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the kinetochore to the centromere is essential for genome maintenance, yet the highly repetitive nature of satellite regional centromeres limits our understanding of their chromatin organization.", "language": "english", "position": {"atoms": [{"position_id": 4144, "txt": "The attachment of the kinetochore to the centromere is essential for genome maintenance, yet the highly repetitive nature of satellite regional centromeres limits our understanding of their chromatin organization.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[6]/div[2]/div/div"}]}, "tags": [], "label": "abstract", "web_segment_id": 20, "global_sentence_id": 20, "edu_l1_label": "IOS"}, {"txt": " We demonstrate that single-molecule chromatin fiber sequencing (Fiber-seq) can uniquely co-resolve kinetochore and surrounding chromatin architectures along point centromeres, revealing largely homogeneous single-molecule kinetochore occupancy.", "language": "english", "position": {"atoms": [{"position_id": 4145, "txt": " We demonstrate that single-molecule chromatin fiber sequencing (Fiber-seq) can uniquely co-resolve kinetochore and surrounding chromatin architectures along point centromeres, revealing largely homogeneous single-molecule kinetochore occupancy.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[6]/div[2]/div/div"}]}, "tags": [], "label": "abstract", "web_segment_id": 20, "global_sentence_id": 21, "edu_l1_label": "IOS"}, {"txt": " In contrast, the application of Fiber-seq to regional centromeres exposed marked per-molecule heterogeneity in their chromatin organization.", "language": "english", "position": {"atoms": [{"position_id": 4146, "txt": " In contrast, the application of Fiber-seq to regional centromeres exposed marked per-molecule heterogeneity in their chromatin organization.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[6]/div[2]/div/div"}]}, "tags": [], "label": "abstract", "web_segment_id": 20, "global_sentence_id": 22, "edu_l1_label": "IOS"}, {"txt": " Regional centromere cores uniquely contain a dichotomous chromatin organization (dichromatin) composed of compacted nucleosome arrays punctuated with highly accessible chromatin patches.", "language": "english", "position": {"atoms": [{"position_id": 4147, "txt": " Regional centromere cores uniquely contain a dichotomous chromatin organization (dichromatin) composed of compacted nucleosome arrays punctuated with highly accessible chromatin patches.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[6]/div[2]/div/div"}]}, "tags": [], "label": "abstract", "web_segment_id": 20, "global_sentence_id": 23, "edu_l1_label": "IOS"}, {"txt": " CENP-B occupancy phases dichromatin to the underlying alpha-satellite repeat within centromere cores but is not necessary for dichromatin formation.", "language": "english", "position": {"atoms": [{"position_id": 4148, "txt": " CENP-B occupancy phases dichromatin to the underlying alpha-satellite repeat within centromere cores but is not necessary for dichromatin formation.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[6]/div[2]/div/div"}]}, "tags": [], "label": "abstract", "web_segment_id": 20, "global_sentence_id": 24, "edu_l1_label": "IOS"}, {"txt": " Centromere core dichromatin is conserved between humans and primates, including along regional centromeres lacking satellite repeats.", "language": "english", "position": {"atoms": [{"position_id": 4149, "txt": " Centromere core dichromatin is conserved between humans and primates, including along regional centromeres lacking satellite repeats.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[6]/div[2]/div/div"}]}, "tags": [], "label": "abstract", "web_segment_id": 20, "global_sentence_id": 25, "edu_l1_label": "IOS"}, {"txt": " Overall, the chromatin organization of regional centromeres is defined by marked per-molecule heterogeneity, buffering kinetochore attachment 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are composed of ∼125 bp point centromeres built on a single CENP-A nucleosome, whereas human centromeres are composed of regional centromeres that occupy ∼171 bp alpha-satellite repeat units organized into higher-order repeats (HORs) that can span several megabases on each chromosome.", "language": "english", "position": {"atoms": [{"position_id": 4173, "txt": " For example, ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]"}, {"position_id": 4175, "txt": "Saccharomyces cerevisiae", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/em[1]"}, {"position_id": 4177, "txt": " centromeres are composed of ∼125 bp point centromeres built on a single CENP-A nucleosome, whereas human centromeres are composed of regional centromeres that occupy ∼171 bp alpha-satellite repeat units organized into higher-order repeats (HORs) that can span several megabases on each chromosome.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/em[1]"}]}, "tags": ["em"], "label": "content", "web_segment_id": 32, "global_sentence_id": 39, "edu_l1_label": "IOS"}, {"txt": " These alpha-satellite HORs serve as the genetic substrate for kinetochore attachment to the human genome within the centromere core,1,2 and kinetochore interactions within the centromere core are modulated by several DNA-binding proteins, including the sequence-specific DNA-binding protein CENP-B3,4 and the histone H3 variant CENP-A.5 Imaging and genomic studies have demonstrated that kinetochore attachment is limited to only a small portion of the alpha-satellite HOR array, which is marked by CENP-A and CENP-B occupancy along the autosomes and X chromosome6,7 and hypo-CpG methylation8,9,10 (i.e., the centromere core or “centromere dip region” [CDR]).", "language": "english", "position": {"atoms": [{"position_id": 4178, "txt": " These alpha-satellite HORs serve as the 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4212, "txt": "9", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/a[9]/span/span/sup"}, {"position_id": 4214, "txt": ",", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/sup[5]"}, {"position_id": 4216, "txt": "10", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/a[10]/span/span/sup"}, {"position_id": 4218, "txt": " (i.e., the centromere core or “centromere dip region” [CDR]).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/a[10]"}]}, "tags": ["em"], "label": "content", "web_segment_id": 32, "global_sentence_id": 40, "edu_l1_label": "IOS"}, {"txt": " However, in vivo chromatin compaction and organization within this region remain largely unresolved, with somewhat contradictory chromatin features appearing to localize to the centromere core.", "language": "english", "position": {"atoms": [{"position_id": 4219, "txt": " However, ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/a[10]"}, {"position_id": 4221, "txt": "in vivo", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/em[2]"}, {"position_id": 4223, "txt": " chromatin compaction and organization within this region remain largely unresolved, with somewhat contradictory chromatin features appearing to localize to the centromere core.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/em[2]"}]}, "tags": ["em"], "label": "content", "web_segment_id": 32, "global_sentence_id": 41, "edu_l1_label": "IOS"}, {"txt": " For example, the centromere core contains a unique patterning of histones referred to as “centro-chromatin,” which is composed of both centromere-specific CENP-A nucleosomes and H3 nucleosomes dimethylated on Lys4 (H3K4me2)11 that are often associated with euchromatic portions of the genome.12 Despite the presence of these H3K4me2 histones, the centromere core is thought to contain condensed chromatin arrays in vivo,13 which are proposed to arise from CENP-A-mediated nucleosome condensation14 as well as other kinetochore proteins bridging and compacting neighboring nucleosomes.15,16,17 However, the chromatin compaction of centro-chromatin in vivo remains largely unknown.", "language": "english", "position": {"atoms": [{"position_id": 4224, "txt": " For example, the centromere core contains a unique patterning of histones referred to as “centro-chromatin,” which is composed of both centromere-specific CENP-A nucleosomes and H3 nucleosomes dimethylated on Lys4 (H3K4me2)", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/em[2]"}, {"position_id": 4226, "txt": "11", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/a[11]/span/span/sup"}, {"position_id": 4228, "txt": " that are often associated with euchromatic portions of the genome.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/a[11]"}, {"position_id": 4230, "txt": "12", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/a[12]/span/span/sup"}, {"position_id": 4232, "txt": " Despite the presence of these H3K4me2 histones, the centromere core is thought to contain condensed chromatin arrays ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/a[12]"}, {"position_id": 4234, "txt": "in vivo", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/em[3]"}, {"position_id": 4236, "txt": ",", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/em[3]"}, {"position_id": 4238, "txt": "13", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/a[13]/span/span/sup"}, {"position_id": 4240, "txt": " which are proposed to arise from CENP-A-mediated nucleosome condensation", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/a[13]"}, {"position_id": 4242, "txt": "14", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/a[14]/span/span/sup"}, {"position_id": 4244, "txt": " as well as other kinetochore proteins bridging and compacting neighboring nucleosomes.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/a[14]"}, {"position_id": 4246, "txt": "15", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/a[15]/span/span/sup"}, {"position_id": 4248, "txt": ",", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/sup[6]"}, {"position_id": 4250, "txt": "16", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/a[16]/span/span/sup"}, {"position_id": 4252, "txt": ",", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/sup[7]"}, {"position_id": 4254, "txt": "17", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/a[17]/span/span/sup"}, {"position_id": 4256, "txt": " However, the chromatin compaction of centro-chromatin ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/a[17]"}, {"position_id": 4258, "txt": "in vivo", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/em[4]"}, {"position_id": 4260, "txt": " remains largely unknown.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[1]/em[4]"}]}, "tags": ["em"], "label": "content", "web_segment_id": 32, "global_sentence_id": 42, "edu_l1_label": "IOS"}, {"txt": "Resolving exactly how chromatin is organized along individual chromatin fibers within the centromere, as well as the relationship between kinetochore binding and chromatin organization, has been challenging due to the highly repetitive DNA content of alpha-satellite HORs.13 Specifically, centromeres are systematically unresolved in most reference genomes, and short-read sequencing-based chromatin profiling methods cannot uniquely resolve chromatin architectures across these repetitive DNA arrays (Figure S1A).", "language": "english", "position": {"atoms": [{"position_id": 4262, "txt": "Resolving exactly how chromatin is organized along individual chromatin fibers within the centromere, as well as the relationship between kinetochore binding and chromatin organization, has been challenging due to the highly repetitive DNA content of alpha-satellite HORs.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[2]"}, {"position_id": 4264, "txt": "13", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[2]/a[1]/span/span/sup"}, {"position_id": 4266, "txt": " Specifically, centromeres are systematically unresolved in most reference genomes, and short-read sequencing-based chromatin profiling methods cannot uniquely resolve chromatin architectures across these repetitive DNA arrays (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[2]/a[1]"}, {"position_id": 4268, "txt": "Figure S1", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[2]/a[2]/span/span"}, {"position_id": 4270, "txt": "A).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[2]/a[2]"}]}, "tags": [], "label": "content", "web_segment_id": 33, "global_sentence_id": 43, "edu_l1_label": "IOS"}, {"txt": " In addition, short-read sequencing-based chromatin profiling methods are inherently unable to resolve how multiple chromatin features are positioned along a single chromatin fiber, as these methods inherently massively fragment chromatin fibers in the process of studying them.", "language": "english", "position": {"atoms": [{"position_id": 4271, "txt": " In addition, short-read sequencing-based chromatin profiling methods are inherently unable to resolve how multiple chromatin features are positioned along a single chromatin fiber, as these methods inherently massively fragment chromatin fibers in the process of studying them.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[2]/a[2]"}]}, "tags": [], "label": "content", "web_segment_id": 33, "global_sentence_id": 44, "edu_l1_label": "IOS"}, {"txt": "The completion of the first telomere-to-telomere (T2T) human reference genome,18 in combination with emerging methyltransferase-based single-molecule long-read chromatin profiling methods,19,20,21,22 opens the possibility of studying 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"/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/div/sup[1]"}, {"position_id": 4283, "txt": "20", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/div/a[3]/span/span/sup"}, {"position_id": 4285, "txt": ",", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/div/sup[2]"}, {"position_id": 4287, "txt": "21", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/div/a[4]/span/span/sup"}, {"position_id": 4289, "txt": ",", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/div/sup[3]"}, {"position_id": 4291, "txt": "22", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/div/a[5]/span/span/sup"}, {"position_id": 4293, "txt": " opens the possibility of studying chromatin features across centromeres at single-molecule and single-nucleotide resolution.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/div/a[5]"}]}, "tags": [], "label": "content", "web_segment_id": 34, "global_sentence_id": 45, "edu_l1_label": "IOS"}, {"txt": " Specifically, non-specific adenine methyltransferase (m6A-MTase)-based chromatin profiling methods (i.e., single-molecule chromatin fiber sequencing [Fiber-seq]) enable nucleotide-precise mappings of chromatin accessibility, protein occupancy, nucleosome positioning, and CpG methylation along multi-kilobase chromatin fibers19,23 (Figures S1B and S1C).", "language": "english", "position": {"atoms": [{"position_id": 4294, "txt": " Specifically, non-specific adenine methyltransferase (m6A-MTase)-based chromatin profiling methods (i.e., single-molecule chromatin fiber sequencing [Fiber-seq]) enable nucleotide-precise mappings of chromatin accessibility, protein occupancy, nucleosome positioning, and CpG methylation along multi-kilobase chromatin fibers", 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"/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/div/a[8]"}]}, "tags": [], "label": "content", "web_segment_id": 34, "global_sentence_id": 46, "edu_l1_label": "IOS"}, {"txt": " Fiber-seq utilizes a non-specific m6A-MTase24 to stencil the chromatin architecture of individual multi-kilobase fibers onto their underlying DNA templates via methylated adenines (Figure 1A), which is a non-endogenous DNA modification in humans.25,26 The genetic and chromatin architecture of each fiber is directly read using highly accurate single-molecule PacBio HiFi long-read DNA sequencing, which is capable of accurately distinguishing m6A- and mCpG-modified bases at single-nucleotide resolution.23,27 We have previously established that both the CpG methylation pattern and chromatin accessibility patterns derived from Fiber-seq data are highly reproducible between replicates23 and show strong agreement with orthogonal methods genome wide, such as bisulfite sequencing 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"/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/div/a[10]"}, {"position_id": 4317, "txt": "25", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/div/a[11]/span/span/sup"}, {"position_id": 4319, "txt": ",", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/div/sup[5]"}, {"position_id": 4321, "txt": "26", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/div/a[12]/span/span/sup"}, {"position_id": 4323, "txt": " The genetic and chromatin architecture of each fiber is directly read using highly accurate single-molecule PacBio HiFi long-read DNA sequencing, which is capable of accurately distinguishing m6A- and mCpG-modified bases at single-nucleotide resolution.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/div/a[12]"}, {"position_id": 4325, "txt": "23", "x": 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sequencing and ATAC-seq.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/div/a[15]"}, {"position_id": 4337, "txt": "19", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/div/a[16]/span/span/sup"}, {"position_id": 4339, "txt": ",", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/div/sup[7]"}, {"position_id": 4341, "txt": "23", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/div/a[17]/span/span/sup"}, {"position_id": 4343, "txt": ",", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/div/sup[8]"}, {"position_id": 4345, "txt": "28", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/div/a[18]/span/span/sup"}, {"position_id": 4347, "txt": ",", "x": 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Resolution of kinetochore and surrounding chromatin architectures along point centromeres", "language": "english", "position": {"atoms": [{"position_id": 4351, "txt": "Figure 1", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/figure/span[2]/span/p/span"}, {"position_id": 4353, "txt": ". Resolution of kinetochore and surrounding chromatin architectures along point centromeres", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/figure/span[2]/span/p/span"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 36, "global_sentence_id": 49, "edu_l1_label": "EDU_O"}, {"txt": "(A) Schematic for mapping the chromatin occupancy of point centromeres within the yeast S. cerevisiae using Fiber-seq.", "language": "english", "position": {"atoms": [{"position_id": 4355, "txt": "(A) Schematic for mapping the chromatin occupancy of point centromeres within the yeast ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/figure/span[2]/span/div[1]"}, {"position_id": 4357, "txt": "S. cerevisiae", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/figure/span[2]/span/div[1]/em"}, {"position_id": 4359, "txt": " using Fiber-seq.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/figure/span[2]/span/div[1]/em"}]}, "tags": ["img", "em"], "label": "figure_title", "web_segment_id": 37, "global_sentence_id": 50, "edu_l1_label": "EDU_O"}, {"txt": "(B) Locus displaying single-molecule chromatin architectures of the S. cerevisiae chromosome III point centromere, alongside Cap Analysis of Gene Expression (CAGE) sequencing data and gene annotations.", "language": "english", "position": {"atoms": [{"position_id": 4361, "txt": "(B) Locus displaying single-molecule chromatin architectures of the ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/figure/span[2]/span/div[2]"}, {"position_id": 4363, "txt": "S. cerevisiae", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/figure/span[2]/span/div[2]/em"}, {"position_id": 4365, "txt": " chromosome III point centromere, alongside Cap Analysis of Gene Expression (CAGE) sequencing data and gene annotations.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/figure/span[2]/span/div[2]/em"}]}, "tags": ["img", "em"], "label": "figure_title", "web_segment_id": 38, "global_sentence_id": 51, "edu_l1_label": "EDU_O"}, {"txt": " Each gray bar is a single Fiber-seq read, with purple dashes representing sites of m6A-modified bases along that read.", "language": "english", "position": {"atoms": [{"position_id": 4366, "txt": " Each gray bar is a single Fiber-seq read, with purple dashes representing sites of m6A-modified bases along that read.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/figure/span[2]/span/div[2]/em"}]}, "tags": ["em", "img"], "label": "figure_title", "web_segment_id": 38, "global_sentence_id": 52, "edu_l1_label": "EDU_O"}, {"txt": " Note the large patches of chromatin accessibility that correspond to CAGE-positive gene promoters as well as those immediately adjacent to the centromere.", "language": "english", "position": {"atoms": [{"position_id": 4367, "txt": " Note the large patches of chromatin accessibility that correspond to CAGE-positive gene promoters as well as those immediately adjacent to the centromere.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/figure/span[2]/span/div[2]/em"}]}, "tags": ["em", "img"], "label": "figure_title", "web_segment_id": 38, "global_sentence_id": 53, "edu_l1_label": "EDU_O"}, {"txt": "(C) Heatmap displaying average Fiber-seq m6A signal surrounding each of the S. cerevisiae point centromeres.", "language": "english", "position": {"atoms": [{"position_id": 4369, "txt": "(C) Heatmap displaying average Fiber-seq m6A signal surrounding each of the ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/figure/span[2]/span/div[3]"}, {"position_id": 4371, "txt": "S. cerevisiae", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/figure/span[2]/span/div[3]/em"}, {"position_id": 4373, "txt": " point centromeres.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/figure/span[2]/span/div[3]/em"}]}, "tags": ["img", "em"], "label": "figure_title", "web_segment_id": 39, "global_sentence_id": 54, "edu_l1_label": "EDU_O"}, {"txt": "(D) (Top) Zoom-in of the per-nucleotide Fiber-seq signal of the S. cerevisiae chromosome III point centromere in relation to the CDEI, CDEII, and CDEIII elements.", "language": "english", "position": {"atoms": [{"position_id": 4375, "txt": "(D) (Top) Zoom-in of the per-nucleotide Fiber-seq signal of the ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/figure/span[2]/span/div[4]"}, {"position_id": 4377, "txt": "S. cerevisiae", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/figure/span[2]/span/div[4]/em[1]"}, {"position_id": 4379, "txt": " chromosome III point centromere in relation to the CDEI, CDEII, and CDEIII elements.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/figure/span[2]/span/div[4]/em[1]"}]}, "tags": ["img", "em"], "label": "figure_title", "web_segment_id": 40, "global_sentence_id": 55, "edu_l1_label": "EDU_O"}, {"txt": " (Bottom) Cryo-EM structure of the yeast complete S. cerevisiae inner kinetochore bound to the chromosome III point centromere (PDB:", "language": "english", "position": {"atoms": [{"position_id": 4380, "txt": " (Bottom) Cryo-EM structure of the yeast complete ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/figure/span[2]/span/div[4]/em[1]"}, {"position_id": 4382, "txt": "S. cerevisiae", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/figure/span[2]/span/div[4]/em[2]"}, {"position_id": 4384, "txt": " inner kinetochore bound to the chromosome III point centromere (PDB:", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/figure/span[2]/span/div[4]/em[2]"}]}, "tags": ["img", "em"], "label": "figure_title", "web_segment_id": 40, "global_sentence_id": 56, "edu_l1_label": "EDU_O"}, {"txt": " 8OW130), with the DNA colored according to the m6A-MTase sensitivity measured via Fiber-seq on S. cerevisiae.", "language": "english", "position": {"atoms": [{"position_id": 4385, "txt": " ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/figure/span[2]/span/div[4]/em[2]"}, {"position_id": 4387, "txt": "8OW1", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/figure/span[2]/span/div[4]/a[1]/span/span"}, {"position_id": 4389, "txt": "30", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/figure/span[2]/span/div[4]/a[2]/span/span/sup"}, {"position_id": 4391, "txt": "), with the DNA colored according to the m6A-MTase sensitivity measured via Fiber-seq on ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/figure/span[2]/span/div[4]/a[2]"}, {"position_id": 4393, "txt": "S. cerevisiae", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/figure/span[2]/span/div[4]/em[3]"}, {"position_id": 4395, "txt": ".", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[1]/div[3]/figure/span[2]/span/div[4]/em[3]"}]}, "tags": ["img", "em"], "label": "figure_title", "web_segment_id": 40, "global_sentence_id": 57, "edu_l1_label": "EDU_O"}, {"txt": "Results", "language": "english", "position": {"atoms": [{"position_id": 4397, "txt": "Results", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/h2"}]}, "tags": ["h2"], "label": "title1", "web_segment_id": 41, "global_sentence_id": 58, "edu_l1_label": "BOS"}, {"txt": "Single-molecule chromatin architectures of kinetochore-bound point centromeres", "language": "english", "position": {"atoms": [{"position_id": 4399, "txt": "Single-molecule chromatin architectures of kinetochore-bound point centromeres", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/h3"}]}, "tags": ["h3"], "label": "title2", "web_segment_id": 42, "global_sentence_id": 59, "edu_l1_label": "IOS"}, {"txt": "To map the chromatin architecture of centromeres at single-molecule and near-single-nucleotide resolution, we first applied Fiber-seq to budding yeast Saccharomyces cerevisiae (Figure 1A), which contain a point centromere along each chromosome.31,32 Similar to humans, the yeast inner kinetochore directly interacts with DNA via a centromere-associated inner kinetochore (CCAN) complex, which contains the histone H3 variant CENP-A (Cse4)31 in addition to the yeast-specific centromere binding factor 1 (Cbf1)33 and the yeast-specific multiprotein complex CBF3.34 Each yeast centromere is organized into three centromere DNA elements (CDEs) (CDEI, CDEII, and CDEIII), and cryoelectron microscopy (cryo-EM) structures and nuclease digestions of the yeast CCAN complex have shown that the yeast CCAN embeds ∼160 bp of DNA within this complex.35,30 Application of Fiber-seq to asynchronously growing Saccharomyces cerevisiae cells revealed a discrete change in chromatin structure immediately overlapping the CDEI–III elements (Figures 1B and 1C).", "language": "english", "position": {"atoms": [{"position_id": 4401, "txt": "To map the chromatin architecture of centromeres at single-molecule and near-single-nucleotide resolution, we first applied Fiber-seq to budding yeast ", "x": 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"/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/sup[1]"}, {"position_id": 4415, "txt": "32", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/a[3]/span/span/sup"}, {"position_id": 4417, "txt": " Similar to humans, the yeast inner kinetochore directly interacts with DNA via a centromere-associated inner kinetochore (CCAN) complex, which contains the histone H3 variant CENP-A (Cse4)", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/a[3]"}, {"position_id": 4419, "txt": "31", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/a[4]/span/span/sup"}, {"position_id": 4421, "txt": " in addition to the yeast-specific centromere binding factor 1 (Cbf1)", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/a[4]"}, {"position_id": 4423, "txt": "33", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/a[5]/span/span/sup"}, {"position_id": 4425, "txt": " and the yeast-specific multiprotein complex CBF3.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/a[5]"}, {"position_id": 4427, "txt": "34", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/a[6]/span/span/sup"}, {"position_id": 4429, "txt": " Each yeast centromere is organized into three centromere DNA elements (CDEs) (CDEI, CDEII, and CDEIII), and cryoelectron microscopy (cryo-EM) structures and nuclease digestions of the yeast CCAN complex have shown that the yeast CCAN embeds ∼160 bp of DNA within this complex.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/a[6]"}, {"position_id": 4431, "txt": "35", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/a[7]/span/span/sup"}, {"position_id": 4433, "txt": ",", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/sup[2]"}, {"position_id": 4435, "txt": "30", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/a[8]/span/span/sup"}, {"position_id": 4437, "txt": " Application of Fiber-seq to asynchronously growing ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/a[8]"}, {"position_id": 4439, "txt": "Saccharomyces cerevisiae", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/em[2]"}, {"position_id": 4441, "txt": " cells revealed a discrete change in chromatin structure immediately overlapping the CDEI–III elements (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/em[2]"}, {"position_id": 4443, "txt": "Figures 1", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/a[9]/span/span"}, {"position_id": 4445, "txt": "B and 1C).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/a[9]"}]}, "tags": ["em"], "label": "content", "web_segment_id": 43, "global_sentence_id": 60, "edu_l1_label": "IOS"}, {"txt": " Specifically, >90% of chromatin fibers overlapping the yeast centromere contained a well-positioned MTase-protected region overlapping the CDEI–III elements.", "language": "english", "position": {"atoms": [{"position_id": 4446, "txt": " Specifically, >90% of chromatin fibers overlapping the yeast centromere contained a well-positioned MTase-protected region overlapping the CDEI–III elements.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/a[9]"}]}, "tags": [], "label": "content", "web_segment_id": 43, "global_sentence_id": 61, "edu_l1_label": "IOS"}, {"txt": " This MTase-protected region was significantly larger than the standard nucleosome footprint size observed genome wide, perfectly aligned with the cryo-EM structure of the yeast inner kinetochore (Figure 1D), and was disrupted upon Cse4 destabilization.36 Notably, yeast centromeres were frequently flanked by MTase-sensitive patches (MSPs) of chromatin that mirror the size of traditional gene-regulatory elements (Figures 1B and 1C), indicating that the yeast CCAN is associated with marked alterations in the local chromatin architecture.", "language": "english", "position": {"atoms": [{"position_id": 4447, "txt": " This MTase-protected region was significantly larger than the standard nucleosome footprint size observed genome wide, perfectly aligned with the cryo-EM structure of the yeast inner kinetochore (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/a[9]"}, {"position_id": 4449, "txt": "Figure 1", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/a[10]/span/span"}, {"position_id": 4451, "txt": "D), and was disrupted upon Cse4 destabilization.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/a[10]"}, {"position_id": 4453, "txt": "36", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/a[11]/span/span/sup"}, {"position_id": 4455, "txt": " Notably, yeast centromeres were frequently flanked by MTase-sensitive patches (MSPs) of chromatin that mirror the size of traditional gene-regulatory elements (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/a[11]"}, {"position_id": 4457, "txt": "Figures 1", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/a[12]/span/span"}, {"position_id": 4459, "txt": "B and 1C), indicating that the yeast CCAN is associated with marked alterations in the local chromatin architecture.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/a[12]"}]}, "tags": [], "label": "content", "web_segment_id": 43, "global_sentence_id": 62, "edu_l1_label": "IOS"}, {"txt": " Together, these findings reveal that Fiber-seq can resolve the chromatin architecture of the CCAN at single-molecule and near-single-nucleotide resolution and that individual fibers demonstrate homogeneous CCAN occupancy that frequently abuts patches of accessible chromatin.", "language": "english", "position": {"atoms": [{"position_id": 4460, "txt": " Together, these findings reveal that Fiber-seq can resolve the chromatin architecture of the CCAN at single-molecule and near-single-nucleotide resolution and that individual fibers demonstrate homogeneous CCAN occupancy that frequently abuts patches of accessible chromatin.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[1]/div/a[12]"}]}, "tags": [], "label": "content", "web_segment_id": 43, "global_sentence_id": 63, "edu_l1_label": "IOS"}, {"txt": "Dichotomous chromatin marks the centromere core in humans", "language": "english", "position": {"atoms": [{"position_id": 4462, "txt": "Dichotomous chromatin marks the centromere core in humans", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/h3"}]}, "tags": ["h3"], "label": "title2", "web_segment_id": 44, "global_sentence_id": 64, "edu_l1_label": "IOS"}, {"txt": "We next sought to investigate the chromatin architecture of human centromeres by applying Fiber-seq to the human hydatidiform mole CHM13 cell line,37 the same line used for constructing the first human T2T reference genome.9,18 We observed that coupling long-read epigenome maps (Table S1) with paired fully sequenced and assembled genome maps from the same individual enabled us to uniquely map the chromatin architecture of all centromeres in CHM13 cells (Figure 2), overcoming the substantial diversity between individuals38 that is enriched within these highly repetitive genomic regions.", "language": "english", "position": {"atoms": [{"position_id": 4464, "txt": "We next sought to investigate the chromatin architecture of human centromeres by applying Fiber-seq to the human hydatidiform mole CHM13 cell line,", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/div"}, {"position_id": 4466, "txt": "37", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/div/a[1]/span/span/sup"}, {"position_id": 4468, "txt": " the same line used for constructing the first human T2T reference genome.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/div/a[1]"}, {"position_id": 4470, "txt": "9", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/div/a[2]/span/span/sup"}, {"position_id": 4472, "txt": ",", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/div/sup[1]"}, {"position_id": 4474, "txt": "18", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/div/a[3]/span/span/sup"}, {"position_id": 4476, "txt": " We observed that coupling long-read epigenome maps (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/div/a[3]"}, {"position_id": 4478, "txt": "Table S1", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/div/a[4]/span/span"}, {"position_id": 4480, "txt": ") with paired fully sequenced and assembled genome maps from the same individual enabled us to uniquely map the chromatin architecture of all centromeres in CHM13 cells (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/div/a[4]"}, {"position_id": 4482, "txt": "Figure 2", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/div/a[5]/span/span"}, {"position_id": 4484, "txt": "), overcoming the substantial diversity between individuals", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/div/a[5]"}, {"position_id": 4486, "txt": "38", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/div/a[6]/span/span/sup"}, {"position_id": 4488, "txt": " that is enriched within these highly repetitive genomic regions.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/div/a[6]"}]}, "tags": [], "label": "content", "web_segment_id": 45, "global_sentence_id": 65, "edu_l1_label": "IOS"}, {"txt": " Notably, in stark contrast to the yeast point centromeres, CHM13 regional centromeres lacked homogeneously positioned chromatin (Figure 2A).", "language": "english", "position": {"atoms": [{"position_id": 4489, "txt": " Notably, in stark contrast to the yeast point centromeres, CHM13 regional centromeres lacked homogeneously positioned chromatin (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/div/a[6]"}, {"position_id": 4491, "txt": "Figure 2", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/div/a[7]/span/span"}, {"position_id": 4493, "txt": "A).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/div/a[7]"}]}, "tags": [], "label": "content", "web_segment_id": 45, "global_sentence_id": 66, "edu_l1_label": "IOS"}, {"txt": " However, similar to the region immediately proximal to the yeast point centromere nucleosome, CHM13 centromere cores contained markedly altered chromatin structures not observed elsewhere in the human genome.", "language": "english", "position": {"atoms": [{"position_id": 4494, "txt": " However, similar to the region immediately proximal to the yeast point centromere nucleosome, CHM13 centromere cores contained markedly altered chromatin structures not observed elsewhere in the human genome.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/div/a[7]"}]}, "tags": [], "label": "content", "web_segment_id": 45, "global_sentence_id": 67, "edu_l1_label": "IOS"}, {"txt": " Specifically, the nucleosome architecture of CHM13 centromere cores diverged from that observed elsewhere in the human genome, containing mononucleosome footprints markedly smaller than the average nucleosome footprint size outside of the centromere core (Figure S1D), consistent with a large population of these centromere core mononucleosomes containing CENP-A, which is known to wrap only 121 bp of DNA in humans.13,39,40 In addition, the centromere core contained some of the most compacted nucleosome arrays within the human genome, with nearly 50% of all nucleosome footprints within the centromere core being di-nucleosomal in size (i.e., >210 bp), consistent with prior observations41, (Figures 2B and 2C).", "language": "english", "position": {"atoms": [{"position_id": 4495, "txt": " Specifically, the nucleosome architecture of CHM13 centromere cores diverged from that observed elsewhere in the human genome, containing mononucleosome footprints markedly smaller than the average nucleosome footprint size outside of the centromere core (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/div/a[7]"}, {"position_id": 4497, "txt": "Figure S1", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/div/a[8]/span/span"}, {"position_id": 4499, "txt": "D), consistent with a large population of these centromere core mononucleosomes containing CENP-A, which is known to wrap only 121 bp of DNA in humans.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/div/a[8]"}, {"position_id": 4501, "txt": "13", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/div/a[9]/span/span/sup"}, {"position_id": 4503, "txt": ",", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/div/sup[2]"}, {"position_id": 4505, "txt": "39", "x": 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and non-centromeric regions (Figure S1E), possibly reflecting unique CCAN footprints within this region.", "language": "english", "position": {"atoms": [{"position_id": 4522, "txt": " Of note, the size of di-nucleosome footprints within the centromere core appears distinct relative to other centromeric and non-centromeric regions (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/div/a[13]"}, {"position_id": 4524, "txt": "Figure S1", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/div/a[14]/span/span"}, {"position_id": 4526, "txt": "E), possibly reflecting unique CCAN footprints within this region.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/div/a[14]"}]}, "tags": [], "label": "content", "web_segment_id": 45, "global_sentence_id": 69, "edu_l1_label": "IOS"}, {"txt": "<img 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Dichotomous accessible chromatin patches mark human CHM13 centromere cores", "language": "english", "position": {"atoms": [{"position_id": 4528, "txt": "Figure 2", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/figure/span[2]/span/p/span"}, {"position_id": 4530, "txt": ". Dichotomous accessible chromatin patches mark human CHM13 centromere cores", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/figure/span[2]/span/p/span"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 47, "global_sentence_id": 71, "edu_l1_label": "EDU_O"}, {"txt": "(A) Genomic locus of chromosome 5 centromere showing satellite repeats, bulk CpG methylation, Fiber-seq-identified di-nucleosome footprint density, Fiber-seq-identified accessible chromatin patch density, and the density of Fiber-seq inferred regulatory elements (FIREs).", "language": "english", "position": {"atoms": [{"position_id": 4532, "txt": "(A) Genomic locus of chromosome 5 centromere showing satellite repeats, bulk CpG methylation, Fiber-seq-identified di-nucleosome footprint density, Fiber-seq-identified accessible chromatin patch density, and the density of Fiber-seq inferred regulatory elements (FIREs).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/figure/span[2]/span/div[1]"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 48, "global_sentence_id": 72, "edu_l1_label": "EDU_O"}, {"txt": " Fiber-seq tracks generated by aggregating single-molecule data at each base along the genome.", "language": "english", "position": {"atoms": [{"position_id": 4533, "txt": " Fiber-seq tracks generated by aggregating single-molecule data at each base along the genome.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/figure/span[2]/span/div[1]"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 48, "global_sentence_id": 73, "edu_l1_label": "EDU_O"}, {"txt": " On the bottom are individual Fiber-seq reads (gray bars) with m6A-modified bases in purple delineating single-molecule chromatin architectures within euchromatic and heterochromatic regions.", "language": "english", "position": {"atoms": [{"position_id": 4534, "txt": " On the bottom are individual Fiber-seq reads (gray bars) with m6A-modified bases in purple delineating single-molecule chromatin architectures within euchromatic and heterochromatic regions.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/figure/span[2]/span/div[1]"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 48, "global_sentence_id": 74, "edu_l1_label": "EDU_O"}, {"txt": "(B) Average density of di-nucleosome footprints and accessible chromatin patches within various genomic regions (∗p < 0.01 Mann-Whitney).", "language": "english", "position": {"atoms": [{"position_id": 4536, "txt": "(B) Average density of di-nucleosome footprints and accessible chromatin patches within various genomic regions (∗", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/figure/span[2]/span/div[2]"}, 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"/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/figure/span[2]/span/div[4]"}, {"position_id": 4546, "txt": "p", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/figure/span[2]/span/div[4]/em"}, {"position_id": 4548, "txt": " < 0.01 Mann-Whitney).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/figure/span[2]/span/div[4]/em"}]}, "tags": ["img", "em"], "label": "figure_title", "web_segment_id": 51, "global_sentence_id": 77, "edu_l1_label": "EDU_O"}, {"txt": "(E) Estimated total number of accessible chromatin patches along each chromosome’s centromere core versus the length of that chromosome.", "language": "english", "position": {"atoms": [{"position_id": 4550, "txt": "(E) Estimated total number of accessible chromatin patches along each chromosome’s centromere core versus the length of that chromosome.", "x": 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"web_segment_id": 52, "global_sentence_id": 79, "edu_l1_label": "EDU_O"}, {"txt": "See also Figure S1 and Table S1.", "language": "english", "position": {"atoms": [{"position_id": 4557, "txt": "See also ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/figure/span[2]/span/div[6]"}, {"position_id": 4559, "txt": "Figure S1", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/figure/span[2]/span/div[6]/a[1]/span/span"}, {"position_id": 4561, "txt": " and ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/figure/span[2]/span/div[6]/a[1]"}, {"position_id": 4563, "txt": "Table S1", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/figure/span[2]/span/div[6]/a[2]/span/span"}, {"position_id": 4565, "txt": ".", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[1]/figure/span[2]/span/div[6]/a[2]"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 53, "global_sentence_id": 80, "edu_l1_label": "EDU_O"}, {"txt": "Notably, similar to yeast point centromeres, regional centromere cores in humans were also markedly enriched for large MSPs of chromatin, forming some of the most accessible chromatin domains within the entire human genome (Figures 2B and 2C).", "language": "english", "position": {"atoms": [{"position_id": 4567, "txt": "Notably, similar to yeast point centromeres, regional centromere cores in humans were also markedly enriched for large MSPs of chromatin, forming some of the most accessible chromatin domains within the entire human genome (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[2]"}, {"position_id": 4569, "txt": "Figures 2", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[2]/a[1]/span/span"}, {"position_id": 4571, "txt": "B and 2C).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[2]/a[1]"}]}, "tags": [], "label": "content", "web_segment_id": 54, "global_sentence_id": 81, "edu_l1_label": "IOS"}, {"txt": " However, in stark contrast to traditional heterochromatin or euchromatin domains, individual chromatin fibers originating from the centromere core contained both tightly compacted nucleosome arrays and highly accessible chromatin features abutting each other (Figures 2A and 2C).", "language": "english", "position": {"atoms": [{"position_id": 4572, "txt": " However, in stark contrast to traditional heterochromatin or euchromatin domains, individual chromatin fibers originating from the centromere core contained both tightly compacted nucleosome arrays and highly accessible chromatin features abutting each other (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[2]/a[1]"}, {"position_id": 4574, "txt": "Figures 2", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[2]/a[2]/span/span"}, {"position_id": 4576, "txt": "A and 2C).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[2]/a[2]"}]}, "tags": [], "label": "content", "web_segment_id": 54, "global_sentence_id": 82, "edu_l1_label": "IOS"}, {"txt": "Accessible chromatin patches were infrequently observed within alpha-satellite regions outside of the centromere core, indicating that they are a unique feature of kinetochore binding.", "language": "english", "position": {"atoms": [{"position_id": 4578, "txt": "Accessible chromatin patches were infrequently observed within alpha-satellite regions outside of the centromere core, indicating that they are a unique feature of kinetochore binding.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[3]"}]}, "tags": [], "label": "content", "web_segment_id": 55, "global_sentence_id": 83, "edu_l1_label": "IOS"}, {"txt": " Although these accessible chromatin patches were heterogeneously placed across individual chromatin fibers within the centromere core, these patches nonetheless clustered along individual chromatin fibers within the centromere core (Figure 2D).", "language": "english", "position": {"atoms": [{"position_id": 4579, "txt": " Although these accessible chromatin patches were heterogeneously placed across individual chromatin fibers within the centromere core, these patches nonetheless clustered along individual chromatin fibers within the centromere core (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[3]"}, {"position_id": 4581, "txt": "Figure 2", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[3]/a[1]/span/span"}, {"position_id": 4583, "txt": "D).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[3]/a[1]"}]}, "tags": [], "label": "content", "web_segment_id": 55, "global_sentence_id": 84, "edu_l1_label": "IOS"}, {"txt": " In addition, each chromosome molecule contains only 6–28 accessible chromatin patches within its 80–220 kbp centromere core (Figure 2E), a value that mirrors estimates of the number of kinetochore microtubules that form on individual human centromeres.43,44 Notably, longer chromosomes have significantly more accessible chromatin patches than shorter chromosomes, and after controlling for chromosome length, we observed that chromosomes with the highest rate of missegregation in human RPE-1 cells42 had among the lowest amounts of accessible chromatin patches (Figure 2E).", "language": "english", "position": {"atoms": [{"position_id": 4584, "txt": " In addition, each chromosome molecule contains only 6–28 accessible chromatin patches within its 80–220 kbp centromere core (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[3]/a[1]"}, {"position_id": 4586, "txt": "Figure 2", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[3]/a[2]/span/span"}, {"position_id": 4588, "txt": "E), a value that mirrors estimates of the number of kinetochore microtubules that form on individual human centromeres.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[3]/a[2]"}, {"position_id": 4590, "txt": "43", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[3]/a[3]/span/span/sup"}, {"position_id": 4592, "txt": ",", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[3]/sup"}, {"position_id": 4594, "txt": "44", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[3]/a[4]/span/span/sup"}, {"position_id": 4596, "txt": " Notably, longer chromosomes have significantly more accessible chromatin patches than shorter chromosomes, and after controlling for chromosome length, we observed that chromosomes with the highest rate of missegregation in human RPE-1 cells", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[3]/a[4]"}, {"position_id": 4598, "txt": "42", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[3]/a[5]/span/span/sup"}, {"position_id": 4600, "txt": " had among the lowest amounts of accessible chromatin patches (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[3]/a[5]"}, {"position_id": 4602, "txt": "Figure 2", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[3]/a[6]/span/span"}, {"position_id": 4604, "txt": "E).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[3]/a[6]"}]}, "tags": [], "label": "content", "web_segment_id": 55, "global_sentence_id": 85, "edu_l1_label": "IOS"}, {"txt": " Together, these findings establish that the centromere core in human CHM13 cells contains a dichotomous chromatin organization (i.e., dichromatin) not found elsewhere in the genome, which is characterized by highly accessible chromatin patches and large di-nucleosome-sized footprints, the combination of which likely directly relates to kinetochore attachment and function within the centromere core.", "language": "english", "position": {"atoms": [{"position_id": 4605, "txt": " Together, these findings establish that the centromere core in human CHM13 cells contains a dichotomous chromatin organization (i.e., dichromatin) not found elsewhere in the genome, which is characterized by highly accessible chromatin patches and large di-nucleosome-sized footprints, the combination of which likely directly relates to kinetochore attachment and function within the centromere core.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[2]/div[3]/a[6]"}]}, "tags": [], "label": "content", "web_segment_id": 55, "global_sentence_id": 86, "edu_l1_label": "IOS"}, {"txt": "CENP-B guides centromere core dichromatin to mirror the alpha-satellite DNA repeat", "language": "english", "position": {"atoms": [{"position_id": 4607, "txt": "CENP-B guides centromere core dichromatin to mirror the alpha-satellite DNA repeat", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/h3"}]}, "tags": ["h3"], "label": "title2", "web_segment_id": 56, "global_sentence_id": 87, "edu_l1_label": "IOS"}, {"txt": "We next sought to investigate the impact that the alpha-satellite repeat sequence has on dichromatin formation within CHM13 centromere cores.", "language": "english", "position": {"atoms": [{"position_id": 4609, "txt": "We next sought to investigate the impact that the alpha-satellite repeat sequence has on dichromatin formation within CHM13 centromere cores.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div"}]}, "tags": [], "label": "content", "web_segment_id": 57, "global_sentence_id": 88, "edu_l1_label": "IOS"}, {"txt": " The 171 bp alpha-satellite repeat is known to preferentially position CENP-A containing nucleosomes both in vitro and in vivo,40,45 so we first sought to identify whether we could observe this preferential positioning along extended alpha-satellite arrays using Fiber-seq data.", "language": "english", "position": {"atoms": [{"position_id": 4610, "txt": " The 171 bp alpha-satellite repeat is known to preferentially position CENP-A containing nucleosomes both ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div"}, {"position_id": 4612, "txt": "in vitro", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div/em[1]"}, {"position_id": 4614, "txt": " and ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div/em[1]"}, {"position_id": 4616, "txt": "in vivo", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div/em[2]"}, {"position_id": 4618, "txt": ",", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div/em[2]"}, {"position_id": 4620, "txt": "40", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div/a[1]/span/span/sup"}, {"position_id": 4622, "txt": ",", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div/sup[1]"}, {"position_id": 4624, "txt": "45", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div/a[2]/span/span/sup"}, {"position_id": 4626, "txt": " so we first sought to identify whether we could observe this preferential positioning along extended alpha-satellite arrays using Fiber-seq data.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div/a[2]"}]}, "tags": ["em"], "label": "content", "web_segment_id": 57, "global_sentence_id": 89, "edu_l1_label": "IOS"}, {"txt": " To identify the most commonly represented spacing of m6A-modified bases (i.e., the chromatin/nucleosome repeat unit length), we applied a Fourier transform to m6A-modified bases present along each fiber.", "language": "english", "position": {"atoms": [{"position_id": 4627, "txt": " To identify the most commonly represented spacing of m6A-modified bases (i.e., the chromatin/nucleosome repeat unit length), we applied a Fourier transform to m6A-modified bases present along each fiber.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div/a[2]"}]}, "tags": [], "label": "content", "web_segment_id": 57, "global_sentence_id": 90, "edu_l1_label": "IOS"}, {"txt": " Importantly, this approach for measuring nucleosome positioning within the centromere is not subject to prior mapping biases, as is observed with short-read methods like MNase-seq.", "language": "english", "position": {"atoms": [{"position_id": 4628, "txt": " Importantly, this approach for measuring nucleosome positioning within the centromere is not subject to prior mapping biases, as is observed with short-read methods like MNase-seq.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div/a[2]"}]}, "tags": [], "label": "content", "web_segment_id": 57, "global_sentence_id": 91, "edu_l1_label": "IOS"}, {"txt": " We observed that chromatin fibers originating from euchromatic and non-alpha-satellite heterochromatic genomic regions have nucleosomes repeating every ∼179–190 bp (Figures 3A, 3B, and S2), consistent with prior reports.46,47 In contrast, centromere core alpha-satellite regions contained a nucleosome repeat unit of 170 bp, mirroring the underlying repeat length of alpha-satellite DNA (Figures 3A and 3B).", "language": "english", "position": {"atoms": [{"position_id": 4629, "txt": " We observed that chromatin fibers originating from euchromatic and non-alpha-satellite heterochromatic genomic regions have nucleosomes repeating every ∼179–190 bp (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div/a[2]"}, {"position_id": 4631, "txt": "Figures 3", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div/a[3]/span/span"}, {"position_id": 4633, "txt": "A, 3B, and ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div/a[3]"}, {"position_id": 4635, "txt": "S2", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div/a[4]/span/span"}, {"position_id": 4637, "txt": "), consistent with prior reports.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div/a[4]"}, {"position_id": 4639, "txt": "46", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div/a[5]/span/span/sup"}, {"position_id": 4641, "txt": ",", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div/sup[2]"}, {"position_id": 4643, "txt": "47", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div/a[6]/span/span/sup"}, {"position_id": 4645, "txt": " In contrast, centromere core alpha-satellite regions contained a nucleosome repeat unit of 170 bp, mirroring the underlying repeat length of alpha-satellite DNA (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div/a[6]"}, {"position_id": 4647, "txt": "Figures 3", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div/a[7]/span/span"}, {"position_id": 4649, "txt": "A and 3B).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div/a[7]"}]}, "tags": [], "label": "content", "web_segment_id": 57, "global_sentence_id": 92, "edu_l1_label": "IOS"}, {"txt": " This reveals that the predominant positioning of nucleosome arrays within the centromere core is directly related to the size of the underlying alpha-satellite repeat.", "language": "english", "position": {"atoms": [{"position_id": 4650, "txt": " This reveals that the predominant positioning of nucleosome arrays within the centromere core is directly related to the size of the underlying alpha-satellite repeat.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div/a[7]"}]}, "tags": [], "label": "content", "web_segment_id": 57, "global_sentence_id": 93, "edu_l1_label": "IOS"}, {"txt": " However, inactive alpha-satellite HORs, as well as divergent/monomeric alpha-satellite HORs, contained a nucleosome repeat unit of 190–193 bp (Figure 3B), indicating that the alpha-satellite repeat in and of itself is not sufficient for enabling chromatin to mirror the underlying DNA repeat.", "language": "english", "position": {"atoms": [{"position_id": 4651, "txt": " However, inactive alpha-satellite HORs, as well as divergent/monomeric alpha-satellite HORs, contained a nucleosome repeat unit of 190–193 bp (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div/a[7]"}, {"position_id": 4653, "txt": "Figure 3", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div/a[8]/span/span"}, {"position_id": 4655, "txt": "B), indicating that the alpha-satellite repeat in and of itself is not sufficient for enabling chromatin to mirror the underlying DNA repeat.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/div/a[8]"}]}, "tags": [], "label": "content", "web_segment_id": 57, "global_sentence_id": 94, "edu_l1_label": "IOS"}, {"txt": "<img https://wcd-image-bucket-test.oss-cn-zhangjiakou.aliyuncs.com/raw/3vzkHM2TEuufhSAhl4Aw8Cu.jpeg", "language": "english", "position": {"atoms": [{"position_id": 790, "txt": "<img https://wcd-image-bucket-test.oss-cn-zhangjiakou.aliyuncs.com/raw/3vzkHM2TEuufhSAhl4Aw8Cu.jpeg", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/figure/span[1]/img"}]}, "tags": ["img"], "label": "figure", "web_segment_id": 58, "global_sentence_id": 95, "edu_l1_label": "EDU_O"}, {"txt": "Figure 3. Centromere core chromatin mirrors the alpha-satellite DNA repeat", "language": "english", "position": {"atoms": [{"position_id": 4657, "txt": "Figure 3", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/figure/span[2]/span/p/span"}, {"position_id": 4659, "txt": ". Centromere core chromatin mirrors the alpha-satellite DNA repeat", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/figure/span[2]/span/p/span"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 59, "global_sentence_id": 96, "edu_l1_label": "EDU_O"}, {"txt": "(A) Box-and-whisker plots of the chromatin repeat lengths from various genomic regions.", "language": "english", "position": {"atoms": [{"position_id": 4661, "txt": "(A) Box-and-whisker plots of the chromatin repeat lengths from various genomic regions.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/figure/span[2]/span/div[1]"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 60, "global_sentence_id": 97, "edu_l1_label": "EDU_O"}, {"txt": " Specifically, m6A-marked chromatin features from individual chromatin fibers were subjected to Fourier transform, and the per-molecule spectral densities were then aggregated across different fibers from the same genomic region.", "language": "english", "position": {"atoms": [{"position_id": 4662, "txt": " Specifically, m6A-marked chromatin features from individual chromatin fibers were subjected to Fourier transform, and the per-molecule spectral densities were then aggregated across different fibers from the same genomic region.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/figure/span[2]/span/div[1]"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 60, "global_sentence_id": 98, "edu_l1_label": "EDU_O"}, {"txt": "(B) Heatmap of the median spectral density for various chromatin repeat lengths and the peak chromatin repeat length(s) from fibers contained within the euchromatic genome or various satellite repeat regions.", "language": "english", "position": {"atoms": [{"position_id": 4664, "txt": "(B) Heatmap of the median spectral density for various chromatin repeat lengths and the peak chromatin repeat length(s) from fibers contained within the euchromatic genome or various satellite repeat regions.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/figure/span[2]/span/div[2]"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 61, "global_sentence_id": 99, "edu_l1_label": "EDU_O"}, {"txt": " The satellite DNA repeat unit for each region is also indicated.", "language": "english", "position": {"atoms": [{"position_id": 4665, "txt": " The satellite DNA repeat unit for each region is also indicated.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/figure/span[2]/span/div[2]"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 61, "global_sentence_id": 100, "edu_l1_label": "EDU_O"}, {"txt": "(C) Plot showing the average distance between CENP-B boxes along each centromere core within CHM13 cells alongside a heatmap of the median spectral density for the centromere core and euchromatic regions along each centromere.", "language": "english", "position": {"atoms": [{"position_id": 4667, "txt": "(C) Plot showing the average distance between CENP-B boxes along each centromere core within CHM13 cells alongside a heatmap of the median spectral density for the centromere core and euchromatic regions along each centromere.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/figure/span[2]/span/div[3]"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 62, "global_sentence_id": 101, "edu_l1_label": "EDU_O"}, {"txt": "See also Figure S2.", "language": "english", "position": {"atoms": [{"position_id": 4669, "txt": "See also ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/figure/span[2]/span/div[4]"}, {"position_id": 4671, "txt": "Figure S2", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/figure/span[2]/span/div[4]/a/span/span"}, {"position_id": 4673, "txt": ".", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[1]/figure/span[2]/span/div[4]/a"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 63, "global_sentence_id": 102, "edu_l1_label": "EDU_O"}, {"txt": "In addition to CENP-A, alpha-satellite repeats within centromere cores in humans are also bound by the sequence-specific DNA-binding protein CENP-B, which occupies a non-palindromic A/T-rich 17 bp CENP-B box3,4 that predominantly punctuates alternating repeats within alpha-satellite HORs48 (Figures 3C and S3A).", "language": "english", "position": {"atoms": [{"position_id": 4675, "txt": "In addition to CENP-A, alpha-satellite repeats within centromere cores in humans are also bound by the sequence-specific DNA-binding protein CENP-B, which occupies a non-palindromic A/T-rich 17 bp CENP-B box", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div"}, {"position_id": 4677, "txt": "3", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[1]/span/span/sup"}, {"position_id": 4679, "txt": ",", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/sup[1]"}, {"position_id": 4681, "txt": "4", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[2]/span/span/sup"}, {"position_id": 4683, "txt": " that predominantly punctuates alternating repeats within alpha-satellite HORs", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[2]"}, {"position_id": 4685, "txt": "48", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[3]/span/span/sup"}, {"position_id": 4687, "txt": " (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[3]"}, {"position_id": 4689, "txt": "Figures 3", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[4]/span/span"}, {"position_id": 4691, "txt": "C and ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[4]"}, {"position_id": 4693, "txt": "S3", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[5]/span/span"}, {"position_id": 4695, "txt": "A).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[5]"}]}, "tags": [], "label": "content", "web_segment_id": 64, "global_sentence_id": 103, "edu_l1_label": "IOS"}, {"txt": " CENP-B occupancy is known to induce neighboring nucleosome positioning along these repeats in vitro,49,50 and CpG methylation is a known modifier of CENP-B affinity and occupancy in vitro.51,52 Given these features, we next sought to determine whether CENP-B occupancy could be playing a role in the phasing of dichromatin to the alpha-satellite repeat within the centromere core.", "language": "english", "position": {"atoms": [{"position_id": 4696, "txt": " CENP-B occupancy is known to induce neighboring nucleosome positioning along these repeats ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[5]"}, {"position_id": 4698, "txt": "in vitro", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/em[1]"}, {"position_id": 4700, "txt": ",", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/em[1]"}, {"position_id": 4702, "txt": "49", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[6]/span/span/sup"}, {"position_id": 4704, "txt": ",", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/sup[2]"}, {"position_id": 4706, "txt": "50", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[7]/span/span/sup"}, {"position_id": 4708, "txt": " and CpG methylation is a known modifier of CENP-B affinity and occupancy ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[7]"}, {"position_id": 4710, "txt": "in vitro", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/em[2]"}, {"position_id": 4712, "txt": ".", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/em[2]"}, {"position_id": 4714, "txt": "51", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[8]/span/span/sup"}, {"position_id": 4716, "txt": ",", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/sup[3]"}, {"position_id": 4718, "txt": "52", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[9]/span/span/sup"}, {"position_id": 4720, "txt": " Given these features, we next sought to determine whether CENP-B occupancy could be playing a role in the phasing of dichromatin to the alpha-satellite repeat within the centromere core.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[9]"}]}, "tags": ["em"], "label": "content", "web_segment_id": 64, "global_sentence_id": 104, "edu_l1_label": "IOS"}, {"txt": " CENP-B occupancy along the CENP-B box is readily resolved in vitro using DNaseI footprinting,49 and we similarly found that CENP-B occupancy can be resolved in vivo using Fiber-seq (Figures 4A and 4B).", "language": "english", "position": {"atoms": [{"position_id": 4721, "txt": " CENP-B occupancy along the CENP-B box is readily resolved ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[9]"}, {"position_id": 4723, "txt": "in vitro", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/em[3]"}, {"position_id": 4725, "txt": " using DNaseI footprinting,", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/em[3]"}, {"position_id": 4727, "txt": "49", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[10]/span/span/sup"}, {"position_id": 4729, "txt": " and we similarly found that CENP-B occupancy can be resolved ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[10]"}, {"position_id": 4731, "txt": "in vivo", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/em[4]"}, {"position_id": 4733, "txt": " using Fiber-seq (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/em[4]"}, {"position_id": 4735, "txt": "Figures 4", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[11]/span/span"}, {"position_id": 4737, "txt": "A and 4B).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[11]"}]}, "tags": ["em"], "label": "content", "web_segment_id": 64, "global_sentence_id": 105, "edu_l1_label": "IOS"}, {"txt": " Specifically, CENP-B boxes located within the centromere core demonstrate occupancy with an MTase footprint that mirrors the in vitro CENP-B DNaseI footprint and the protein-DNA contacts within the crystal structure of the CENP-B-DNA complex3,49,53 (Figure 4B).", "language": "english", "position": {"atoms": [{"position_id": 4738, "txt": " Specifically, CENP-B boxes located within the centromere core demonstrate occupancy with an MTase footprint that mirrors the ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[11]"}, {"position_id": 4740, "txt": "in vitro", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/em[5]"}, {"position_id": 4742, "txt": " CENP-B DNaseI footprint and the protein-DNA contacts within the crystal structure of the CENP-B-DNA complex", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/em[5]"}, {"position_id": 4744, "txt": "3", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[12]/span/span/sup"}, {"position_id": 4746, "txt": ",", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/sup[4]"}, {"position_id": 4748, "txt": "49", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[13]/span/span/sup"}, {"position_id": 4750, "txt": ",", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/sup[5]"}, {"position_id": 4752, "txt": "53", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[14]/span/span/sup"}, {"position_id": 4754, "txt": " (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[14]"}, {"position_id": 4756, "txt": "Figure 4", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[15]/span/span"}, {"position_id": 4758, "txt": "B).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[15]"}]}, "tags": ["em"], "label": "content", "web_segment_id": 64, "global_sentence_id": 106, "edu_l1_label": "IOS"}, {"txt": " Furthermore, consistent with prior in vitro findings,51,52 we observed that CpG methylation at even one of the 2 CpG di-nucleotides within the CENP-B box largely abrogates CENP-B occupancy within the centromere core in vivo (Figures 4B, 4C, and S3B), indicating that CpG methylation plays a dominant role in modulating CENP-B occupancy within the centromere core.", "language": "english", "position": {"atoms": [{"position_id": 4759, "txt": " Furthermore, consistent with prior ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[15]"}, {"position_id": 4761, "txt": "in vitro", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/em[6]"}, {"position_id": 4763, "txt": " findings,", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/em[6]"}, {"position_id": 4765, "txt": "51", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[16]/span/span/sup"}, {"position_id": 4767, "txt": ",", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/sup[6]"}, {"position_id": 4769, "txt": "52", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[17]/span/span/sup"}, {"position_id": 4771, "txt": " we observed that CpG methylation at even one of the 2 CpG di-nucleotides within the CENP-B box largely abrogates CENP-B occupancy within the centromere core ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[17]"}, {"position_id": 4773, "txt": "in vivo", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/em[7]"}, {"position_id": 4775, "txt": " (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/em[7]"}, {"position_id": 4777, "txt": "Figures 4", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[18]/span/span"}, {"position_id": 4779, "txt": "B, 4C, and ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[18]"}, {"position_id": 4781, "txt": "S3", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[19]/span/span"}, {"position_id": 4783, "txt": "B), indicating that CpG methylation plays a dominant role in modulating CENP-B occupancy within the centromere core.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[19]"}]}, "tags": ["em"], "label": "content", "web_segment_id": 64, "global_sentence_id": 107, "edu_l1_label": "IOS"}, {"txt": " Notably, we found that CENP-B boxes that lack CpG methylation within the centromere core preferentially overlap accessible chromatin patches and position nucleosomes immediately adjacent to them (Figures S3C and S3D), thereby organizing dichromatin within the centromere core relative to the underlying alpha-satellite DNA repeat.", "language": "english", "position": {"atoms": [{"position_id": 4784, "txt": " Notably, we found that CENP-B boxes that lack CpG methylation within the centromere core preferentially overlap accessible chromatin patches and position nucleosomes immediately adjacent to them (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[19]"}, {"position_id": 4786, "txt": "Figures S3", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[20]/span/span"}, {"position_id": 4788, "txt": "C and S3D), thereby organizing dichromatin within the centromere core relative to the underlying alpha-satellite DNA repeat.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[20]"}]}, "tags": [], "label": "content", "web_segment_id": 64, "global_sentence_id": 108, "edu_l1_label": "IOS"}, {"txt": " However, this feature was limited to the centromere core, as CENP-B boxes outside of the centromere core were largely unoccupied, irrespective of their CpG methylation status (Figure 4C), with weak CENP-B occupancy only observed at sporadic unmethylated CENP-B boxes located within alpha-satellite HORs flanking the centromere core, a pattern consistent with prior imaging studies.7 Together, these findings suggest a model whereby CENP-B occupancy at hypo-CpG-methylated CENP-B boxes within the centromere core organizes the chromatin architecture to mirror the underlying alpha-satellite repeat.", "language": "english", "position": {"atoms": [{"position_id": 4789, "txt": " However, this feature was limited to the centromere core, as CENP-B boxes outside of the centromere core were largely unoccupied, irrespective of their CpG methylation status (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[20]"}, {"position_id": 4791, "txt": "Figure 4", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[21]/span/span"}, {"position_id": 4793, "txt": "C), with weak CENP-B occupancy only observed at sporadic unmethylated CENP-B boxes located within alpha-satellite HORs flanking the centromere core, a pattern consistent with prior imaging studies.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[21]"}, {"position_id": 4795, "txt": "7", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[22]/span/span/sup"}, {"position_id": 4797, "txt": " Together, these findings suggest a model whereby CENP-B occupancy at hypo-CpG-methylated CENP-B boxes within the centromere core organizes the chromatin architecture to mirror the underlying alpha-satellite repeat.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/div/a[22]"}]}, "tags": [], "label": "content", "web_segment_id": 64, "global_sentence_id": 109, "edu_l1_label": "IOS"}, {"txt": "<img 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CENP-B selectively occupies and phases dichromatin within the centromere core", "language": "english", "position": {"atoms": [{"position_id": 4799, "txt": "Figure 4", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/figure/span[2]/span/p/span"}, {"position_id": 4801, "txt": ". CENP-B selectively occupies and phases dichromatin within the centromere core", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/figure/span[2]/span/p/span"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 66, "global_sentence_id": 111, "edu_l1_label": "EDU_O"}, {"txt": "(A) Genomic locus showing bulk CpG methylation and per-molecule m6A-marked chromatin architectures and CpG methylations demonstrating single-molecule footprints at centromere core CENP-B boxes.", "language": "english", "position": {"atoms": [{"position_id": 4803, "txt": "(A) Genomic locus showing bulk CpG methylation and per-molecule m6A-marked chromatin architectures and CpG methylations demonstrating single-molecule footprints at centromere core CENP-B boxes.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/figure/span[2]/span/div[1]"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 67, "global_sentence_id": 112, "edu_l1_label": "EDU_O"}, {"txt": "(B) Structure of CENP-B bound to a CENP-B box (PDB:", "language": "english", "position": {"atoms": [{"position_id": 4805, "txt": "(B) Structure of CENP-B bound to a CENP-B box (PDB:", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/figure/span[2]/span/div[2]"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 68, "global_sentence_id": 113, "edu_l1_label": "EDU_O"}, {"txt": " 1HLV53), as well as in vitro DNaseI footprint of a CENP-B-occupied CENP-B box relative to aggregate m6A methylation profile at centromere core CENP-B boxes containing various levels of methylated CpGs (mCpGs).", "language": "english", "position": {"atoms": [{"position_id": 4806, "txt": " ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/figure/span[2]/span/div[2]"}, {"position_id": 4808, "txt": "1HLV", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/figure/span[2]/span/div[2]/a[1]/span/span"}, {"position_id": 4810, "txt": "53", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/figure/span[2]/span/div[2]/a[2]/span/span/sup"}, {"position_id": 4812, "txt": "), as well as ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/figure/span[2]/span/div[2]/a[2]"}, {"position_id": 4814, "txt": "in vitro", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/figure/span[2]/span/div[2]/em"}, {"position_id": 4816, "txt": " DNaseI footprint of a CENP-B-occupied CENP-B box relative to aggregate m6A methylation profile at centromere core CENP-B boxes containing various levels of methylated CpGs (mCpGs).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/figure/span[2]/span/div[2]/em"}]}, "tags": ["img", "em"], "label": "figure_title", "web_segment_id": 68, "global_sentence_id": 114, "edu_l1_label": "EDU_O"}, {"txt": "(C) Box-and-whisker plots of footprint scores at CENP-B boxes within various satellite regions as a function of mCpG status at the CENP-B box.", "language": "english", "position": {"atoms": [{"position_id": 4818, "txt": "(C) Box-and-whisker plots of footprint scores at CENP-B boxes within various satellite regions as a function of mCpG status at the CENP-B box.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/figure/span[2]/span/div[3]"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 69, "global_sentence_id": 115, "edu_l1_label": "EDU_O"}, {"txt": " Higher scores quantitatively indicate greater CENP-B occupancy (∗p < 0.01 Mann-Whitney).", "language": "english", "position": {"atoms": [{"position_id": 4819, "txt": " Higher scores quantitatively indicate greater CENP-B occupancy (∗", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/figure/span[2]/span/div[3]"}, {"position_id": 4821, "txt": "p", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/figure/span[2]/span/div[3]/em"}, {"position_id": 4823, "txt": " < 0.01 Mann-Whitney).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/figure/span[2]/span/div[3]/em"}]}, "tags": ["img", "em"], "label": "figure_title", "web_segment_id": 69, "global_sentence_id": 116, "edu_l1_label": "EDU_O"}, {"txt": "(D) Average density of di-nucleosome footprints and accessible chromatin patches within various genomic regions along the Y chromosome from HG002 using Fiber-seq data from the GM24385 cell line.", "language": "english", "position": {"atoms": [{"position_id": 4825, "txt": "(D) Average density of di-nucleosome footprints and accessible chromatin patches within various genomic regions along the Y chromosome from HG002 using Fiber-seq data from the GM24385 cell line.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/figure/span[2]/span/div[4]"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 70, "global_sentence_id": 117, "edu_l1_label": "EDU_O"}, {"txt": "(E) Heatmap of the median spectral density for centromere core and euchromatic regions along the Y chromosome from HG002 using Fiber-seq data from the GM24385 cell line.", "language": "english", "position": {"atoms": [{"position_id": 4827, "txt": "(E) Heatmap of the median spectral density for centromere core and euchromatic regions along the Y chromosome from HG002 using Fiber-seq data from the GM24385 cell line.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/figure/span[2]/span/div[5]"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 71, "global_sentence_id": 118, "edu_l1_label": "EDU_O"}, {"txt": "See also Figure S3.", "language": "english", "position": {"atoms": [{"position_id": 4829, "txt": "See also ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/figure/span[2]/span/div[6]"}, {"position_id": 4831, "txt": "Figure S3", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/figure/span[2]/span/div[6]/a/span/span"}, {"position_id": 4833, "txt": ".", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[2]/figure/span[2]/span/div[6]/a"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 72, "global_sentence_id": 119, "edu_l1_label": "EDU_O"}, {"txt": "To disentangle the role of CENP-B in dichromatin formation, we evaluated chromatin architectures along the Y chromosome centromere, which is formed along alpha-satellite repeats that lack CENP-B boxes.54 The application of Fiber-seq to 46,XY GM24385 cells followed by mapping to the complete GM24385 reference genome (i.e., HG002)10 demonstrated a marked enrichment in both compacted di-nucleosome footprints and large patches of accessible chromatin within the Y chromosome centromere core (Figures 4D and S3E).", "language": "english", "position": {"atoms": [{"position_id": 4835, "txt": "To disentangle the role of CENP-B in dichromatin formation, we evaluated chromatin architectures along the Y chromosome centromere, which is formed along alpha-satellite repeats that lack CENP-B boxes.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[3]"}, {"position_id": 4837, "txt": "54", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[3]/a[1]/span/span/sup"}, {"position_id": 4839, "txt": " The application of Fiber-seq to 46,XY GM24385 cells followed by mapping to the complete GM24385 reference genome (i.e., HG002)", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[3]/a[1]"}, {"position_id": 4841, "txt": "10", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[3]/a[2]/span/span/sup"}, {"position_id": 4843, "txt": " demonstrated a marked enrichment in both compacted di-nucleosome footprints and large patches of accessible chromatin within the Y chromosome centromere core (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[3]/a[2]"}, {"position_id": 4845, "txt": "Figures 4", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[3]/a[3]/span/span"}, {"position_id": 4847, "txt": "D and ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[3]/a[3]"}, {"position_id": 4849, "txt": "S3", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[3]/a[4]/span/span"}, {"position_id": 4851, "txt": "E).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[3]/a[4]"}]}, "tags": [], "label": "content", "web_segment_id": 73, "global_sentence_id": 120, "edu_l1_label": "IOS"}, {"txt": " However, in contrast to studies using the short-read sequencing method,40 higher-order chromatin organization within the centromere core region of chromosome Y did not mirror the underlying alpha-satellite repeat unit but rather was a continuation of the canonical chromatin repeat unit observed throughout the rest of the HG002 genome (Figure 4E).", "language": "english", "position": {"atoms": [{"position_id": 4852, "txt": " However, in contrast to studies using the short-read sequencing method,", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[3]/a[4]"}, {"position_id": 4854, "txt": "40", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[3]/a[5]/span/span/sup"}, {"position_id": 4856, "txt": " higher-order chromatin organization within the centromere core region of chromosome Y did not mirror the underlying alpha-satellite repeat unit but rather was a continuation of the canonical chromatin repeat unit observed throughout the rest of the HG002 genome (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[3]/a[5]"}, {"position_id": 4858, "txt": "Figure 4", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[3]/a[6]/span/span"}, {"position_id": 4860, "txt": "E).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[3]/a[6]"}]}, "tags": [], "label": "content", "web_segment_id": 73, "global_sentence_id": 121, "edu_l1_label": "IOS"}, {"txt": " Together, these findings indicate that the phasing of chromatin architectures along the alpha-satellite HOR is intricately intertwined with that of CENP-B occupancy and that dichromatin formation within these regions can form irrespective of CENP-B.", "language": "english", "position": {"atoms": [{"position_id": 4861, "txt": " Together, these findings indicate that the phasing of chromatin architectures along the alpha-satellite HOR is intricately intertwined with that of CENP-B occupancy and that dichromatin formation within these regions can form irrespective of CENP-B.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[3]/div[3]/a[6]"}]}, "tags": [], "label": "content", "web_segment_id": 73, "global_sentence_id": 122, "edu_l1_label": "IOS"}, {"txt": "Centromere core dichromatin architecture is conserved across highly divergent regional centromeres", "language": "english", "position": {"atoms": [{"position_id": 4863, "txt": "Centromere core dichromatin architecture is conserved across highly divergent regional centromeres", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/h3"}]}, "tags": ["h3"], "label": "title2", "web_segment_id": 74, "global_sentence_id": 123, "edu_l1_label": "IOS"}, {"txt": "We next sought to evaluate the conservation of centromere core dichromatin architecture between multiple human genomes, as the underlying DNA sequence and structure of each centromere can markedly differ between individuals.38 To accomplish this, we applied Fiber-seq to CHM1 and GM24385 cells, as a reference genome for all centromeres within both of these cells was recently resolved.38 Notably, centromere core regions (i.e., hypo-CpG-methylated regions) within each centromere markedly diverge in both their sequence content and location when compared to CHM13 cells (Figures 5A, 5B, and S4).", "language": "english", "position": {"atoms": [{"position_id": 4865, "txt": "We next sought to evaluate the conservation of centromere core dichromatin architecture between multiple human genomes, as the underlying DNA sequence and structure of each centromere can markedly differ between individuals.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/div"}, {"position_id": 4867, "txt": "38", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/div/a[1]/span/span/sup"}, {"position_id": 4869, "txt": " To accomplish this, we applied Fiber-seq to CHM1 and GM24385 cells, as a reference genome for all centromeres within both of these cells was recently resolved.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/div/a[1]"}, {"position_id": 4871, "txt": "38", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/div/a[2]/span/span/sup"}, {"position_id": 4873, "txt": " Notably, centromere core regions (i.e., hypo-CpG-methylated regions) within each centromere markedly diverge in both their sequence content and location when compared to CHM13 cells (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/div/a[2]"}, {"position_id": 4875, "txt": "Figures 5", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/div/a[3]/span/span"}, {"position_id": 4877, "txt": "A, 5B, and ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/div/a[3]"}, {"position_id": 4879, "txt": "S4", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/div/a[4]/span/span"}, {"position_id": 4881, "txt": ").", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/div/a[4]"}]}, "tags": [], "label": "content", "web_segment_id": 75, "global_sentence_id": 124, "edu_l1_label": "IOS"}, {"txt": " However, despite the sequence divergence of centromere cores within CHM13 cells or between CHM13 cells and CHM1 and GM24385 cells, these centromere core regions are still marked by dichromatin—exhibiting both compacted di-nucleosome footprints as well as large patches of accessible chromatin intermingled along the same chromatin fiber (Figures 5B, 5C, and S4A).", "language": "english", "position": {"atoms": [{"position_id": 4882, "txt": " However, despite the sequence divergence of centromere cores within CHM13 cells or between CHM13 cells and CHM1 and GM24385 cells, these centromere core regions are still marked by dichromatin—exhibiting both compacted di-nucleosome footprints as well as large patches of accessible chromatin intermingled along the same chromatin fiber (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/div/a[4]"}, {"position_id": 4884, "txt": "Figures 5", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/div/a[5]/span/span"}, {"position_id": 4886, "txt": "B, 5C, and ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/div/a[5]"}, {"position_id": 4888, "txt": "S4", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/div/a[6]/span/span"}, {"position_id": 4890, "txt": "A).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/div/a[6]"}]}, "tags": [], "label": "content", "web_segment_id": 75, "global_sentence_id": 125, "edu_l1_label": "IOS"}, {"txt": " In addition, the higher-order chromatin organization along the autosomes and X chromosome within CHM1 and GM24385 cells (i.e., centromeres that contain CENP-B boxes) similarly displayed a chromatin repeat unit of 170 bp selectively within centromere cores (Figures S4B and S4C).", "language": "english", "position": {"atoms": [{"position_id": 4891, "txt": " In addition, the higher-order chromatin organization along the autosomes and X chromosome within CHM1 and GM24385 cells (i.e., centromeres that contain CENP-B boxes) similarly displayed a chromatin repeat unit of 170 bp selectively within centromere cores (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/div/a[6]"}, {"position_id": 4893, "txt": "Figures S4", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/div/a[7]/span/span"}, {"position_id": 4895, "txt": "B and S4C).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/div/a[7]"}]}, "tags": [], "label": "content", "web_segment_id": 75, "global_sentence_id": 126, "edu_l1_label": "IOS"}, {"txt": " Together, these findings demonstrate that dichromatin is a conserved feature of chromatin compaction within the centromere core in humans.", "language": "english", "position": {"atoms": [{"position_id": 4896, "txt": " Together, these findings demonstrate that dichromatin is a conserved feature of chromatin compaction within the centromere core in humans.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/div/a[7]"}]}, "tags": [], "label": "content", "web_segment_id": 75, "global_sentence_id": 127, "edu_l1_label": "IOS"}, {"txt": "<img https://wcd-image-bucket-test.oss-cn-zhangjiakou.aliyuncs.com/raw/246x3a31cqOV3UTQcj1axcgA.jpeg", "language": "english", "position": {"atoms": [{"position_id": 997, "txt": "<img https://wcd-image-bucket-test.oss-cn-zhangjiakou.aliyuncs.com/raw/246x3a31cqOV3UTQcj1axcgA.jpeg", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/figure/span[1]/img"}]}, "tags": ["img"], "label": "figure", "web_segment_id": 76, "global_sentence_id": 128, "edu_l1_label": "EDU_O"}, {"txt": "Figure 5. Dichromatin is a conserved feature of centromere core chromatin in humans", "language": "english", "position": {"atoms": [{"position_id": 4898, "txt": "Figure 5", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/figure/span[2]/span/p/span"}, {"position_id": 4900, "txt": ". Dichromatin is a conserved feature of centromere core chromatin in humans", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/figure/span[2]/span/p/span"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 77, "global_sentence_id": 129, "edu_l1_label": "EDU_O"}, {"txt": "(A and B) Genomic locus showing chromosome 5 centromere in both CHM13 (A) and CHM1 (B) cells, including CpG methylation and accessible chromatin patches.", "language": "english", "position": {"atoms": [{"position_id": 4902, "txt": "(A and B) Genomic locus showing chromosome 5 centromere in both CHM13 (A) and CHM1 (B) cells, including CpG methylation and accessible chromatin patches.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/figure/span[2]/span/div[1]"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 78, "global_sentence_id": 130, "edu_l1_label": "EDU_O"}, {"txt": " (Bottom) Single-molecule chromatin architecture along individual alpha-satellite repeats within centromere core and non-core alpha-satellite repeats.", "language": "english", "position": {"atoms": [{"position_id": 4903, "txt": " (Bottom) Single-molecule chromatin architecture along individual alpha-satellite repeats within centromere core and non-core alpha-satellite repeats.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/figure/span[2]/span/div[1]"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 78, "global_sentence_id": 131, "edu_l1_label": "EDU_O"}, {"txt": "(C) Hexbin plot showing the single-molecule density of di-nucleosome footprints and accessible chromatin patches within various CHM1 centromere cores and surrounding regions.", "language": "english", "position": {"atoms": [{"position_id": 4905, "txt": "(C) Hexbin plot showing the single-molecule density of di-nucleosome footprints and accessible chromatin patches within various CHM1 centromere cores and surrounding regions.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/figure/span[2]/span/div[2]"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 79, "global_sentence_id": 132, "edu_l1_label": "EDU_O"}, {"txt": "See also Figure S4.", "language": "english", "position": {"atoms": [{"position_id": 4907, "txt": "See also ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/figure/span[2]/span/div[3]"}, {"position_id": 4909, "txt": "Figure S4", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/figure/span[2]/span/div[3]/a/span/span"}, {"position_id": 4911, "txt": ".", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[1]/figure/span[2]/span/div[3]/a"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 80, "global_sentence_id": 133, "edu_l1_label": "EDU_O"}, {"txt": "To understand if dichromatin is a feature of regional centromeres that lack alpha-satellite repeats, we next applied Fiber-seq to resolve chromatin architectures within gibbon centromeres.", "language": "english", "position": {"atoms": [{"position_id": 4913, "txt": "To understand if dichromatin is a feature of regional centromeres that lack alpha-satellite repeats, we next applied Fiber-seq to resolve chromatin architectures within gibbon centromeres.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div"}]}, "tags": [], "label": "content", "web_segment_id": 81, "global_sentence_id": 134, "edu_l1_label": "IOS"}, {"txt": " Gibbons have undergone rapid karyotypic evolution accompanied by the inactivation of many ancestral centromeres and the formation of evolutionary new centromeres55 that are largely composed of transposable elements that lack CENP-B boxes and alpha-satellite repeats.56 We first assembled and validated the sequence of five centromeres from the eastern hoolock gibbon (Hoolock leuconedys) by applying Oxford Nanopore (ONT) sequencing, Hi-C, Fiber-seq, and CENP-A Cleavage Under Targets & Release Using Nuclease (CUT&RUN) to a 38,XX lymphoblastoid cell line derived from Betty57 (Figure 6A).", "language": "english", "position": {"atoms": [{"position_id": 4914, "txt": " Gibbons have undergone rapid karyotypic evolution accompanied by the inactivation of many ancestral centromeres and the formation of evolutionary new centromeres", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div"}, {"position_id": 4916, "txt": "55", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div/a[1]/span/span/sup"}, {"position_id": 4918, "txt": " that are largely composed of transposable elements that lack CENP-B boxes and alpha-satellite repeats.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div/a[1]"}, {"position_id": 4920, "txt": "56", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div/a[2]/span/span/sup"}, {"position_id": 4922, "txt": " We first assembled and validated the sequence of five centromeres from the eastern hoolock gibbon (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div/a[2]"}, {"position_id": 4924, "txt": "Hoolock leuconedys", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div/em"}, {"position_id": 4926, "txt": ") by applying Oxford Nanopore (ONT) sequencing, Hi-C, Fiber-seq, and CENP-A Cleavage Under Targets & Release Using Nuclease (CUT&RUN) to a 38,XX lymphoblastoid cell line derived from Betty", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div/em"}, {"position_id": 4928, "txt": "57", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div/a[3]/span/span/sup"}, {"position_id": 4930, "txt": " (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div/a[3]"}, {"position_id": 4932, "txt": "Figure 6", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div/a[4]/span/span"}, {"position_id": 4934, "txt": "A).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div/a[4]"}]}, "tags": ["em"], "label": "content", "web_segment_id": 81, "global_sentence_id": 135, "edu_l1_label": "IOS"}, {"txt": " These centromeres contained hypo-CpG-methylated regions corresponding to sites of CENP-A occupancy (Figures 6B and S5).", "language": "english", "position": {"atoms": [{"position_id": 4935, "txt": " These centromeres contained hypo-CpG-methylated regions corresponding to sites of CENP-A occupancy (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div/a[4]"}, {"position_id": 4937, "txt": "Figures 6", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div/a[5]/span/span"}, {"position_id": 4939, "txt": "B and ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div/a[5]"}, {"position_id": 4941, "txt": "S5", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div/a[6]/span/span"}, {"position_id": 4943, "txt": ").", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div/a[6]"}]}, "tags": [], "label": "content", "web_segment_id": 81, "global_sentence_id": 136, "edu_l1_label": "IOS"}, {"txt": " However, the sequence of these centromere cores was largely derived from transposable elements, not alpha-satellite repeats.", "language": "english", "position": {"atoms": [{"position_id": 4944, "txt": " However, the sequence of these centromere cores was largely derived from transposable elements, not alpha-satellite repeats.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div/a[6]"}]}, "tags": [], "label": "content", "web_segment_id": 81, "global_sentence_id": 137, "edu_l1_label": "IOS"}, {"txt": " Notably, despite the lack of alpha-satellite repeats within these centromere cores, these regions were still marked by dichromatin—exhibiting both compacted di-nucleosome footprints and clustered patches of accessible chromatin intermingled along the same chromatin fibers (Figures 6B, 6C, and S5E).", "language": "english", "position": {"atoms": [{"position_id": 4945, "txt": " Notably, despite the lack of alpha-satellite repeats within these centromere cores, these regions were still marked by dichromatin—exhibiting both compacted di-nucleosome footprints and clustered patches of accessible chromatin intermingled along the same chromatin fibers (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div/a[6]"}, {"position_id": 4947, "txt": "Figures 6", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div/a[7]/span/span"}, {"position_id": 4949, "txt": "B, 6C, and ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div/a[7]"}, {"position_id": 4951, "txt": "S5", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div/a[8]/span/span"}, {"position_id": 4953, "txt": "E).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div/a[8]"}]}, "tags": [], "label": "content", "web_segment_id": 81, "global_sentence_id": 138, "edu_l1_label": "IOS"}, {"txt": " Unlike human autosomes, the higher-order chromatin organization within the eastern hoolock gibbon centromere core regions appeared to be a continuation of the canonical chromatin repeat unit observed within flanking regions, albeit less organized owing to the dichromatin features (Figure 6D).", "language": "english", "position": {"atoms": [{"position_id": 4954, "txt": " Unlike human autosomes, the higher-order chromatin organization within the eastern hoolock gibbon centromere core regions appeared to be a continuation of the canonical chromatin repeat unit observed within flanking regions, albeit less organized owing to the dichromatin features (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div/a[8]"}, {"position_id": 4956, "txt": "Figure 6", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div/a[9]/span/span"}, {"position_id": 4958, "txt": "D).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div/a[9]"}]}, "tags": [], "label": "content", "web_segment_id": 81, "global_sentence_id": 139, "edu_l1_label": "IOS"}, {"txt": " Together, these findings demonstrate that dichromatin is a conserved feature of centromere core chromatin compaction, irrespective of the underlying DNA sequence.", "language": "english", "position": {"atoms": [{"position_id": 4959, "txt": " Together, these findings demonstrate that dichromatin is a conserved feature of centromere core chromatin compaction, irrespective of the underlying DNA sequence.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/div/a[9]"}]}, "tags": [], "label": "content", "web_segment_id": 81, "global_sentence_id": 140, "edu_l1_label": "IOS"}, {"txt": "<img https://wcd-image-bucket-test.oss-cn-zhangjiakou.aliyuncs.com/raw/2CgnEyZhllN3LnHJyLOBlU.jpeg", "language": "english", "position": {"atoms": [{"position_id": 1054, "txt": "<img https://wcd-image-bucket-test.oss-cn-zhangjiakou.aliyuncs.com/raw/2CgnEyZhllN3LnHJyLOBlU.jpeg", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/figure/span[1]/img"}]}, "tags": ["img"], "label": "figure", "web_segment_id": 82, "global_sentence_id": 141, "edu_l1_label": "EDU_O"}, {"txt": "Figure 6. Centromere core dichromatin architecture does not require alpha-satellite repeats", "language": "english", "position": {"atoms": [{"position_id": 4961, "txt": "Figure 6", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/figure/span[2]/span/p/span"}, {"position_id": 4963, "txt": ". Centromere core dichromatin architecture does not require alpha-satellite repeats", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/figure/span[2]/span/p/span"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 83, "global_sentence_id": 142, "edu_l1_label": "EDU_O"}, {"txt": "(A) Schematic for Fiber-seq in a lymphoblastoid cell line from the eastern hoolock gibbon (Hoolock leuconedys) Betty.", "language": "english", "position": {"atoms": [{"position_id": 4965, "txt": "(A) Schematic for Fiber-seq in a lymphoblastoid cell line from the eastern hoolock gibbon (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/figure/span[2]/span/div[1]"}, {"position_id": 4967, "txt": "Hoolock leuconedys", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/figure/span[2]/span/div[1]/em[1]"}, {"position_id": 4969, "txt": ") Betty.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/figure/span[2]/span/div[1]/em[1]"}]}, "tags": ["img", "em"], "label": "figure_title", "web_segment_id": 84, "global_sentence_id": 143, "edu_l1_label": "EDU_O"}, {"txt": " Ultralong-read Nanopore sequencing was used for de novo genome assembly, which was validated using the contigs assembled using Fiber-seq data.", "language": "english", "position": {"atoms": [{"position_id": 4970, "txt": " Ultralong-read Nanopore sequencing was used for ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/figure/span[2]/span/div[1]/em[1]"}, {"position_id": 4972, "txt": "de novo", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/figure/span[2]/span/div[1]/em[2]"}, {"position_id": 4974, "txt": " genome assembly, which was validated using the contigs assembled using Fiber-seq data.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/figure/span[2]/span/div[1]/em[2]"}]}, "tags": ["em", "img"], "label": "figure_title", "web_segment_id": 84, "global_sentence_id": 144, "edu_l1_label": "EDU_O"}, {"txt": " CENP-A CUT&RUN was used to identify centromere cores along validated assembly regions.", "language": "english", "position": {"atoms": [{"position_id": 4975, "txt": " CENP-A CUT&RUN was used to identify centromere cores along validated assembly regions.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/figure/span[2]/span/div[1]/em[2]"}]}, "tags": ["em", "img"], "label": "figure_title", "web_segment_id": 84, "global_sentence_id": 145, "edu_l1_label": "EDU_O"}, {"txt": "(B) Genomic locus showing chromosome 8 centromere, including different repeat classes, CpG methylation, CENP-A CUT&RUN, and Fiber-seq-derived di-nucleosome footprint density, and chromatin accessibility.", "language": "english", "position": {"atoms": [{"position_id": 4977, "txt": "(B) Genomic locus showing chromosome 8 centromere, including different repeat classes, CpG methylation, CENP-A CUT&RUN, and Fiber-seq-derived di-nucleosome footprint density, and chromatin accessibility.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/figure/span[2]/span/div[2]"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 85, "global_sentence_id": 146, "edu_l1_label": "EDU_O"}, {"txt": " (Bottom) Single-molecule chromatin architecture from pericentromeric gene-regulatory elements, centromere core, and heterochromatin.", "language": "english", "position": {"atoms": [{"position_id": 4978, "txt": " (Bottom) Single-molecule chromatin architecture from pericentromeric gene-regulatory elements, centromere core, and heterochromatin.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/figure/span[2]/span/div[2]"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 85, "global_sentence_id": 147, "edu_l1_label": "EDU_O"}, {"txt": "(C) Hexbin plot showing the single-molecule density of di-nucleosome footprints and accessible chromatin patches within centromere core and flanking regions.", "language": "english", "position": {"atoms": [{"position_id": 4980, "txt": "(C) Hexbin plot showing the single-molecule density of di-nucleosome footprints and accessible chromatin patches within centromere core and flanking regions.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/figure/span[2]/span/div[3]"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 86, "global_sentence_id": 148, "edu_l1_label": "EDU_O"}, {"txt": "(D) Box-and-whisker plots of the chromatin repeat lengths from centromere core and flanking regions.", "language": "english", "position": {"atoms": [{"position_id": 4982, "txt": "(D) Box-and-whisker plots of the chromatin repeat lengths from centromere core and flanking regions.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/figure/span[2]/span/div[4]"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 87, "global_sentence_id": 149, "edu_l1_label": "EDU_O"}, {"txt": " On the bottom the peak chromatin repeat unit as well as the medial spectral density at that repeat unit are indicated, showing that chromatin is more disorganized within the centromere core.", "language": "english", "position": {"atoms": [{"position_id": 4983, "txt": " On the bottom the peak chromatin repeat unit as well as the medial spectral density at that repeat unit are indicated, showing that chromatin is more disorganized within the centromere core.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/figure/span[2]/span/div[4]"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 87, "global_sentence_id": 150, "edu_l1_label": "EDU_O"}, {"txt": "See also Figure S5.", "language": "english", "position": {"atoms": [{"position_id": 4985, "txt": "See also ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/figure/span[2]/span/div[5]"}, {"position_id": 4987, "txt": "Figure S5", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/figure/span[2]/span/div[5]/a/span/span"}, {"position_id": 4989, "txt": ".", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[2]/section[4]/div[2]/figure/span[2]/span/div[5]/a"}]}, "tags": ["img"], "label": "figure_title", "web_segment_id": 88, "global_sentence_id": 151, "edu_l1_label": "EDU_O"}, {"txt": "Discussion", "language": "english", "position": {"atoms": [{"position_id": 4991, "txt": "Discussion", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/h2"}]}, "tags": ["h2"], "label": "title1", "web_segment_id": 89, "global_sentence_id": 152, "edu_l1_label": "BOS"}, {"txt": "We demonstrate that pairing complete reference centromere genome assemblies with Fiber-seq enables the delineation of chromatin architectures within centromeres at single-molecule and near-single-nucleotide resolution.", "language": "english", "position": {"atoms": [{"position_id": 4993, "txt": "We demonstrate that pairing complete reference centromere genome assemblies with Fiber-seq enables the delineation of chromatin architectures within centromeres at single-molecule and near-single-nucleotide resolution.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[1]"}]}, "tags": [], "label": "content", "web_segment_id": 90, "global_sentence_id": 153, "edu_l1_label": "IOS"}, {"txt": " Application of Fiber-seq to four human and non-human primate samples with complete centromere assemblies exposed a unique form of chromatin compaction within the centromere cores that is not observed elsewhere along the genome.", "language": "english", "position": {"atoms": [{"position_id": 4994, "txt": " Application of Fiber-seq to four human and non-human primate samples with complete centromere assemblies exposed a unique form of chromatin compaction within the centromere cores that is not observed elsewhere along the genome.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[1]"}]}, "tags": [], "label": "content", "web_segment_id": 90, "global_sentence_id": 154, "edu_l1_label": "IOS"}, {"txt": " Specifically, centromere cores simultaneously contain both the most accessible and compacted chromatin in the genome, with these dichotomous chromatin features both present along individual chromatin fibers.", "language": "english", "position": {"atoms": [{"position_id": 4995, "txt": " Specifically, centromere cores simultaneously contain both the most accessible and compacted chromatin in the genome, with these dichotomous chromatin features both present along individual chromatin fibers.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[1]"}]}, "tags": [], "label": "content", "web_segment_id": 90, "global_sentence_id": 155, "edu_l1_label": "IOS"}, {"txt": " In addition, unlike traditional euchromatic regulatory elements, accessible chromatin patches within the centromere core are heterogeneously positioned across individual chromatin fibers.", "language": "english", "position": {"atoms": [{"position_id": 4996, "txt": " In addition, unlike traditional euchromatic regulatory elements, accessible chromatin patches within the centromere core are heterogeneously positioned across individual chromatin fibers.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[1]"}]}, "tags": [], "label": "content", "web_segment_id": 90, "global_sentence_id": 156, "edu_l1_label": "IOS"}, {"txt": " These dichotomous features of chromatin compaction within the centromere core diverge from the standard model of heterochromatin and euchromatin compaction and are hence termed dichromatin.", "language": "english", "position": {"atoms": [{"position_id": 4997, "txt": " These dichotomous features of chromatin compaction within the centromere core diverge from the standard model of heterochromatin and euchromatin compaction and are hence termed dichromatin.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[1]"}]}, "tags": [], "label": "content", "web_segment_id": 90, "global_sentence_id": 157, "edu_l1_label": "IOS"}, {"txt": " Further work will elucidate the role of dichromatin both within and outside the centromere.", "language": "english", "position": {"atoms": [{"position_id": 4998, "txt": " Further work will elucidate the role of dichromatin both within and outside the centromere.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[1]"}]}, "tags": [], "label": "content", "web_segment_id": 90, "global_sentence_id": 158, "edu_l1_label": "IOS"}, {"txt": "These accessible chromatin patches that punctuate the centromere core create a highly plastic chromatin topology at the region of kinetochore attachment that is readily exposed to proteins essential for maintaining the centromere core.58 Specifically, whereas the surrounding chromatin within the centromere is marked by tightly compacted nucleosome arrays that often stretch >20 kb in length,17 the centromere core contains highly heterogeneous chromatin with clustered accessible chromatin patches often disrupting the ability of compacted nucleosome arrays to extend beyond ∼1 kb in length.", "language": "english", "position": {"atoms": [{"position_id": 5000, "txt": "These accessible chromatin patches that punctuate the centromere core create a highly plastic chromatin topology at the region of kinetochore attachment that is readily exposed to proteins essential for maintaining the centromere core.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[2]"}, {"position_id": 5002, "txt": "58", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[2]/a[1]/span/span/sup"}, {"position_id": 5004, "txt": " Specifically, whereas the surrounding chromatin within the centromere is marked by tightly compacted nucleosome arrays that often stretch >20 kb in length,", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[2]/a[1]"}, {"position_id": 5006, "txt": "17", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[2]/a[2]/span/span/sup"}, {"position_id": 5008, "txt": " the centromere core contains highly heterogeneous chromatin with clustered accessible chromatin patches often disrupting the ability of compacted nucleosome arrays to extend beyond ∼1 kb in length.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[2]/a[2]"}]}, "tags": [], "label": "content", "web_segment_id": 91, "global_sentence_id": 159, "edu_l1_label": "IOS"}, {"txt": "The clustering of these patches along human autosome and chromosome X centromeres potentially reflects the action of bound CENP-B homodimers59 binding to and bridging distinct CENP-B boxes in close physical proximity along the alpha-satellite array.49,60 However, these accessible chromatin patches nonetheless cluster along centromeres that lack CENP-B occupancy, albeit to a lesser degree, indicating that CENP-B occupancy may simply exist as a mechanism for stabilizing this inherent property of chromatin within the centromere core.", "language": "english", "position": {"atoms": [{"position_id": 5010, "txt": "The clustering of these patches along human autosome and chromosome X centromeres potentially reflects the action of bound CENP-B homodimers", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[3]"}, {"position_id": 5012, "txt": "59", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[3]/a[1]/span/span/sup"}, {"position_id": 5014, "txt": " binding to and bridging distinct CENP-B boxes in close physical proximity along the alpha-satellite array.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[3]/a[1]"}, {"position_id": 5016, "txt": "49", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[3]/a[2]/span/span/sup"}, {"position_id": 5018, "txt": ",", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[3]/sup"}, {"position_id": 5020, "txt": "60", "x": 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"txt": " Notably, although CENP-B boxes selectively phase surrounding chromatin to mirror the underlying alpha-satellite repeat, this phasing phenomenon was only observed on centromeres containing occupied CENP-B boxes and was not necessary for dichromatin formation in the centromere core.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[3]/a[3]"}]}, "tags": [], "label": "content", "web_segment_id": 92, "global_sentence_id": 161, "edu_l1_label": "IOS"}, {"txt": " The basic alpha-satellite repeat unit across species (i.e., 171 bp in primates, 186 bp in the fish Sparus aurata, 155 bp in both Arabidopsis and maize, and 340 bp in pigs)61 is well documented to reflect mono- or di-nucleosome lengths, and our findings suggest that the evolutionary pressure for this may, in fact, be to mediate the clustering of these accessible chromatin patches within the centromere core via the stochastic occupancy of dimeric CENP-B proteins at nearby CENP-B boxes 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"/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[4]/em[2]"}, {"position_id": 5050, "txt": "Figure 1", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[4]/a[1]/span/span"}, {"position_id": 5052, "txt": "B), and these patterns differ between centromeres (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[4]/a[1]"}, {"position_id": 5054, "txt": "Figure 1", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[4]/a[2]/span/span"}, {"position_id": 5056, "txt": "D), highlighting a need for our structural understanding of the yeast CCAN to account for these chromosome-to-chromosome and fiber-to-fiber dynamics.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[4]/a[2]"}]}, "tags": ["em"], "label": "content", "web_segment_id": 93, "global_sentence_id": 165, "edu_l1_label": "IOS"}, {"txt": " Furthermore, protein occupancy footprints at the yeast point centromeres markedly extend beyond the CDEI–III elements (Figure 1D), suggesting that Cse4 and Cbf1 rarely solo occupy the yeast centromere outside of a CCAN complex and that neighboring sequences may play a role in stabilizing CCAN occupancy.", "language": "english", "position": {"atoms": [{"position_id": 5057, "txt": " Furthermore, protein occupancy footprints at the yeast point centromeres markedly extend beyond the CDEI–III elements (", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[4]/a[2]"}, {"position_id": 5059, "txt": "Figure 1", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[4]/a[3]/span/span"}, {"position_id": 5061, "txt": "D), suggesting that Cse4 and Cbf1 rarely solo occupy the yeast centromere outside of a CCAN complex and that neighboring sequences may play a role in stabilizing CCAN occupancy.", "x": 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"content", "web_segment_id": 94, "global_sentence_id": 168, "edu_l1_label": "IOS"}, {"txt": " Furthermore, dichromatin can assemble within centromere cores that lack alpha-satellite repeats, indicating that functional conservation within centromeres is mediated at the level of chromatin, not DNA.", "language": "english", "position": {"atoms": [{"position_id": 5069, "txt": " Furthermore, dichromatin can assemble within centromere cores that lack alpha-satellite repeats, indicating that functional conservation within centromeres is mediated at the level of chromatin, not DNA.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[5]/a[1]"}]}, "tags": [], "label": "content", "web_segment_id": 94, "global_sentence_id": 169, "edu_l1_label": "IOS"}, {"txt": " This likely enables centromeres to have a large degree of plasticity in terms of their underlying DNA sequence while maintaining their overall chromatin structure.", "language": "english", "position": {"atoms": [{"position_id": 5070, "txt": " This likely enables centromeres to have a large degree of plasticity in terms of their underlying DNA sequence while maintaining their overall chromatin structure.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[5]/a[1]"}]}, "tags": [], "label": "content", "web_segment_id": 94, "global_sentence_id": 170, "edu_l1_label": "IOS"}, {"txt": " These findings are consistent with the centromere paradox61 and raise additional questions as to how the centromere core remains faithfully localized to a specific region along the genome despite its predilection to form along divergent sequences.", "language": "english", "position": {"atoms": [{"position_id": 5071, "txt": " These findings are consistent with the centromere paradox", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/div[5]/a[1]"}, {"position_id": 5073, "txt": "61", "x": 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able to determine the specific identity of the proteins that cause them.", "language": "english", "position": {"atoms": [{"position_id": 5079, "txt": "One of the limitations with Fiber-seq is that although we can observe protein footprints, we are not able to determine the specific identity of the proteins that cause them.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/section/div"}]}, "tags": [], "label": "content", "web_segment_id": 96, "global_sentence_id": 173, "edu_l1_label": "IOS"}, {"txt": " For example, within both human and gibbon centromeres, we see that the centromere core is selectively populated by a 250–300 bp footprint (Figures S1E and S5F).", "language": "english", "position": {"atoms": [{"position_id": 5080, "txt": " For example, within both human and gibbon centromeres, we see that the centromere core is selectively populated by a 250–300 bp footprint (", "x": 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CENP-A di-nucleosome.15 However, future work is needed to evaluate this hypothesis.", "language": "english", "position": {"atoms": [{"position_id": 5089, "txt": " This footprint size is markedly larger than that of the human inner kinetochore bound to a single CENP-A nucleosome", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/section/div/a[2]"}, {"position_id": 5091, "txt": "63", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/section/div/a[3]/span/span/sup"}, {"position_id": 5093, "txt": " and raises suspicion that CCAN occupancy ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/section/div/a[3]"}, {"position_id": 5095, "txt": "in vivo", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[3]/section/div/em"}, {"position_id": 5097, "txt": " includes a bridged CENP-A di-nucleosome.", "x": 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[{"position_id": 5116, "txt": "The Hia5 enzyme is available upon request.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[4]/section[2]/div"}]}, "tags": [], "label": "content", "web_segment_id": 101, "global_sentence_id": 181, "edu_l1_label": "EDU_O"}, {"txt": "Data and code availability", "language": "english", "position": {"atoms": [{"position_id": 5118, "txt": "Data and code availability", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[4]/section[3]/h3"}]}, "tags": ["h3"], "label": "title2", "web_segment_id": 102, "global_sentence_id": 182, "edu_l1_label": "EDU_O"}, {"txt": "All data used for this paper are available at GEO:", "language": "english", "position": {"atoms": [{"position_id": 5120, "txt": "All data used for this paper are available at GEO:", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[4]/section[3]/div"}]}, "tags": [], "label": "content", "web_segment_id": 103, "global_sentence_id": 183, "edu_l1_label": "EDU_O"}, {"txt": " GSE226394.", "language": "english", "position": {"atoms": [{"position_id": 5121, "txt": " ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[4]/section[3]/div"}, {"position_id": 5123, "txt": "GSE226394", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[4]/section[3]/div/a[1]/span/span"}, {"position_id": 5125, "txt": ".", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[4]/section[3]/div/a[1]"}]}, "tags": [], "label": "content", "web_segment_id": 103, "global_sentence_id": 184, "edu_l1_label": "EDU_O"}, {"txt": " All code used for this paper is available at the following Zenodo repository:", "language": "english", "position": {"atoms": [{"position_id": 5126, "txt": " All code used for this paper is available at the following Zenodo repository:", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[4]/section[3]/div/a[1]"}]}, "tags": [], "label": "content", "web_segment_id": 103, "global_sentence_id": 185, "edu_l1_label": "EDU_O"}, {"txt": " https://zenodo.org/record/7686305.", "language": "english", "position": {"atoms": [{"position_id": 5127, "txt": " ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[4]/section[3]/div/a[1]"}, {"position_id": 5129, "txt": "https://zenodo.org/record/7686305", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[4]/section[3]/div/a[2]/span/span"}, {"position_id": 5131, "txt": ".", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[4]/section[3]/div/a[2]"}]}, "tags": [], "label": "content", "web_segment_id": 103, "global_sentence_id": 186, "edu_l1_label": "EDU_O"}, {"txt": "Acknowledgments", "language": "english", "position": {"atoms": [{"position_id": 5133, "txt": "Acknowledgments", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[5]/h2"}]}, "tags": ["h2"], "label": "title1", "web_segment_id": 104, "global_sentence_id": 187, "edu_l1_label": "IOS"}, {"txt": "We thank Steven Henikoff, Stirling Churchman, and John Stamatoyannopoulos for their helpful comments and feedback.", "language": "english", "position": {"atoms": [{"position_id": 5135, "txt": "We thank Steven Henikoff, Stirling Churchman, and John Stamatoyannopoulos for their helpful comments and feedback.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[5]/div"}]}, "tags": [], "label": "content", "web_segment_id": 105, "global_sentence_id": 188, "edu_l1_label": "EDU_O"}, {"txt": " We are grateful to Nam Pho and the research computing group at the University of Washington for computational assistance.", "language": "english", "position": {"atoms": [{"position_id": 5136, "txt": " We are grateful to Nam Pho and the research computing group at the University of Washington for computational assistance.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[5]/div"}]}, "tags": [], "label": "content", "web_segment_id": 105, "global_sentence_id": 189, "edu_l1_label": "EDU_O"}, {"txt": " We thank the Telomere-to-Telomere (T2T) consortium for generating a complete reference genome of CHM13 cells, as well as the Y chromosome of HG002.", "language": "english", "position": {"atoms": [{"position_id": 5137, "txt": " We thank the Telomere-to-Telomere (T2T) consortium for generating a complete reference genome of CHM13 cells, as well as the Y chromosome of HG002.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[5]/div"}]}, "tags": [], "label": "content", "web_segment_id": 105, "global_sentence_id": 190, "edu_l1_label": "EDU_O"}, {"txt": " This research was supported by NIH grants 1DP5OD029630 and 1U01HG013744 to A.B.S. and a 2021 Catalytic Collaborations pilot grant from the Brotman Baty Institute for Precision Medicine.", "language": "english", "position": {"atoms": [{"position_id": 5138, "txt": " This research was supported by ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[5]/div"}, {"position_id": 5140, "txt": "NIH", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[5]/div/span[1]"}, {"position_id": 5142, "txt": " grants ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[5]/div/span[1]"}, {"position_id": 5144, "txt": "1DP5OD029630", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[5]/div/a[1]/span/span"}, {"position_id": 5146, "txt": " and ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[5]/div/a[1]"}, {"position_id": 5148, "txt": "1U01HG013744", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[5]/div/a[2]/span/span"}, {"position_id": 5150, "txt": " to A.B.S. and a 2021 Catalytic Collaborations pilot grant from the ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[5]/div/a[2]"}, {"position_id": 5152, "txt": "Brotman Baty Institute", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[5]/div/span[2]"}, {"position_id": 5154, "txt": " for Precision Medicine.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[5]/div/span[2]"}]}, "tags": [], "label": "content", "web_segment_id": 105, "global_sentence_id": 191, "edu_l1_label": "EDU_O"}, {"txt": " A.B.S. holds a Career Award for Medical Scientists from the Burroughs Wellcome Fund and is a Pew Biomedical Scholar.", "language": "english", "position": {"atoms": [{"position_id": 5155, "txt": " A.B.S. holds a Career Award for Medical Scientists from the ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[5]/div/span[2]"}, {"position_id": 5157, "txt": "Burroughs Wellcome Fund", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[5]/div/span[3]"}, {"position_id": 5159, "txt": " and is a Pew Biomedical Scholar.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[5]/div/span[3]"}]}, "tags": [], "label": "content", "web_segment_id": 105, "global_sentence_id": 192, "edu_l1_label": "EDU_O"}, {"txt": " S.B. and S.H. were supported by NIH R35 GM149357, and S.B. is also an investigator of the Howard Hughes Medical Institute.", "language": "english", "position": {"atoms": [{"position_id": 5160, "txt": " S.B. and S.H. were supported by NIH ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[5]/div/span[3]"}, {"position_id": 5162, "txt": "R35 GM149357", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[5]/div/a[3]/span/span"}, {"position_id": 5164, "txt": ", and S.B. is also an investigator of the Howard Hughes Medical Institute.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[5]/div/a[3]"}]}, "tags": [], "label": "content", "web_segment_id": 105, "global_sentence_id": 193, "edu_l1_label": "EDU_O"}, {"txt": "Author contributions", "language": "english", "position": {"atoms": [{"position_id": 5166, "txt": "Author contributions", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[6]/h2"}]}, "tags": ["h2"], "label": "title1", "web_segment_id": 106, "global_sentence_id": 194, "edu_l1_label": "IOS"}, {"txt": "A.B.S., J.R., G.A.H., Y.M., S.H., K.M.M., and B.J.M. designed and performed the experiments.", "language": "english", "position": {"atoms": [{"position_id": 5168, "txt": "A.B.S., J.R., G.A.H., Y.M., S.H., K.M.M., and B.J.M. designed and performed the experiments.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[6]/div"}]}, "tags": [], "label": "content", "web_segment_id": 107, "global_sentence_id": 195, "edu_l1_label": "EDU_O"}, {"txt": " A.B.S., D.D., A.E.S.C., G.A.H., G.A.L., E.E.E., R.J.O., and T.R. performed the computational analyses.", "language": "english", "position": {"atoms": [{"position_id": 5169, "txt": " A.B.S., D.D., A.E.S.C., G.A.H., G.A.L., E.E.E., R.J.O., and T.R. performed the computational analyses.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[6]/div"}]}, "tags": [], "label": "content", "web_segment_id": 107, "global_sentence_id": 196, "edu_l1_label": "EDU_O"}, {"txt": " A.B.S. and D.D. wrote the manuscript.", "language": "english", "position": {"atoms": [{"position_id": 5170, "txt": " A.B.S. and D.D. wrote the manuscript.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[6]/div"}]}, "tags": [], "label": "content", "web_segment_id": 107, "global_sentence_id": 197, "edu_l1_label": "EDU_O"}, {"txt": "Declaration of interests", "language": "english", "position": {"atoms": [{"position_id": 5172, "txt": "Declaration of interests", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[7]/h2"}]}, "tags": ["h2"], "label": "title1", "web_segment_id": 108, "global_sentence_id": 198, "edu_l1_label": "IOS"}, {"txt": "A.B.S. is a co-inventor on a patent relating to the Fiber-seq method.", "language": "english", "position": {"atoms": [{"position_id": 5174, "txt": "A.B.S. is a co-inventor on a patent relating to the Fiber-seq method.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[7]/div"}]}, "tags": [], "label": "content", "web_segment_id": 109, "global_sentence_id": 199, "edu_l1_label": "EDU_O"}, {"txt": " E.E.E. is a scientific advisory board member of Variant Bio.", "language": "english", "position": {"atoms": [{"position_id": 5175, "txt": " E.E.E. is a scientific advisory board member of Variant Bio.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[7]/div"}]}, "tags": [], "label": "content", "web_segment_id": 109, "global_sentence_id": 200, "edu_l1_label": "EDU_O"}, {"txt": "STAR★Methods", "language": "english", "position": {"atoms": [{"position_id": 5177, "txt": "STAR★Methods", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/h2"}]}, "tags": ["h2"], "label": "title1", "web_segment_id": 110, "global_sentence_id": 201, "edu_l1_label": "IOS"}, {"txt": "Key resources table", "language": "english", "position": {"atoms": [{"position_id": 5179, "txt": "Key resources table", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[1]/h3"}]}, "tags": ["h3"], "label": "table_title", "web_segment_id": 111, "global_sentence_id": 202, "edu_l1_label": "EDU_O"}, {"txt": "<table <table position_id=\"1206\"><thead position_id=\"1207\"><tr class=\"rowsep-1 valign-bottom\" position_id=\"1208\"><th scope=\"col\" position_id=\"1209\">REAGENT or RESOURCE</th><th scope=\"col\" position_id=\"1210\">SOURCE</th><th scope=\"col\" position_id=\"1211\">IDENTIFIER</th></tr></thead><tbody position_id=\"1212\"><tr class=\"rowsep-1 valign-top\" position_id=\"1213\"><th colspan=\"3\" scope=\"row\" position_id=\"1214\"><strong position_id=\"1215\">Antibodies</strong></th></tr><tr class=\"valign-top\" position_id=\"1216\"><td position_id=\"1217\">CENP-A monoclonal antibody</td><td position_id=\"1218\">Enzo Life Sciences</td><td position_id=\"1219\">ADI-KAM-CC006-E; RRID: AB_2038993</td></tr><tr class=\"valign-top\" position_id=\"1220\"><td position_id=\"1221\">Tri-methyl-histone H3 (Lys4) (C42D8) rabbit monoclonal antibody</td><td position_id=\"1222\">Cell Signaling Technology</td><td position_id=\"1223\">9751; RRID: AB_2616028</td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1224\"><td position_id=\"1225\">rabbit (DA1E) monoclonal antibody IgG XP isotype control</td><td position_id=\"1226\">Cell Signaling Technology</td><td position_id=\"1227\">66362; RRID: AB_2924329</td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1228\"><th colspan=\"3\" scope=\"row\" position_id=\"1229\"><strong position_id=\"1230\">Chemicals, peptides, and recombinant proteins</strong></th></tr><tr class=\"valign-top\" position_id=\"1231\"><td position_id=\"1232\">AmnioMax C-100 Basal Medium</td><td position_id=\"1233\">Invitrogen</td><td position_id=\"1234\">12558011</td></tr><tr class=\"valign-top\" position_id=\"1235\"><td position_id=\"1236\">Hia5 MTase</td><td position_id=\"1237\">Stergachis et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib19\" data-xocs-content-type=\"reference\" href=\"#bib19\" name=\"bbib19\" position_id=\"1238\"><span class=\"anchor-text-container\" position_id=\"1239\"><span class=\"anchor-text\" position_id=\"1240\"><sup position_id=\"1241\">19</sup></span></span></a></td><td position_id=\"1242\">N/A</td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1243\"><td position_id=\"1244\">S-adenosylmethionine</td><td position_id=\"1245\">NEB</td><td position_id=\"1246\">B9003S</td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1247\"><th colspan=\"3\" scope=\"row\" position_id=\"1248\"><strong position_id=\"1249\">Critical commercial assays</strong></th></tr><tr class=\"valign-top\" position_id=\"1250\"><td position_id=\"1251\">Promega Wizard HMW DNA Extraction Kit A2920</td><td position_id=\"1252\">Promega</td><td position_id=\"1253\">A2920</td></tr><tr class=\"valign-top\" position_id=\"1254\"><td position_id=\"1255\">SMRTbell prep kit 3.0</td><td position_id=\"1256\">PacBio</td><td position_id=\"1257\">N/A</td></tr><tr class=\"valign-top\" position_id=\"1258\"><td position_id=\"1259\">Sequel II SMRT Cell</td><td position_id=\"1260\">PacBio</td><td position_id=\"1261\">N/A</td></tr><tr class=\"valign-top\" position_id=\"1262\"><td position_id=\"1263\">ONT ligation Sequencing Kit</td><td position_id=\"1264\">ONT</td><td position_id=\"1265\">LSK109</td></tr><tr class=\"valign-top\" position_id=\"1266\"><td position_id=\"1267\">Ultra-Long DNA Sequencing Kit</td><td position_id=\"1268\">ONT</td><td position_id=\"1269\">SQK-ULK001</td></tr><tr class=\"valign-top\" position_id=\"1270\"><td position_id=\"1271\">Omni-C Proximity Ligation Assay</td><td position_id=\"1272\">Dovetail</td><td position_id=\"1273\">N/A</td></tr><tr class=\"valign-top\" position_id=\"1274\"><td position_id=\"1275\">CUT&amp;RUN Assay Kit</td><td position_id=\"1276\">Cell Signaling Technology</td><td position_id=\"1277\">86652</td></tr><tr class=\"valign-top\" position_id=\"1278\"><td position_id=\"1279\">DNA purification with spin columns kit</td><td position_id=\"1280\">Cell Signaling Technology</td><td position_id=\"1281\">14209</td></tr><tr class=\"valign-top\" position_id=\"1282\"><td position_id=\"1283\">NEBNext Ultra II DNA Library Prep Kit for Illumina</td><td position_id=\"1284\">NEB</td><td position_id=\"1285\">E7645S</td></tr><tr class=\"valign-top\" position_id=\"1286\"><td position_id=\"1287\">Nanobind UL Library Prep Kit</td><td position_id=\"1288\">Circulomics</td><td position_id=\"1289\">NB-900-601-01)</td></tr><tr class=\"valign-top\" position_id=\"1290\"><td position_id=\"1291\">Nanobind Library Prep</td><td position_id=\"1292\">Circulomics</td><td position_id=\"1293\">LBP-ULN-001</td></tr><tr class=\"valign-top\" position_id=\"1294\"><td position_id=\"1295\">Nanobind CBB Big DNA Kit</td><td position_id=\"1296\">Circulomics</td><td position_id=\"1297\">NB-900-001-01</td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1298\"><td position_id=\"1299\">Nanobind UHMW DNA Extraction</td><td position_id=\"1300\">Circulomics</td><td position_id=\"1301\">EXT-CLU-001</td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1302\"><th colspan=\"3\" scope=\"row\" position_id=\"1303\"><strong position_id=\"1304\">Deposited data</strong></th></tr><tr class=\"valign-top\" position_id=\"1305\"><td position_id=\"1306\">CHM13 Fiber-seq</td><td position_id=\"1307\">GSM7074431</td><td position_id=\"1308\">GEO: <a class=\"anchor anchor-primary\" href=\"http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE226394\" target=\"_blank\" position_id=\"1309\"><span class=\"anchor-text-container\" position_id=\"1310\"><span class=\"anchor-text\" position_id=\"1311\">GSE226394</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1312\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1313\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1314\"><td position_id=\"1315\">CHM1 Fiber-seq</td><td position_id=\"1316\">GSM7074432</td><td position_id=\"1317\">GEO: <a class=\"anchor anchor-primary\" href=\"http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE226394\" target=\"_blank\" position_id=\"1318\"><span class=\"anchor-text-container\" position_id=\"1319\"><span class=\"anchor-text\" position_id=\"1320\">GSE226394</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1321\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1322\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1323\"><td position_id=\"1324\">GM14385/HG002 Fiber-seq</td><td position_id=\"1325\">GSM7074433</td><td position_id=\"1326\">GEO: <a class=\"anchor anchor-primary\" href=\"http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE226394\" target=\"_blank\" position_id=\"1327\"><span class=\"anchor-text-container\" position_id=\"1328\"><span class=\"anchor-text\" position_id=\"1329\">GSE226394</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1330\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1331\"/></svg></span></a></td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1332\"><td position_id=\"1333\">HLE Fiber-seq</td><td position_id=\"1334\">GSM7074434</td><td position_id=\"1335\">GEO: <a class=\"anchor anchor-primary\" href=\"http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE226394\" target=\"_blank\" position_id=\"1336\"><span class=\"anchor-text-container\" position_id=\"1337\"><span class=\"anchor-text\" position_id=\"1338\">GSE226394</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1339\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1340\"/></svg></span></a></td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1341\"><th colspan=\"3\" scope=\"row\" position_id=\"1342\"><strong position_id=\"1343\">Experimental models: Cell lines</strong></th></tr><tr class=\"valign-top\" position_id=\"1344\"><td position_id=\"1345\">CHM13 Cells</td><td position_id=\"1346\">Gift from Eichler lab, University of Washington</td><td position_id=\"1347\">N/A</td></tr><tr class=\"valign-top\" position_id=\"1348\"><td position_id=\"1349\">CHM1 Cells</td><td position_id=\"1350\">Gift from Eichler lab, University of Washington</td><td position_id=\"1351\">N/A</td></tr><tr class=\"valign-top\" position_id=\"1352\"><td position_id=\"1353\">HLE Cells</td><td position_id=\"1354\">Gift from O’Neil lab, University of Connecticut</td><td position_id=\"1355\">N/A</td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1356\"><td position_id=\"1357\">GM24385</td><td position_id=\"1358\">Coriell</td><td position_id=\"1359\">N/A</td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1360\"><th colspan=\"3\" scope=\"row\" position_id=\"1361\"><strong position_id=\"1362\">Experimental models: Organisms/strains</strong></th></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1363\"><td position_id=\"1364\"><em position_id=\"1365\">Saccharomyces cerevisiae</em> cells SBY3/W303</td><td position_id=\"1366\">Gift from Biggins lab, Fred Hutchinson Cancer Center</td><td position_id=\"1367\">N/A</td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1368\"><th colspan=\"3\" scope=\"row\" position_id=\"1369\"><strong position_id=\"1370\">Software and algorithms</strong></th></tr><tr class=\"valign-top\" position_id=\"1371\"><td position_id=\"1372\">Custom code</td><td position_id=\"1373\"/><td position_id=\"1374\"><a class=\"anchor anchor-primary\" href=\"https://zenodo.org/record/7686305\" target=\"_blank\" position_id=\"1375\"><span class=\"anchor-text-container\" position_id=\"1376\"><span class=\"anchor-text\" position_id=\"1377\">https://zenodo.org/record/7686305</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1378\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1379\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1380\"><td position_id=\"1381\">pbmm2</td><td position_id=\"1382\"/><td position_id=\"1383\"><a class=\"anchor anchor-primary\" href=\"https://github.com/PacificBiosciences/pbmm2\" target=\"_blank\" position_id=\"1384\"><span class=\"anchor-text-container\" position_id=\"1385\"><span class=\"anchor-text\" position_id=\"1386\">https://github.com/PacificBiosciences/pbmm2</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1387\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1388\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1389\"><td position_id=\"1390\">fibertools</td><td position_id=\"1391\">Jha et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib27\" data-xocs-content-type=\"reference\" href=\"#bib27\" name=\"bbib27\" position_id=\"1392\"><span class=\"anchor-text-container\" position_id=\"1393\"><span class=\"anchor-text\" position_id=\"1394\"><sup position_id=\"1395\">27</sup></span></span></a></td><td position_id=\"1396\"><a class=\"anchor anchor-primary\" href=\"https://github.com/fiberseq/fibertools-rs\" target=\"_blank\" position_id=\"1397\"><span class=\"anchor-text-container\" position_id=\"1398\"><span class=\"anchor-text\" position_id=\"1399\">https://github.com/fiberseq/fibertools-rs</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1400\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1401\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1402\"><td position_id=\"1403\">jasmine</td><td position_id=\"1404\"/><td position_id=\"1405\"><a class=\"anchor anchor-primary\" href=\"https://github.com/PacificBiosciences/jasmine\" target=\"_blank\" position_id=\"1406\"><span class=\"anchor-text-container\" position_id=\"1407\"><span class=\"anchor-text\" position_id=\"1408\">https://github.com/PacificBiosciences/jasmine</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1409\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1410\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1411\"><td position_id=\"1412\"><em position_id=\"1413\">primrose</em></td><td position_id=\"1414\"/><td position_id=\"1415\"><a class=\"anchor anchor-primary\" href=\"https://github.com/mattoslmp/primrose\" target=\"_blank\" position_id=\"1416\"><span class=\"anchor-text-container\" position_id=\"1417\"><span class=\"anchor-text\" position_id=\"1418\">https://github.com/mattoslmp/primrose</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1419\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1420\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1421\"><td position_id=\"1422\"><em position_id=\"1423\">pb-CpG-tools</em></td><td position_id=\"1424\"/><td position_id=\"1425\"><a class=\"anchor anchor-primary\" href=\"https://github.com/PacificBiosciences/pb-CpG-tools\" target=\"_blank\" position_id=\"1426\"><span class=\"anchor-text-container\" position_id=\"1427\"><span class=\"anchor-text\" position_id=\"1428\">https://github.com/PacificBiosciences/pb-CpG-tools</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1429\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1430\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1431\"><td position_id=\"1432\">scipy</td><td position_id=\"1433\">Virtanen et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib62\" data-xocs-content-type=\"reference\" href=\"#bib62\" name=\"bbib62\" position_id=\"1434\"><span class=\"anchor-text-container\" position_id=\"1435\"><span class=\"anchor-text\" position_id=\"1436\"><sup position_id=\"1437\">64</sup></span></span></a></td><td position_id=\"1438\"><a class=\"anchor anchor-primary\" href=\"https://anaconda.org/anaconda/scipy\" target=\"_blank\" position_id=\"1439\"><span class=\"anchor-text-container\" position_id=\"1440\"><span class=\"anchor-text\" position_id=\"1441\">https://anaconda.org/anaconda/scipy</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1442\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1443\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1444\"><td position_id=\"1445\">fimo</td><td position_id=\"1446\">Grant et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib60\" data-xocs-content-type=\"reference\" href=\"#bib60\" name=\"bbib60\" position_id=\"1447\"><span class=\"anchor-text-container\" position_id=\"1448\"><span class=\"anchor-text\" position_id=\"1449\"><sup position_id=\"1450\">65</sup></span></span></a></td><td position_id=\"1451\"><a class=\"anchor anchor-primary\" href=\"https://meme-suite.org/meme/doc/fimo.html\" target=\"_blank\" position_id=\"1452\"><span class=\"anchor-text-container\" position_id=\"1453\"><span class=\"anchor-text\" position_id=\"1454\">https://meme-suite.org/meme/doc/fimo.html</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1455\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1456\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1457\"><td position_id=\"1458\">samtools</td><td position_id=\"1459\">Li et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib63\" data-xocs-content-type=\"reference\" href=\"#bib63\" name=\"bbib63\" position_id=\"1460\"><span class=\"anchor-text-container\" position_id=\"1461\"><span class=\"anchor-text\" position_id=\"1462\"><sup position_id=\"1463\">66</sup></span></span></a></td><td position_id=\"1464\"><a class=\"anchor anchor-primary\" href=\"http://www.htslib.org/\" target=\"_blank\" position_id=\"1465\"><span class=\"anchor-text-container\" position_id=\"1466\"><span class=\"anchor-text\" position_id=\"1467\">http://www.htslib.org/</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1468\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1469\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1470\"><td position_id=\"1471\">pilon</td><td position_id=\"1472\">Walker et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib64\" data-xocs-content-type=\"reference\" href=\"#bib64\" name=\"bbib64\" position_id=\"1473\"><span class=\"anchor-text-container\" position_id=\"1474\"><span class=\"anchor-text\" position_id=\"1475\"><sup position_id=\"1476\">67</sup></span></span></a></td><td position_id=\"1477\"><a class=\"anchor anchor-primary\" href=\"https://github.com/broadinstitute/pilon\" target=\"_blank\" position_id=\"1478\"><span class=\"anchor-text-container\" position_id=\"1479\"><span class=\"anchor-text\" position_id=\"1480\">https://github.com/broadinstitute/pilon</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1481\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1482\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1483\"><td position_id=\"1484\">PURGEhaplotigs</td><td position_id=\"1485\">Roach et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib65\" data-xocs-content-type=\"reference\" href=\"#bib65\" name=\"bbib65\" position_id=\"1486\"><span class=\"anchor-text-container\" position_id=\"1487\"><span class=\"anchor-text\" position_id=\"1488\"><sup position_id=\"1489\">68</sup></span></span></a></td><td position_id=\"1490\"><a class=\"anchor anchor-primary\" href=\"https://github.com/dfguan/purge_haplotigs\" target=\"_blank\" position_id=\"1491\"><span class=\"anchor-text-container\" position_id=\"1492\"><span class=\"anchor-text\" position_id=\"1493\">https://github.com/dfguan/purge_haplotigs</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1494\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1495\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1496\"><td position_id=\"1497\">Juicer</td><td position_id=\"1498\">Durand et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib66\" data-xocs-content-type=\"reference\" href=\"#bib66\" name=\"bbib66\" position_id=\"1499\"><span class=\"anchor-text-container\" position_id=\"1500\"><span class=\"anchor-text\" position_id=\"1501\"><sup position_id=\"1502\">69</sup></span></span></a></td><td position_id=\"1503\"><a class=\"anchor anchor-primary\" href=\"https://github.com/aidenlab/juicer\" target=\"_blank\" position_id=\"1504\"><span class=\"anchor-text-container\" position_id=\"1505\"><span class=\"anchor-text\" position_id=\"1506\">https://github.com/aidenlab/juicer</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1507\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1508\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1509\"><td position_id=\"1510\">Assembly Tools</td><td position_id=\"1511\">Durand et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib66\" data-xocs-content-type=\"reference\" href=\"#bib66\" name=\"bbib66\" position_id=\"1512\"><span class=\"anchor-text-container\" position_id=\"1513\"><span class=\"anchor-text\" position_id=\"1514\"><sup position_id=\"1515\">69</sup></span></span></a></td><td position_id=\"1516\"><a class=\"anchor anchor-primary\" href=\"https://github.com/aidenlab/juicer\" target=\"_blank\" position_id=\"1517\"><span class=\"anchor-text-container\" position_id=\"1518\"><span class=\"anchor-text\" position_id=\"1519\">https://github.com/aidenlab/juicer</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1520\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1521\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1522\"><td position_id=\"1523\">TGS-GapCloser</td><td position_id=\"1524\"/><td position_id=\"1525\"><a class=\"anchor anchor-primary\" href=\"https://github.com/BGI-Qingdao/TGS-GapCloser\" target=\"_blank\" position_id=\"1526\"><span class=\"anchor-text-container\" position_id=\"1527\"><span class=\"anchor-text\" position_id=\"1528\">https://github.com/BGI-Qingdao/TGS-GapCloser</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1529\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1530\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1531\"><td position_id=\"1532\">LASTZ</td><td position_id=\"1533\"/><td position_id=\"1534\"><a class=\"anchor anchor-primary\" href=\"https://github.com/lastz/lastz\" target=\"_blank\" position_id=\"1535\"><span class=\"anchor-text-container\" position_id=\"1536\"><span class=\"anchor-text\" position_id=\"1537\">https://github.com/lastz/lastz</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1538\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1539\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1540\"><td position_id=\"1541\">Emboss</td><td position_id=\"1542\">Rice et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib67\" data-xocs-content-type=\"reference\" href=\"#bib67\" name=\"bbib67\" position_id=\"1543\"><span class=\"anchor-text-container\" position_id=\"1544\"><span class=\"anchor-text\" position_id=\"1545\"><sup position_id=\"1546\">70</sup></span></span></a></td><td position_id=\"1547\"><a class=\"anchor anchor-primary\" href=\"http://emboss.sourceforge.net/\" target=\"_blank\" position_id=\"1548\"><span class=\"anchor-text-container\" position_id=\"1549\"><span class=\"anchor-text\" position_id=\"1550\">http://emboss.sourceforge.net/</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1551\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1552\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1553\"><td position_id=\"1554\">cutadapt</td><td position_id=\"1555\">Martin<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib68\" data-xocs-content-type=\"reference\" href=\"#bib68\" name=\"bbib68\" position_id=\"1556\"><span class=\"anchor-text-container\" position_id=\"1557\"><span class=\"anchor-text\" position_id=\"1558\"><sup position_id=\"1559\">71</sup></span></span></a></td><td position_id=\"1560\"><a class=\"anchor anchor-primary\" href=\"https://cutadapt.readthedocs.io/\" target=\"_blank\" position_id=\"1561\"><span class=\"anchor-text-container\" position_id=\"1562\"><span class=\"anchor-text\" position_id=\"1563\">https://cutadapt.readthedocs.io/</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1564\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1565\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1566\"><td position_id=\"1567\">MACS</td><td position_id=\"1568\">Zhang et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib69\" data-xocs-content-type=\"reference\" href=\"#bib69\" name=\"bbib69\" position_id=\"1569\"><span class=\"anchor-text-container\" position_id=\"1570\"><span class=\"anchor-text\" position_id=\"1571\"><sup position_id=\"1572\">72</sup></span></span></a></td><td position_id=\"1573\"><a class=\"anchor anchor-primary\" href=\"https://github.com/macs3-project/MACS\" target=\"_blank\" position_id=\"1574\"><span class=\"anchor-text-container\" position_id=\"1575\"><span class=\"anchor-text\" position_id=\"1576\">https://github.com/macs3-project/MACS</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1577\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1578\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1579\"><td position_id=\"1580\">hifiasm</td><td position_id=\"1581\">Cheng et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib70\" data-xocs-content-type=\"reference\" href=\"#bib70\" name=\"bbib70\" position_id=\"1582\"><span class=\"anchor-text-container\" position_id=\"1583\"><span class=\"anchor-text\" position_id=\"1584\"><sup position_id=\"1585\">73</sup></span></span></a></td><td position_id=\"1586\"><a class=\"anchor anchor-primary\" href=\"https://github.com/chhylp123/hifiasm\" target=\"_blank\" position_id=\"1587\"><span class=\"anchor-text-container\" position_id=\"1588\"><span class=\"anchor-text\" position_id=\"1589\">https://github.com/chhylp123/hifiasm</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1590\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1591\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1592\"><td position_id=\"1593\">RepeatMasker</td><td position_id=\"1594\"/><td position_id=\"1595\"><a class=\"anchor anchor-primary\" href=\"http://www.repeatmasker.org/\" target=\"_blank\" position_id=\"1596\"><span class=\"anchor-text-container\" position_id=\"1597\"><span class=\"anchor-text\" position_id=\"1598\">http://www.repeatmasker.org/</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1599\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1600\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1601\"><td position_id=\"1602\">Bonito</td><td position_id=\"1603\"/><td position_id=\"1604\"><a class=\"anchor anchor-primary\" href=\"https://github.com/nanoporetech/bonito\" target=\"_blank\" position_id=\"1605\"><span class=\"anchor-text-container\" position_id=\"1606\"><span class=\"anchor-text\" position_id=\"1607\">https://github.com/nanoporetech/bonito</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1608\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1609\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1610\"><td position_id=\"1611\">Remora</td><td position_id=\"1612\"/><td position_id=\"1613\"><a class=\"anchor anchor-primary\" href=\"https://github.com/nanoporetech/remora\" target=\"_blank\" position_id=\"1614\"><span class=\"anchor-text-container\" position_id=\"1615\"><span class=\"anchor-text\" position_id=\"1616\">https://github.com/nanoporetech/remora</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1617\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1618\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1619\"><td position_id=\"1620\">modbam2bed</td><td position_id=\"1621\"/><td position_id=\"1622\"><a class=\"anchor anchor-primary\" href=\"https://github.com/nanoporetech/modbam2bed\" target=\"_blank\" position_id=\"1623\"><span class=\"anchor-text-container\" position_id=\"1624\"><span class=\"anchor-text\" position_id=\"1625\">https://github.com/nanoporetech/modbam2bed</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1626\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1627\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1628\"><td position_id=\"1629\">bedtools</td><td position_id=\"1630\">Quinlan and Hall<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib71\" data-xocs-content-type=\"reference\" href=\"#bib71\" name=\"bbib71\" position_id=\"1631\"><span class=\"anchor-text-container\" position_id=\"1632\"><span class=\"anchor-text\" position_id=\"1633\"><sup position_id=\"1634\">74</sup></span></span></a></td><td position_id=\"1635\"><a class=\"anchor anchor-primary\" href=\"https://bedtools.readthedocs.io/\" target=\"_blank\" position_id=\"1636\"><span class=\"anchor-text-container\" position_id=\"1637\"><span class=\"anchor-text\" position_id=\"1638\">https://bedtools.readthedocs.io/</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1639\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1640\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1641\"><td position_id=\"1642\">bedops</td><td position_id=\"1643\">Neph et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib72\" data-xocs-content-type=\"reference\" href=\"#bib72\" name=\"bbib72\" position_id=\"1644\"><span class=\"anchor-text-container\" position_id=\"1645\"><span class=\"anchor-text\" position_id=\"1646\"><sup position_id=\"1647\">75</sup></span></span></a></td><td position_id=\"1648\"><a class=\"anchor anchor-primary\" href=\"https://bedops.readthedocs.io/en/latest/\" target=\"_blank\" position_id=\"1649\"><span class=\"anchor-text-container\" position_id=\"1650\"><span class=\"anchor-text\" position_id=\"1651\">https://bedops.readthedocs.io/en/latest/</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1652\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1653\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1654\"><td position_id=\"1655\">Guppy</td><td position_id=\"1656\">ONT</td><td position_id=\"1657\">N/A</td></tr><tr class=\"valign-top\" position_id=\"1658\"><td position_id=\"1659\">Flye</td><td position_id=\"1660\">Kolmogorov et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib73\" data-xocs-content-type=\"reference\" href=\"#bib73\" name=\"bbib73\" position_id=\"1661\"><span class=\"anchor-text-container\" position_id=\"1662\"><span class=\"anchor-text\" position_id=\"1663\"><sup position_id=\"1664\">76</sup></span></span></a></td><td position_id=\"1665\"><a class=\"anchor anchor-primary\" href=\"https://github.com/mikolmogorov/Flye\" target=\"_blank\" position_id=\"1666\"><span class=\"anchor-text-container\" position_id=\"1667\"><span class=\"anchor-text\" position_id=\"1668\">https://github.com/mikolmogorov/Flye</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1669\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1670\"/></svg></span></a></td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1671\"><td position_id=\"1672\">BWA</td><td position_id=\"1673\">Li and Durbin<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib74\" data-xocs-content-type=\"reference\" href=\"#bib74\" name=\"bbib74\" position_id=\"1674\"><span class=\"anchor-text-container\" position_id=\"1675\"><span class=\"anchor-text\" position_id=\"1676\"><sup position_id=\"1677\">77</sup></span></span></a></td><td position_id=\"1678\"><a class=\"anchor anchor-primary\" href=\"https://github.com/lh3/bwa\" target=\"_blank\" position_id=\"1679\"><span class=\"anchor-text-container\" position_id=\"1680\"><span class=\"anchor-text\" position_id=\"1681\">https://github.com/lh3/bwa</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1682\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1683\"/></svg></span></a></td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1684\"><th colspan=\"3\" scope=\"row\" position_id=\"1685\"><strong position_id=\"1686\">Other</strong></th></tr><tr class=\"valign-top\" position_id=\"1687\"><td position_id=\"1688\">Sage Science PippinHT platform</td><td position_id=\"1689\">Sage Science</td><td position_id=\"1690\">ELF0001</td></tr><tr class=\"valign-top\" position_id=\"1691\"><td position_id=\"1692\">Megaruptor</td><td position_id=\"1693\">Diagenode Diagnostics</td><td position_id=\"1694\">N/A</td></tr></tbody></table>", "language": "english", "position": {"atoms": [{"position_id": 1206, "txt": "<table <table position_id=\"1206\"><thead position_id=\"1207\"><tr class=\"rowsep-1 valign-bottom\" position_id=\"1208\"><th scope=\"col\" position_id=\"1209\">REAGENT or RESOURCE</th><th scope=\"col\" position_id=\"1210\">SOURCE</th><th scope=\"col\" position_id=\"1211\">IDENTIFIER</th></tr></thead><tbody position_id=\"1212\"><tr class=\"rowsep-1 valign-top\" position_id=\"1213\"><th colspan=\"3\" scope=\"row\" position_id=\"1214\"><strong position_id=\"1215\">Antibodies</strong></th></tr><tr class=\"valign-top\" position_id=\"1216\"><td position_id=\"1217\">CENP-A monoclonal antibody</td><td position_id=\"1218\">Enzo Life Sciences</td><td position_id=\"1219\">ADI-KAM-CC006-E; RRID: AB_2038993</td></tr><tr class=\"valign-top\" position_id=\"1220\"><td position_id=\"1221\">Tri-methyl-histone H3 (Lys4) (C42D8) rabbit monoclonal antibody</td><td position_id=\"1222\">Cell Signaling Technology</td><td position_id=\"1223\">9751; RRID: AB_2616028</td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1224\"><td position_id=\"1225\">rabbit (DA1E) monoclonal antibody IgG XP isotype control</td><td position_id=\"1226\">Cell Signaling Technology</td><td position_id=\"1227\">66362; RRID: AB_2924329</td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1228\"><th colspan=\"3\" scope=\"row\" position_id=\"1229\"><strong position_id=\"1230\">Chemicals, peptides, and recombinant proteins</strong></th></tr><tr class=\"valign-top\" position_id=\"1231\"><td position_id=\"1232\">AmnioMax C-100 Basal Medium</td><td position_id=\"1233\">Invitrogen</td><td position_id=\"1234\">12558011</td></tr><tr class=\"valign-top\" position_id=\"1235\"><td position_id=\"1236\">Hia5 MTase</td><td position_id=\"1237\">Stergachis et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib19\" data-xocs-content-type=\"reference\" href=\"#bib19\" name=\"bbib19\" position_id=\"1238\"><span class=\"anchor-text-container\" position_id=\"1239\"><span class=\"anchor-text\" position_id=\"1240\"><sup position_id=\"1241\">19</sup></span></span></a></td><td position_id=\"1242\">N/A</td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1243\"><td position_id=\"1244\">S-adenosylmethionine</td><td position_id=\"1245\">NEB</td><td position_id=\"1246\">B9003S</td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1247\"><th colspan=\"3\" scope=\"row\" position_id=\"1248\"><strong position_id=\"1249\">Critical commercial assays</strong></th></tr><tr class=\"valign-top\" position_id=\"1250\"><td position_id=\"1251\">Promega Wizard HMW DNA Extraction Kit A2920</td><td position_id=\"1252\">Promega</td><td position_id=\"1253\">A2920</td></tr><tr class=\"valign-top\" position_id=\"1254\"><td position_id=\"1255\">SMRTbell prep kit 3.0</td><td position_id=\"1256\">PacBio</td><td position_id=\"1257\">N/A</td></tr><tr class=\"valign-top\" position_id=\"1258\"><td position_id=\"1259\">Sequel II SMRT Cell</td><td position_id=\"1260\">PacBio</td><td position_id=\"1261\">N/A</td></tr><tr class=\"valign-top\" position_id=\"1262\"><td position_id=\"1263\">ONT ligation Sequencing Kit</td><td position_id=\"1264\">ONT</td><td position_id=\"1265\">LSK109</td></tr><tr class=\"valign-top\" position_id=\"1266\"><td position_id=\"1267\">Ultra-Long DNA Sequencing Kit</td><td position_id=\"1268\">ONT</td><td position_id=\"1269\">SQK-ULK001</td></tr><tr class=\"valign-top\" position_id=\"1270\"><td position_id=\"1271\">Omni-C Proximity Ligation Assay</td><td position_id=\"1272\">Dovetail</td><td position_id=\"1273\">N/A</td></tr><tr class=\"valign-top\" position_id=\"1274\"><td position_id=\"1275\">CUT&amp;RUN Assay Kit</td><td position_id=\"1276\">Cell Signaling Technology</td><td position_id=\"1277\">86652</td></tr><tr class=\"valign-top\" position_id=\"1278\"><td position_id=\"1279\">DNA purification with spin columns kit</td><td position_id=\"1280\">Cell Signaling Technology</td><td position_id=\"1281\">14209</td></tr><tr class=\"valign-top\" position_id=\"1282\"><td position_id=\"1283\">NEBNext Ultra II DNA Library Prep Kit for Illumina</td><td position_id=\"1284\">NEB</td><td position_id=\"1285\">E7645S</td></tr><tr class=\"valign-top\" position_id=\"1286\"><td position_id=\"1287\">Nanobind UL Library Prep Kit</td><td position_id=\"1288\">Circulomics</td><td position_id=\"1289\">NB-900-601-01)</td></tr><tr class=\"valign-top\" position_id=\"1290\"><td position_id=\"1291\">Nanobind Library Prep</td><td position_id=\"1292\">Circulomics</td><td position_id=\"1293\">LBP-ULN-001</td></tr><tr class=\"valign-top\" position_id=\"1294\"><td position_id=\"1295\">Nanobind CBB Big DNA Kit</td><td position_id=\"1296\">Circulomics</td><td position_id=\"1297\">NB-900-001-01</td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1298\"><td position_id=\"1299\">Nanobind UHMW DNA Extraction</td><td position_id=\"1300\">Circulomics</td><td position_id=\"1301\">EXT-CLU-001</td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1302\"><th colspan=\"3\" scope=\"row\" position_id=\"1303\"><strong position_id=\"1304\">Deposited data</strong></th></tr><tr class=\"valign-top\" position_id=\"1305\"><td position_id=\"1306\">CHM13 Fiber-seq</td><td position_id=\"1307\">GSM7074431</td><td position_id=\"1308\">GEO: <a class=\"anchor anchor-primary\" href=\"http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE226394\" target=\"_blank\" position_id=\"1309\"><span class=\"anchor-text-container\" position_id=\"1310\"><span class=\"anchor-text\" position_id=\"1311\">GSE226394</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1312\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1313\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1314\"><td position_id=\"1315\">CHM1 Fiber-seq</td><td position_id=\"1316\">GSM7074432</td><td position_id=\"1317\">GEO: <a class=\"anchor anchor-primary\" href=\"http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE226394\" target=\"_blank\" position_id=\"1318\"><span class=\"anchor-text-container\" position_id=\"1319\"><span class=\"anchor-text\" position_id=\"1320\">GSE226394</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1321\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1322\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1323\"><td position_id=\"1324\">GM14385/HG002 Fiber-seq</td><td position_id=\"1325\">GSM7074433</td><td position_id=\"1326\">GEO: <a class=\"anchor anchor-primary\" href=\"http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE226394\" target=\"_blank\" position_id=\"1327\"><span class=\"anchor-text-container\" position_id=\"1328\"><span class=\"anchor-text\" position_id=\"1329\">GSE226394</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1330\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1331\"/></svg></span></a></td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1332\"><td position_id=\"1333\">HLE Fiber-seq</td><td position_id=\"1334\">GSM7074434</td><td position_id=\"1335\">GEO: <a class=\"anchor anchor-primary\" href=\"http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE226394\" target=\"_blank\" position_id=\"1336\"><span class=\"anchor-text-container\" position_id=\"1337\"><span class=\"anchor-text\" position_id=\"1338\">GSE226394</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1339\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1340\"/></svg></span></a></td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1341\"><th colspan=\"3\" scope=\"row\" position_id=\"1342\"><strong position_id=\"1343\">Experimental models: Cell lines</strong></th></tr><tr class=\"valign-top\" position_id=\"1344\"><td position_id=\"1345\">CHM13 Cells</td><td position_id=\"1346\">Gift from Eichler lab, University of Washington</td><td position_id=\"1347\">N/A</td></tr><tr class=\"valign-top\" position_id=\"1348\"><td position_id=\"1349\">CHM1 Cells</td><td position_id=\"1350\">Gift from Eichler lab, University of Washington</td><td position_id=\"1351\">N/A</td></tr><tr class=\"valign-top\" position_id=\"1352\"><td position_id=\"1353\">HLE Cells</td><td position_id=\"1354\">Gift from O’Neil lab, University of Connecticut</td><td position_id=\"1355\">N/A</td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1356\"><td position_id=\"1357\">GM24385</td><td position_id=\"1358\">Coriell</td><td position_id=\"1359\">N/A</td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1360\"><th colspan=\"3\" scope=\"row\" position_id=\"1361\"><strong position_id=\"1362\">Experimental models: Organisms/strains</strong></th></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1363\"><td position_id=\"1364\"><em position_id=\"1365\">Saccharomyces cerevisiae</em> cells SBY3/W303</td><td position_id=\"1366\">Gift from Biggins lab, Fred Hutchinson Cancer Center</td><td position_id=\"1367\">N/A</td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1368\"><th colspan=\"3\" scope=\"row\" position_id=\"1369\"><strong position_id=\"1370\">Software and algorithms</strong></th></tr><tr class=\"valign-top\" position_id=\"1371\"><td position_id=\"1372\">Custom code</td><td position_id=\"1373\"/><td position_id=\"1374\"><a class=\"anchor anchor-primary\" href=\"https://zenodo.org/record/7686305\" target=\"_blank\" position_id=\"1375\"><span class=\"anchor-text-container\" position_id=\"1376\"><span class=\"anchor-text\" position_id=\"1377\">https://zenodo.org/record/7686305</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1378\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1379\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1380\"><td position_id=\"1381\">pbmm2</td><td position_id=\"1382\"/><td position_id=\"1383\"><a class=\"anchor anchor-primary\" href=\"https://github.com/PacificBiosciences/pbmm2\" target=\"_blank\" position_id=\"1384\"><span class=\"anchor-text-container\" position_id=\"1385\"><span class=\"anchor-text\" position_id=\"1386\">https://github.com/PacificBiosciences/pbmm2</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1387\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1388\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1389\"><td position_id=\"1390\">fibertools</td><td position_id=\"1391\">Jha et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib27\" data-xocs-content-type=\"reference\" href=\"#bib27\" name=\"bbib27\" position_id=\"1392\"><span class=\"anchor-text-container\" position_id=\"1393\"><span class=\"anchor-text\" position_id=\"1394\"><sup position_id=\"1395\">27</sup></span></span></a></td><td position_id=\"1396\"><a class=\"anchor anchor-primary\" href=\"https://github.com/fiberseq/fibertools-rs\" target=\"_blank\" position_id=\"1397\"><span class=\"anchor-text-container\" position_id=\"1398\"><span class=\"anchor-text\" position_id=\"1399\">https://github.com/fiberseq/fibertools-rs</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1400\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1401\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1402\"><td position_id=\"1403\">jasmine</td><td position_id=\"1404\"/><td position_id=\"1405\"><a class=\"anchor anchor-primary\" href=\"https://github.com/PacificBiosciences/jasmine\" target=\"_blank\" position_id=\"1406\"><span class=\"anchor-text-container\" position_id=\"1407\"><span class=\"anchor-text\" position_id=\"1408\">https://github.com/PacificBiosciences/jasmine</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1409\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1410\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1411\"><td position_id=\"1412\"><em position_id=\"1413\">primrose</em></td><td position_id=\"1414\"/><td position_id=\"1415\"><a class=\"anchor anchor-primary\" href=\"https://github.com/mattoslmp/primrose\" target=\"_blank\" position_id=\"1416\"><span class=\"anchor-text-container\" position_id=\"1417\"><span class=\"anchor-text\" position_id=\"1418\">https://github.com/mattoslmp/primrose</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1419\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1420\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1421\"><td position_id=\"1422\"><em position_id=\"1423\">pb-CpG-tools</em></td><td position_id=\"1424\"/><td position_id=\"1425\"><a class=\"anchor anchor-primary\" href=\"https://github.com/PacificBiosciences/pb-CpG-tools\" target=\"_blank\" position_id=\"1426\"><span class=\"anchor-text-container\" position_id=\"1427\"><span class=\"anchor-text\" position_id=\"1428\">https://github.com/PacificBiosciences/pb-CpG-tools</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1429\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1430\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1431\"><td position_id=\"1432\">scipy</td><td position_id=\"1433\">Virtanen et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib62\" data-xocs-content-type=\"reference\" href=\"#bib62\" name=\"bbib62\" position_id=\"1434\"><span class=\"anchor-text-container\" position_id=\"1435\"><span class=\"anchor-text\" position_id=\"1436\"><sup position_id=\"1437\">64</sup></span></span></a></td><td position_id=\"1438\"><a class=\"anchor anchor-primary\" href=\"https://anaconda.org/anaconda/scipy\" target=\"_blank\" position_id=\"1439\"><span class=\"anchor-text-container\" position_id=\"1440\"><span class=\"anchor-text\" position_id=\"1441\">https://anaconda.org/anaconda/scipy</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1442\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1443\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1444\"><td position_id=\"1445\">fimo</td><td position_id=\"1446\">Grant et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib60\" data-xocs-content-type=\"reference\" href=\"#bib60\" name=\"bbib60\" position_id=\"1447\"><span class=\"anchor-text-container\" position_id=\"1448\"><span class=\"anchor-text\" position_id=\"1449\"><sup position_id=\"1450\">65</sup></span></span></a></td><td position_id=\"1451\"><a class=\"anchor anchor-primary\" href=\"https://meme-suite.org/meme/doc/fimo.html\" target=\"_blank\" position_id=\"1452\"><span class=\"anchor-text-container\" position_id=\"1453\"><span class=\"anchor-text\" position_id=\"1454\">https://meme-suite.org/meme/doc/fimo.html</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1455\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1456\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1457\"><td position_id=\"1458\">samtools</td><td position_id=\"1459\">Li et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib63\" data-xocs-content-type=\"reference\" href=\"#bib63\" name=\"bbib63\" position_id=\"1460\"><span class=\"anchor-text-container\" position_id=\"1461\"><span class=\"anchor-text\" position_id=\"1462\"><sup position_id=\"1463\">66</sup></span></span></a></td><td position_id=\"1464\"><a class=\"anchor anchor-primary\" href=\"http://www.htslib.org/\" target=\"_blank\" position_id=\"1465\"><span class=\"anchor-text-container\" position_id=\"1466\"><span class=\"anchor-text\" position_id=\"1467\">http://www.htslib.org/</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1468\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1469\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1470\"><td position_id=\"1471\">pilon</td><td position_id=\"1472\">Walker et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib64\" data-xocs-content-type=\"reference\" href=\"#bib64\" name=\"bbib64\" position_id=\"1473\"><span class=\"anchor-text-container\" position_id=\"1474\"><span class=\"anchor-text\" position_id=\"1475\"><sup position_id=\"1476\">67</sup></span></span></a></td><td position_id=\"1477\"><a class=\"anchor anchor-primary\" href=\"https://github.com/broadinstitute/pilon\" target=\"_blank\" position_id=\"1478\"><span class=\"anchor-text-container\" position_id=\"1479\"><span class=\"anchor-text\" position_id=\"1480\">https://github.com/broadinstitute/pilon</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1481\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1482\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1483\"><td position_id=\"1484\">PURGEhaplotigs</td><td position_id=\"1485\">Roach et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib65\" data-xocs-content-type=\"reference\" href=\"#bib65\" name=\"bbib65\" position_id=\"1486\"><span class=\"anchor-text-container\" position_id=\"1487\"><span class=\"anchor-text\" position_id=\"1488\"><sup position_id=\"1489\">68</sup></span></span></a></td><td position_id=\"1490\"><a class=\"anchor anchor-primary\" href=\"https://github.com/dfguan/purge_haplotigs\" target=\"_blank\" position_id=\"1491\"><span class=\"anchor-text-container\" position_id=\"1492\"><span class=\"anchor-text\" position_id=\"1493\">https://github.com/dfguan/purge_haplotigs</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1494\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1495\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1496\"><td position_id=\"1497\">Juicer</td><td position_id=\"1498\">Durand et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib66\" data-xocs-content-type=\"reference\" href=\"#bib66\" name=\"bbib66\" position_id=\"1499\"><span class=\"anchor-text-container\" position_id=\"1500\"><span class=\"anchor-text\" position_id=\"1501\"><sup position_id=\"1502\">69</sup></span></span></a></td><td position_id=\"1503\"><a class=\"anchor anchor-primary\" href=\"https://github.com/aidenlab/juicer\" target=\"_blank\" position_id=\"1504\"><span class=\"anchor-text-container\" position_id=\"1505\"><span class=\"anchor-text\" position_id=\"1506\">https://github.com/aidenlab/juicer</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1507\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1508\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1509\"><td position_id=\"1510\">Assembly Tools</td><td position_id=\"1511\">Durand et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib66\" data-xocs-content-type=\"reference\" href=\"#bib66\" name=\"bbib66\" position_id=\"1512\"><span class=\"anchor-text-container\" position_id=\"1513\"><span class=\"anchor-text\" position_id=\"1514\"><sup position_id=\"1515\">69</sup></span></span></a></td><td position_id=\"1516\"><a class=\"anchor anchor-primary\" href=\"https://github.com/aidenlab/juicer\" target=\"_blank\" position_id=\"1517\"><span class=\"anchor-text-container\" position_id=\"1518\"><span class=\"anchor-text\" position_id=\"1519\">https://github.com/aidenlab/juicer</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1520\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1521\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1522\"><td position_id=\"1523\">TGS-GapCloser</td><td position_id=\"1524\"/><td position_id=\"1525\"><a class=\"anchor anchor-primary\" href=\"https://github.com/BGI-Qingdao/TGS-GapCloser\" target=\"_blank\" position_id=\"1526\"><span class=\"anchor-text-container\" position_id=\"1527\"><span class=\"anchor-text\" position_id=\"1528\">https://github.com/BGI-Qingdao/TGS-GapCloser</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1529\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1530\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1531\"><td position_id=\"1532\">LASTZ</td><td position_id=\"1533\"/><td position_id=\"1534\"><a class=\"anchor anchor-primary\" href=\"https://github.com/lastz/lastz\" target=\"_blank\" position_id=\"1535\"><span class=\"anchor-text-container\" position_id=\"1536\"><span class=\"anchor-text\" position_id=\"1537\">https://github.com/lastz/lastz</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1538\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1539\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1540\"><td position_id=\"1541\">Emboss</td><td position_id=\"1542\">Rice et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib67\" data-xocs-content-type=\"reference\" href=\"#bib67\" name=\"bbib67\" position_id=\"1543\"><span class=\"anchor-text-container\" position_id=\"1544\"><span class=\"anchor-text\" position_id=\"1545\"><sup position_id=\"1546\">70</sup></span></span></a></td><td position_id=\"1547\"><a class=\"anchor anchor-primary\" href=\"http://emboss.sourceforge.net/\" target=\"_blank\" position_id=\"1548\"><span class=\"anchor-text-container\" position_id=\"1549\"><span class=\"anchor-text\" position_id=\"1550\">http://emboss.sourceforge.net/</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1551\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1552\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1553\"><td position_id=\"1554\">cutadapt</td><td position_id=\"1555\">Martin<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib68\" data-xocs-content-type=\"reference\" href=\"#bib68\" name=\"bbib68\" position_id=\"1556\"><span class=\"anchor-text-container\" position_id=\"1557\"><span class=\"anchor-text\" position_id=\"1558\"><sup position_id=\"1559\">71</sup></span></span></a></td><td position_id=\"1560\"><a class=\"anchor anchor-primary\" href=\"https://cutadapt.readthedocs.io/\" target=\"_blank\" position_id=\"1561\"><span class=\"anchor-text-container\" position_id=\"1562\"><span class=\"anchor-text\" position_id=\"1563\">https://cutadapt.readthedocs.io/</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1564\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1565\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1566\"><td position_id=\"1567\">MACS</td><td position_id=\"1568\">Zhang et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib69\" data-xocs-content-type=\"reference\" href=\"#bib69\" name=\"bbib69\" position_id=\"1569\"><span class=\"anchor-text-container\" position_id=\"1570\"><span class=\"anchor-text\" position_id=\"1571\"><sup position_id=\"1572\">72</sup></span></span></a></td><td position_id=\"1573\"><a class=\"anchor anchor-primary\" href=\"https://github.com/macs3-project/MACS\" target=\"_blank\" position_id=\"1574\"><span class=\"anchor-text-container\" position_id=\"1575\"><span class=\"anchor-text\" position_id=\"1576\">https://github.com/macs3-project/MACS</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1577\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1578\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1579\"><td position_id=\"1580\">hifiasm</td><td position_id=\"1581\">Cheng et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib70\" data-xocs-content-type=\"reference\" href=\"#bib70\" name=\"bbib70\" position_id=\"1582\"><span class=\"anchor-text-container\" position_id=\"1583\"><span class=\"anchor-text\" position_id=\"1584\"><sup position_id=\"1585\">73</sup></span></span></a></td><td position_id=\"1586\"><a class=\"anchor anchor-primary\" href=\"https://github.com/chhylp123/hifiasm\" target=\"_blank\" position_id=\"1587\"><span class=\"anchor-text-container\" position_id=\"1588\"><span class=\"anchor-text\" position_id=\"1589\">https://github.com/chhylp123/hifiasm</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1590\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1591\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1592\"><td position_id=\"1593\">RepeatMasker</td><td position_id=\"1594\"/><td position_id=\"1595\"><a class=\"anchor anchor-primary\" href=\"http://www.repeatmasker.org/\" target=\"_blank\" position_id=\"1596\"><span class=\"anchor-text-container\" position_id=\"1597\"><span class=\"anchor-text\" position_id=\"1598\">http://www.repeatmasker.org/</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1599\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1600\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1601\"><td position_id=\"1602\">Bonito</td><td position_id=\"1603\"/><td position_id=\"1604\"><a class=\"anchor anchor-primary\" href=\"https://github.com/nanoporetech/bonito\" target=\"_blank\" position_id=\"1605\"><span class=\"anchor-text-container\" position_id=\"1606\"><span class=\"anchor-text\" position_id=\"1607\">https://github.com/nanoporetech/bonito</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1608\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1609\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1610\"><td position_id=\"1611\">Remora</td><td position_id=\"1612\"/><td position_id=\"1613\"><a class=\"anchor anchor-primary\" href=\"https://github.com/nanoporetech/remora\" target=\"_blank\" position_id=\"1614\"><span class=\"anchor-text-container\" position_id=\"1615\"><span class=\"anchor-text\" position_id=\"1616\">https://github.com/nanoporetech/remora</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1617\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1618\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1619\"><td position_id=\"1620\">modbam2bed</td><td position_id=\"1621\"/><td position_id=\"1622\"><a class=\"anchor anchor-primary\" href=\"https://github.com/nanoporetech/modbam2bed\" target=\"_blank\" position_id=\"1623\"><span class=\"anchor-text-container\" position_id=\"1624\"><span class=\"anchor-text\" position_id=\"1625\">https://github.com/nanoporetech/modbam2bed</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1626\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1627\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1628\"><td position_id=\"1629\">bedtools</td><td position_id=\"1630\">Quinlan and Hall<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib71\" data-xocs-content-type=\"reference\" href=\"#bib71\" name=\"bbib71\" position_id=\"1631\"><span class=\"anchor-text-container\" position_id=\"1632\"><span class=\"anchor-text\" position_id=\"1633\"><sup position_id=\"1634\">74</sup></span></span></a></td><td position_id=\"1635\"><a class=\"anchor anchor-primary\" href=\"https://bedtools.readthedocs.io/\" target=\"_blank\" position_id=\"1636\"><span class=\"anchor-text-container\" position_id=\"1637\"><span class=\"anchor-text\" position_id=\"1638\">https://bedtools.readthedocs.io/</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1639\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1640\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1641\"><td position_id=\"1642\">bedops</td><td position_id=\"1643\">Neph et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib72\" data-xocs-content-type=\"reference\" href=\"#bib72\" name=\"bbib72\" position_id=\"1644\"><span class=\"anchor-text-container\" position_id=\"1645\"><span class=\"anchor-text\" position_id=\"1646\"><sup position_id=\"1647\">75</sup></span></span></a></td><td position_id=\"1648\"><a class=\"anchor anchor-primary\" href=\"https://bedops.readthedocs.io/en/latest/\" target=\"_blank\" position_id=\"1649\"><span class=\"anchor-text-container\" position_id=\"1650\"><span class=\"anchor-text\" position_id=\"1651\">https://bedops.readthedocs.io/en/latest/</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1652\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1653\"/></svg></span></a></td></tr><tr class=\"valign-top\" position_id=\"1654\"><td position_id=\"1655\">Guppy</td><td position_id=\"1656\">ONT</td><td position_id=\"1657\">N/A</td></tr><tr class=\"valign-top\" position_id=\"1658\"><td position_id=\"1659\">Flye</td><td position_id=\"1660\">Kolmogorov et al.<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib73\" data-xocs-content-type=\"reference\" href=\"#bib73\" name=\"bbib73\" position_id=\"1661\"><span class=\"anchor-text-container\" position_id=\"1662\"><span class=\"anchor-text\" position_id=\"1663\"><sup position_id=\"1664\">76</sup></span></span></a></td><td position_id=\"1665\"><a class=\"anchor anchor-primary\" href=\"https://github.com/mikolmogorov/Flye\" target=\"_blank\" position_id=\"1666\"><span class=\"anchor-text-container\" position_id=\"1667\"><span class=\"anchor-text\" position_id=\"1668\">https://github.com/mikolmogorov/Flye</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1669\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1670\"/></svg></span></a></td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1671\"><td position_id=\"1672\">BWA</td><td position_id=\"1673\">Li and Durbin<a class=\"anchor anchor-primary\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-id=\"bib74\" data-xocs-content-type=\"reference\" href=\"#bib74\" name=\"bbib74\" position_id=\"1674\"><span class=\"anchor-text-container\" position_id=\"1675\"><span class=\"anchor-text\" position_id=\"1676\"><sup position_id=\"1677\">77</sup></span></span></a></td><td position_id=\"1678\"><a class=\"anchor anchor-primary\" href=\"https://github.com/lh3/bwa\" target=\"_blank\" position_id=\"1679\"><span class=\"anchor-text-container\" position_id=\"1680\"><span class=\"anchor-text\" position_id=\"1681\">https://github.com/lh3/bwa</span><svg aria-label=\"Opens in new window\" class=\"icon icon-arrow-up-right-tiny arrow-external-link\" viewBox=\"0 0 8 8\" focusable=\"false\" height=\"20\" position_id=\"1682\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\" position_id=\"1683\"/></svg></span></a></td></tr><tr class=\"rowsep-1 valign-top\" position_id=\"1684\"><th colspan=\"3\" scope=\"row\" position_id=\"1685\"><strong position_id=\"1686\">Other</strong></th></tr><tr class=\"valign-top\" position_id=\"1687\"><td position_id=\"1688\">Sage Science PippinHT platform</td><td position_id=\"1689\">Sage Science</td><td position_id=\"1690\">ELF0001</td></tr><tr class=\"valign-top\" position_id=\"1691\"><td position_id=\"1692\">Megaruptor</td><td position_id=\"1693\">Diagenode Diagnostics</td><td position_id=\"1694\">N/A</td></tr></tbody></table>", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[1]/div/span/div/div/table"}]}, "tags": ["table"], "label": "table", "web_segment_id": 112, "global_sentence_id": 203, "edu_l1_label": "EDU_O"}, {"txt": "Method details", "language": "english", "position": {"atoms": [{"position_id": 5181, "txt": "Method details", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/h3"}]}, "tags": ["h3"], "label": "title2", "web_segment_id": 113, "global_sentence_id": 204, "edu_l1_label": "EDU_O"}, {"txt": "Cell line authentication", "language": "english", "position": {"atoms": [{"position_id": 5183, "txt": "Cell line authentication", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[1]/h4"}]}, "tags": ["h4"], "label": "title3", "web_segment_id": 114, "global_sentence_id": 205, "edu_l1_label": "EDU_O"}, {"txt": "The genetic identity of each cell line was authenticated by comparing the genetic sequencing data against previously published sequencing and assembly data from each sample.", "language": "english", "position": {"atoms": [{"position_id": 5185, "txt": "The genetic identity of each cell line was authenticated by comparing the genetic sequencing data against previously published sequencing and assembly data from each sample.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[1]/div"}]}, "tags": [], "label": "content", "web_segment_id": 115, "global_sentence_id": 206, "edu_l1_label": "EDU_O"}, {"txt": "Single-molecule chromatin fiber sequencing", "language": "english", "position": {"atoms": [{"position_id": 5187, "txt": "Single-molecule chromatin fiber sequencing", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/h4"}]}, "tags": ["h4"], "label": "title3", "web_segment_id": 116, "global_sentence_id": 207, "edu_l1_label": "EDU_O"}, {"txt": "CHM13 cells were grown in AmnioMax C-100 Basal Medium (Invitrogen 12558011), which includes the AmnioMAX C-100 Supplement to approximately 90% confluency at 37°C and 5% CO2.", "language": "english", "position": {"atoms": [{"position_id": 5189, "txt": "CHM13 cells were grown in AmnioMax C-100 Basal Medium (Invitrogen 12558011), which includes the AmnioMAX C-100 Supplement to approximately 90% confluency at 37°C and 5% CO", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]"}, {"position_id": 5191, "txt": "2", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/sub"}, {"position_id": 5193, "txt": ".", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/sub"}]}, "tags": [], "label": "content", "web_segment_id": 117, "global_sentence_id": 208, "edu_l1_label": "EDU_O"}, {"txt": " Growth media was changed daily, and cells were split using 0.25% trypsin (GIbco 25200056).", "language": "english", "position": {"atoms": [{"position_id": 5194, "txt": " Growth media was changed daily, and cells were split using 0.25% trypsin (GIbco 25200056).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/sub"}]}, "tags": [], "label": "content", "web_segment_id": 117, "global_sentence_id": 209, "edu_l1_label": "EDU_O"}, {"txt": " One million CHM13 cells per sample were pelleted at 250 x g for 5 min (4 samples were processed in parallel), and washed once with PBS and then pelleted again at 250 x g for 5 min.", "language": "english", "position": {"atoms": [{"position_id": 5195, "txt": " One million CHM13 cells per sample were pelleted at 250 x g for 5 min (4 samples were processed in parallel), and washed once with PBS and then pelleted again at 250 x g for 5 min.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/sub"}]}, "tags": [], "label": "content", "web_segment_id": 117, "global_sentence_id": 210, "edu_l1_label": "EDU_O"}, {"txt": " Each cell pellet was resuspended in 60 μl Buffer A (15 mM Tris, pH 8.0; 15 mM NaCl; 60 mM KCl; 1mM EDTA, pH 8.0; 0.5 mM EGTA, pH 8.0; 0.5 mM Spermidine) and 60 μl of cold 2X Lysis buffer (0.1% IGEPAL CA-630 in Buffer A) was added and mixed by gentle flicking then kept on ice for 10 min.", "language": "english", "position": {"atoms": [{"position_id": 5196, "txt": " Each cell pellet was resuspended in 60 μl Buffer A (15 mM Tris, pH 8.0; 15 mM NaCl; 60 mM KCl; 1mM EDTA, pH 8.0; 0.5 mM EGTA, pH 8.0; 0.5 mM Spermidine) and 60 μl of cold 2X Lysis buffer (0.1% IGEPAL CA-630 in Buffer A) was added and mixed by gentle flicking then kept on ice for 10 min.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/sub"}]}, "tags": [], "label": "content", "web_segment_id": 117, "global_sentence_id": 211, "edu_l1_label": "EDU_O"}, {"txt": " Samples were then pelleted at 4°C for 5 min at 350 x g and the supernatant was removed.", "language": "english", "position": {"atoms": [{"position_id": 5197, "txt": " Samples were then pelleted at 4°C for 5 min at 350 x g and the supernatant was removed.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/sub"}]}, "tags": [], "label": "content", "web_segment_id": 117, "global_sentence_id": 212, "edu_l1_label": "EDU_O"}, {"txt": " The nuclei pellets were gently resuspended individually with wide bore pipette tips in 57.5 μl Buffer A and moved to a 25°C thermocycler.", "language": "english", "position": {"atoms": [{"position_id": 5198, "txt": " The nuclei pellets were gently resuspended individually with wide bore pipette tips in 57.5 μl Buffer A and moved to a 25°C thermocycler.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/sub"}]}, "tags": [], "label": "content", "web_segment_id": 117, "global_sentence_id": 213, "edu_l1_label": "EDU_O"}, {"txt": " 1 μl of Hia5 MTase (200 U)19 and 1.5 μl 32 mM S-adenosylmethionine (NEB B9003S) (0.8 mM final concentration) were added, then carefully mixed by pipetting the volume up and down 10 times with wide bore tips.", "language": "english", "position": {"atoms": [{"position_id": 5199, "txt": " 1 μl of Hia5 MTase (200 U)", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/sub"}, {"position_id": 5201, "txt": "19", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/a/span/span/sup"}, {"position_id": 5203, "txt": " and 1.5 μl 32 mM S-adenosylmethionine (NEB B9003S) (0.8 mM final concentration) were added, then carefully mixed by pipetting the volume up and down 10 times with wide bore tips.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/a"}]}, "tags": [], "label": "content", "web_segment_id": 117, "global_sentence_id": 214, "edu_l1_label": "EDU_O"}, {"txt": " The reactions were incubated for 10 min at 25°C then stopped with 3 μl of 20% SDS (1% final concentration) and transferred to new 1.5 mL microfuge tubes.", "language": "english", "position": {"atoms": [{"position_id": 5204, "txt": " The reactions were incubated for 10 min at 25°C then stopped with 3 μl of 20% SDS (1% final concentration) and transferred to new 1.5 mL microfuge tubes.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/a"}]}, "tags": [], "label": "content", "web_segment_id": 117, "global_sentence_id": 215, "edu_l1_label": "EDU_O"}, {"txt": " The sample volumes were adjusted to 100 μl by the addition of 37 μl PBS.", "language": "english", "position": {"atoms": [{"position_id": 5205, "txt": " The sample volumes were adjusted to 100 μl by the addition of 37 μl PBS.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/a"}]}, "tags": [], "label": "content", "web_segment_id": 117, "global_sentence_id": 216, "edu_l1_label": "EDU_O"}, {"txt": " To that, 500 μl of HMW Lysis Buffer A (Promega Wizard HMW DNA Extraction Kit A2920) and 3 μl RNAse A (ThermoFisher EN0531) were added.", "language": "english", "position": {"atoms": [{"position_id": 5206, "txt": " To that, 500 μl of HMW Lysis Buffer A (Promega Wizard HMW DNA Extraction Kit A2920) and 3 μl RNAse A (ThermoFisher EN0531) were added.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/a"}]}, "tags": [], "label": "content", "web_segment_id": 117, "global_sentence_id": 217, "edu_l1_label": "EDU_O"}, {"txt": " The tubes were mixed by inverting 7 times and incubated 15 min at 37°C.", "language": "english", "position": {"atoms": [{"position_id": 5207, "txt": " The tubes were mixed by inverting 7 times and incubated 15 min at 37°C.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/a"}]}, "tags": [], "label": "content", "web_segment_id": 117, "global_sentence_id": 218, "edu_l1_label": "EDU_O"}, {"txt": " 20 μl of Proteinase K (Promega Wizard HMW DNA Extraction Kit A2920) was added and the samples mixed by inverting 10 times and incubated 15 min at 56°C followed by chilling on ice for 1 min.", "language": "english", "position": {"atoms": [{"position_id": 5208, "txt": " 20 μl of Proteinase K (Promega Wizard HMW DNA Extraction Kit A2920) was added and the samples mixed by inverting 10 times and incubated 15 min at 56°C followed by chilling on ice for 1 min.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/a"}]}, "tags": [], "label": "content", "web_segment_id": 117, "global_sentence_id": 219, "edu_l1_label": "EDU_O"}, {"txt": " Protein was precipitated by the addition of 200 μl Protein Precipitation Solution (Promega Wizard HMW DNA Extraction Kit A2920).", "language": "english", "position": {"atoms": [{"position_id": 5209, "txt": " Protein was precipitated by the addition of 200 μl Protein Precipitation Solution (Promega Wizard HMW DNA Extraction Kit A2920).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/a"}]}, "tags": [], "label": "content", "web_segment_id": 117, "global_sentence_id": 220, "edu_l1_label": "EDU_O"}, {"txt": " Using a wide bore tip the samples were mixed by drawing up contents from the bottom of the tube and then expelled on the side of the tube 5 times.", "language": "english", "position": {"atoms": [{"position_id": 5210, "txt": " Using a wide bore tip the samples were mixed by drawing up contents from the bottom of the tube and then expelled on the side of the tube 5 times.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/a"}]}, "tags": [], "label": "content", "web_segment_id": 117, "global_sentence_id": 221, "edu_l1_label": "EDU_O"}, {"txt": " Tubes were centrifuged at 16,000g for 5 min.", "language": "english", "position": {"atoms": [{"position_id": 5211, "txt": " Tubes were centrifuged at 16,000g for 5 min.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/a"}]}, "tags": [], "label": "content", "web_segment_id": 117, "global_sentence_id": 222, "edu_l1_label": "EDU_O"}, {"txt": " The supernatant was poured into a new 1.5 ml tube containing 600 μl isopropanol.", "language": "english", "position": {"atoms": [{"position_id": 5212, "txt": " The supernatant was poured into a new 1.5 ml tube containing 600 μl isopropanol.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/a"}]}, "tags": [], "label": "content", "web_segment_id": 117, "global_sentence_id": 223, "edu_l1_label": "EDU_O"}, {"txt": " This was mixed by gentle inversion 10 times, incubated 1 min at room temperature then inverted an additional 10 times.", "language": "english", "position": {"atoms": [{"position_id": 5213, "txt": " This was mixed by gentle inversion 10 times, incubated 1 min at room temperature then inverted an additional 10 times.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/a"}]}, "tags": [], "label": "content", "web_segment_id": 117, "global_sentence_id": 224, "edu_l1_label": "EDU_O"}, {"txt": " DNA was precipitated by centrifugation at 16,000g for 5 min.", "language": "english", "position": {"atoms": [{"position_id": 5214, "txt": " DNA was precipitated by centrifugation at 16,000g for 5 min.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/a"}]}, "tags": [], "label": "content", "web_segment_id": 117, "global_sentence_id": 225, "edu_l1_label": "EDU_O"}, {"txt": " The supernatant was decanted and the pellet washed with the addition of 70% ethanol and centrifuged again at 16,000 g 5 min.", "language": "english", "position": {"atoms": [{"position_id": 5215, "txt": " The supernatant was decanted and the pellet washed with the addition of 70% ethanol and centrifuged again at 16,000 g 5 min.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/a"}]}, "tags": [], "label": "content", "web_segment_id": 117, "global_sentence_id": 226, "edu_l1_label": "EDU_O"}, {"txt": " After the supernatant was decanted, a quick spin was performed to facilitate removal of any residual ethanol.", "language": "english", "position": {"atoms": [{"position_id": 5216, "txt": " After the supernatant was decanted, a quick spin was performed to facilitate removal of any residual ethanol.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/a"}]}, "tags": [], "label": "content", "web_segment_id": 117, "global_sentence_id": 227, "edu_l1_label": "EDU_O"}, {"txt": " Open tubes were air dried on the bench for 15 min.", "language": "english", "position": {"atoms": [{"position_id": 5217, "txt": " Open tubes were air dried on the bench for 15 min.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/a"}]}, "tags": [], "label": "content", "web_segment_id": 117, "global_sentence_id": 228, "edu_l1_label": "EDU_O"}, {"txt": " The DNA was resuspended by the addition of 25 μl 10mM Tris pH 8.0.", "language": "english", "position": {"atoms": [{"position_id": 5218, "txt": " The DNA was resuspended by the addition of 25 μl 10mM Tris pH 8.0.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/a"}]}, "tags": [], "label": "content", "web_segment_id": 117, "global_sentence_id": 229, "edu_l1_label": "EDU_O"}, {"txt": " Tubes were stored overnight in 4°C and the next day were mixed gently by using a wide bore pipette tip, drawing up the sample 5 times and gently expelling the contents on the side of the tube.", "language": "english", "position": {"atoms": [{"position_id": 5219, "txt": " Tubes were stored overnight in 4°C and the next day were mixed gently by using a wide bore pipette tip, drawing up the sample 5 times and gently expelling the contents on the side of the tube.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/a"}]}, "tags": [], "label": "content", "web_segment_id": 117, "global_sentence_id": 230, "edu_l1_label": "EDU_O"}, {"txt": " Samples were then stored at -80°C prior to library construction.", "language": "english", "position": {"atoms": [{"position_id": 5220, "txt": " Samples were then stored at -80°C prior to library construction.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[1]/a"}]}, "tags": [], "label": "content", "web_segment_id": 117, "global_sentence_id": 231, "edu_l1_label": "EDU_O"}, {"txt": "DNA shearing, library construction, and PacBio Sequel II sequencing were performed as previously described.19 with the exception that 15-20 kb fragments were targeted when shearing using the Megaruptor (Diagenode Diagnostics).", "language": "english", "position": {"atoms": [{"position_id": 5222, "txt": "DNA shearing, library construction, and PacBio Sequel II sequencing were performed as previously described.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[2]"}, {"position_id": 5224, "txt": "19", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[2]/a/span/span/sup"}, {"position_id": 5226, "txt": " with the exception that 15-20 kb fragments were targeted when shearing using the Megaruptor (Diagenode Diagnostics).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[2]/div[2]/a"}]}, "tags": [], "label": "content", "web_segment_id": 118, "global_sentence_id": 232, 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"/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[4]/div[4]/em[1]"}, {"position_id": 5319, "txt": " using default parameters.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[4]/div[4]/em[1]"}]}, "tags": ["em"], "label": "content", "web_segment_id": 127, "global_sentence_id": 262, "edu_l1_label": "EDU_O"}, {"txt": " By default, this process is run in the background during fibertools-rs predict-m6A.", "language": "english", "position": {"atoms": [{"position_id": 5320, "txt": " By default, this process is run in the background during ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[4]/div[4]/em[1]"}, {"position_id": 5322, "txt": "fibertools-rs predict-m6A.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[4]/div[4]/em[2]"}]}, "tags": ["em"], "label": "content", "web_segment_id": 127, "global_sentence_id": 263, "edu_l1_label": "EDU_O"}, {"txt": "Nucleosome, MSP, and m6A bigWig tracks were generated by counting total occurrences across all molecules at a bp and dividing by the coverage at that bp.", "language": "english", "position": {"atoms": [{"position_id": 5324, "txt": "Nucleosome, MSP, and m6A bigWig tracks were generated by counting total occurrences across all molecules at a bp and dividing by the coverage at that bp.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[4]/div[5]"}]}, "tags": [], "label": "content", "web_segment_id": 128, "global_sentence_id": 264, "edu_l1_label": "EDU_O"}, {"txt": "Identifying the centromere core/centromere dip region", "language": "english", "position": {"atoms": [{"position_id": 5326, "txt": "Identifying the centromere core/centromere dip region", "x": 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CHM1 annotations were generated as previously described.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[5]/div/a[2]"}, {"position_id": 5338, "txt": "38", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[5]/div/a[3]/span/span/sup"}, {"position_id": 5340, "txt": " For CHM13 and CHM1, alpha satellite repeats less than 25 bp apart were merged together and we only kept alpha satellite stretches ≥ 100 kb.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[5]/div/a[3]"}]}, "tags": [], "label": "content", "web_segment_id": 130, "global_sentence_id": 266, "edu_l1_label": "EDU_O"}, {"txt": " We then made windows of 1190 bp across this region with step size of 170 bp (approximate alpha satellite repeat length).", "language": "english", "position": {"atoms": [{"position_id": 5341, "txt": " We then made windows of 1190 bp across this region with step size of 170 bp (approximate alpha satellite repeat length).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[5]/div/a[3]"}]}, "tags": [], "label": "content", "web_segment_id": 130, "global_sentence_id": 267, "edu_l1_label": "EDU_O"}, {"txt": " We then took the mean CpG methylation frequency across all CpG sites that fall in the window.", "language": "english", "position": {"atoms": [{"position_id": 5342, "txt": " We then took the mean CpG methylation frequency across all CpG sites that fall in the window.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[5]/div/a[3]"}]}, "tags": [], "label": "content", "web_segment_id": 130, "global_sentence_id": 268, "edu_l1_label": "EDU_O"}, {"txt": " We identified all windows that were below the 35th percentile of CpG methylation window frequency, and merged neighboring windows that passed this threshold.", "language": "english", "position": {"atoms": [{"position_id": 5343, "txt": " We identified all windows that were below the 35", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[5]/div/a[3]"}, {"position_id": 5345, "txt": "th", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[5]/div/sup[1]"}, {"position_id": 5347, "txt": " percentile of CpG methylation window frequency, and merged neighboring windows that passed this threshold.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[5]/div/sup[1]"}]}, "tags": [], "label": "content", "web_segment_id": 130, "global_sentence_id": 269, "edu_l1_label": "EDU_O"}, {"txt": " Merged windows that were 1) at least 15 kb in length, 2) had a mean CpG methylation window frequency < 20th percentile, and 3) were not located in the terminal 70 kb of the alpha satellite repeat region were identified as CDRs.", "language": "english", "position": {"atoms": [{"position_id": 5348, "txt": " Merged windows that were 1) at least 15 kb in length, 2) had a mean CpG methylation window frequency < 20", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[5]/div/sup[1]"}, {"position_id": 5350, "txt": "th", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[5]/div/sup[2]"}, {"position_id": 5352, "txt": " percentile, and 3) were not located in the terminal 70 kb of the alpha satellite repeat region were identified as CDRs.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[5]/div/sup[2]"}]}, "tags": [], "label": "content", "web_segment_id": 130, "global_sentence_id": 270, "edu_l1_label": "EDU_O"}, {"txt": " For HG002, CDRs were identified using the same approach, but the threshold to the terminus of the alpha satellite array was lowered to 15 kb.", "language": "english", "position": {"atoms": [{"position_id": 5353, "txt": " For HG002, CDRs were identified using the same approach, but the threshold to the terminus of the alpha satellite array was lowered to 15 kb.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[5]/div/sup[2]"}]}, "tags": [], "label": "content", "web_segment_id": 130, "global_sentence_id": 271, "edu_l1_label": "EDU_O"}, {"txt": " For HLE, we used CENPA CUT&RUN enriched regions to identify the centromere core, as we did not know whether to expect this region to be hypo-CpG methylated.", "language": "english", "position": {"atoms": [{"position_id": 5354, "txt": " For HLE, we used CENPA CUT&RUN enriched regions to identify the centromere core, as we did not know whether to expect this region to be hypo-CpG methylated.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[5]/div/sup[2]"}]}, "tags": [], "label": "content", "web_segment_id": 130, "global_sentence_id": 272, "edu_l1_label": "EDU_O"}, {"txt": "Identification of di-nucleosomes and large MSPs", "language": "english", "position": {"atoms": [{"position_id": 5356, "txt": "Identification of di-nucleosomes and large MSPs", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[6]/h4"}]}, "tags": ["h4"], "label": "title3", "web_segment_id": 131, "global_sentence_id": 273, "edu_l1_label": "EDU_O"}, {"txt": "The cutoff for identifying di-nucleosomes and large MSPs was 210 and 150, respectively.", "language": "english", "position": {"atoms": [{"position_id": 5358, "txt": "The cutoff for identifying di-nucleosomes and large MSPs was 210 and 150, respectively.", "x": 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"position": {"atoms": [{"position_id": 5361, "txt": "Measuring distance between neighboring accessible patches", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[7]/h4"}]}, "tags": ["h4"], "label": "title3", "web_segment_id": 133, "global_sentence_id": 276, "edu_l1_label": "EDU_O"}, {"txt": "To calculate the observed distance between large MSPs we calculated the distance between large MSP start positions.", "language": "english", "position": {"atoms": [{"position_id": 5363, "txt": "To calculate the observed distance between large MSPs we calculated the distance between large MSP start positions.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[7]/div"}]}, "tags": [], "label": "content", "web_segment_id": 134, "global_sentence_id": 277, "edu_l1_label": "EDU_O"}, {"txt": " To calculate the expected distance between large MSPs in the CDR, we first calculated the number of large MSPs fully contained in the CDR and divided by the total number of sequenced bases per CDR to get a large MSP/sequenced bp value.", "language": "english", "position": {"atoms": [{"position_id": 5364, "txt": " To calculate the expected distance between large MSPs in the CDR, we first calculated the number of large MSPs fully contained in the CDR and divided by the total number of sequenced bases per CDR to get a large MSP/sequenced bp value.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[7]/div"}]}, "tags": [], "label": "content", "web_segment_id": 134, "global_sentence_id": 278, "edu_l1_label": "EDU_O"}, {"txt": " We then multiply the resulting value by the length of the respective CDR to get the expected number of large MSPs per CDR.", "language": "english", "position": {"atoms": [{"position_id": 5365, "txt": " We then multiply the resulting value by the length of the respective CDR to get the expected number of large MSPs per CDR.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[7]/div"}]}, "tags": [], "label": "content", "web_segment_id": 134, "global_sentence_id": 279, "edu_l1_label": "EDU_O"}, {"txt": " We divide the length of the CDR by this value to get the expected number of bp between large MSPs within the CDR.", "language": "english", "position": {"atoms": [{"position_id": 5366, "txt": " We divide the length of the CDR by this value to get the expected number of bp between large MSPs within the CDR.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[7]/div"}]}, "tags": [], "label": "content", "web_segment_id": 134, "global_sentence_id": 280, "edu_l1_label": "EDU_O"}, {"txt": "Determining chromatin repeat lengths", "language": "english", "position": {"atoms": [{"position_id": 5368, "txt": "Determining chromatin repeat lengths", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[8]/h4"}]}, "tags": ["h4"], "label": "title3", "web_segment_id": 135, "global_sentence_id": 281, "edu_l1_label": "IOS"}, {"txt": "To determine the chromatin repeat length of individual chromatin fibers, the per-base m6A pattern on each fiber was converted into a binary vector (m6a=1, no-m6a=0).", "language": "english", "position": {"atoms": [{"position_id": 5370, "txt": "To determine the chromatin repeat length of individual chromatin fibers, the per-base m6A pattern on each fiber was converted into a binary vector (m6a=1, no-m6a=0).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[8]/div"}]}, "tags": [], "label": "content", "web_segment_id": 136, "global_sentence_id": 282, "edu_l1_label": "IOS"}, {"txt": " These vectors were then independently analyzed using the scipy.signal.periodogram tool.", "language": "english", "position": {"atoms": [{"position_id": 5371, "txt": " These vectors were then independently analyzed using the ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[8]/div"}, {"position_id": 5373, "txt": "scipy.signal.periodogram", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[8]/div/em"}, {"position_id": 5375, "txt": " tool.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[8]/div/em"}]}, "tags": ["em"], "label": "content", "web_segment_id": 136, "global_sentence_id": 283, "edu_l1_label": "EDU_O"}, {"txt": " This results in spectral density estimations across a vector of frequencies, which is the inverse of the nucleosome repeat length in base-pairs.", "language": "english", "position": {"atoms": [{"position_id": 5376, "txt": " This results in spectral density estimations across a vector of frequencies, which is the inverse of the nucleosome repeat length in base-pairs.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[8]/div/em"}]}, "tags": ["em"], "label": "content", "web_segment_id": 136, "global_sentence_id": 284, "edu_l1_label": "EDU_O"}, {"txt": " Spectral densities derived from multiple fibers originating from similar genomic loci were combined and displayed.", "language": "english", "position": {"atoms": [{"position_id": 5377, "txt": " Spectral densities derived from multiple fibers originating from similar genomic loci were combined and displayed.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[8]/div/em"}]}, "tags": ["em"], "label": "content", "web_segment_id": 136, "global_sentence_id": 285, "edu_l1_label": "EDU_O"}, {"txt": "Delineating CENP-B binding elements and occupancy", "language": "english", "position": {"atoms": [{"position_id": 5379, "txt": "Delineating CENP-B binding 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"position": {"atoms": [{"position_id": 5382, "txt": " Specifically, genomic regions were scanned with this motif using ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[9]/div[1]"}, {"position_id": 5384, "txt": "fimo", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[9]/div[1]/em[1]"}, {"position_id": 5386, "txt": " (version 4.11.2)", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[9]/div[1]/em[1]"}, {"position_id": 5388, "txt": "65", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[9]/div[1]/a/span/span/sup"}, {"position_id": 5390, "txt": " with the ", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[9]/div[1]/a"}, {"position_id": 5392, "txt": "--parse-genomic-coord --qv-thresh --thresh 0.05 --max-stored-scores 1000000", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[9]/div[1]/em[2]"}, {"position_id": 5394, "txt": " flags.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[9]/div[1]/em[2]"}]}, "tags": ["em"], "label": "content", "web_segment_id": 138, "global_sentence_id": 288, "edu_l1_label": "IOS"}, {"txt": " We further filtered motifs to those which contained 2 CpG sites.", "language": "english", "position": {"atoms": [{"position_id": 5395, "txt": " We further filtered motifs to those which contained 2 CpG sites.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[9]/div[1]/em[2]"}]}, "tags": ["em"], "label": "content", "web_segment_id": 138, "global_sentence_id": 289, "edu_l1_label": "IOS"}, {"txt": " To delineate the occupancy of these CENP-B boxes, we intersected CENP-B boxes per-fiber methylation calls.", "language": "english", "position": {"atoms": [{"position_id": 5396, "txt": " To delineate the occupancy of these CENP-B boxes, we intersected CENP-B boxes per-fiber methylation calls.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[9]/div[1]/em[2]"}]}, "tags": ["em"], "label": "content", "web_segment_id": 138, "global_sentence_id": 290, "edu_l1_label": "IOS"}, {"txt": " Specifically, the m6A methylation profile of every region along every fiber overlapping a CENP-B box was converted into a binary profile (m6a=1, no-m6a=0) and stored in an array.", "language": "english", "position": {"atoms": [{"position_id": 5397, "txt": " Specifically, the m6A methylation profile of every region along every fiber overlapping a CENP-B box was converted into a binary profile (m6a=1, no-m6a=0) and stored in an array.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[9]/div[1]/em[2]"}]}, "tags": ["em"], "label": "content", "web_segment_id": 138, "global_sentence_id": 291, "edu_l1_label": "IOS"}, {"txt": " Based on genomic context and/or CpG methylation contexts these arrays were collapsed to form m6A frequency tracks with a rolling average of 10bp.", "language": "english", "position": {"atoms": [{"position_id": 5398, "txt": " Based on genomic context and/or CpG methylation contexts these arrays were collapsed to form m6A frequency tracks with a rolling average of 10bp.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[9]/div[1]/em[2]"}]}, "tags": ["em"], "label": "content", "web_segment_id": 138, "global_sentence_id": 292, "edu_l1_label": "IOS"}, {"txt": "To calculate footprint score distributions, we took all fibers fulfilling a filtering requirement (CpG methylation status/genomic region), 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defined by the mean of the smoothed m6A frequency in the -7 - +1 positions relative to the center of the CENP-B box.", "language": "english", "position": {"atoms": [{"position_id": 5403, "txt": " The CENP-B core score was defined by the mean of the smoothed m6A frequency in the -7 - +1 positions relative to the center of the CENP-B box.", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[9]/div[2]"}]}, "tags": [], "label": "content", "web_segment_id": 139, "global_sentence_id": 296, "edu_l1_label": "IOS"}, {"txt": "Quantifying nucleosome positioning surrounding CENP-B boxes", "language": "english", "position": {"atoms": [{"position_id": 5405, "txt": "Quantifying nucleosome positioning surrounding CENP-B boxes", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[10]/h4"}]}, "tags": ["h4"], "label": "title3", "web_segment_id": 140, "global_sentence_id": 297, "edu_l1_label": "IOS"}, {"txt": "To visualize the association of CENP-B occupancy and surrounding nucleosome positioning we first classified every instance of a chromatin fiber overlapping a CENP-B box by its CpG methylation state (0,1 or 2 mCpGs).", "language": "english", "position": {"atoms": [{"position_id": 5407, "txt": "To visualize the association of CENP-B occupancy and surrounding nucleosome positioning we first classified every instance of a chromatin fiber overlapping a CENP-B box by its CpG methylation state (0,1 or 2 mCpGs).", "x": "/html/body/div[2]/div/div/div/div/div[3]/div[2]/article/div[8]/div[1]/section[8]/section[2]/section[10]/div"}]}, "tags": [], "label": "content", "web_segment_id": 141, "global_sentence_id": 298, "edu_l1_label": "IOS"}, {"txt": " For each overlap, we took the closest (Relative to center of CENPB box) boundary of both the upstream and downstream nucleosome.", "language": "english", "position": {"atoms": [{"position_id": 5408, "txt": " For each overlap, we took 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# Conservation of dichromatin organization along regional centromeres
## Highlights
## Summary
## Graphical abstract
## Keywords
## Introduction
## Results
### Single-molecule chromatin architectures of kinetochore-bound point centromeres
### Dichotomous chromatin marks the centromere core in humans
### CENP-B guides centromere core dichromatin to mirror the alpha-satellite DNA repeat
### Centromere core dichromatin architecture is conserved across highly divergent regional centromeres
## Discussion
## Limitations of the study
## STAR★Methods
### Key resources table
### Method details
#### Cell line authentication
#### Single-molecule chromatin fiber sequencing
#### Yeast strains, yeast fiber-seq and genomic DNA (gDNA) extraction
#### Mapping and identifying single-molecule chromatin features
#### Identifying the centromere core/centromere dip region
#### Identification of di-nucleosomes and large MSPs
#### Measuring distance between neighboring accessible patches
#### Determining chromatin repeat lengths
#### Delineating CENP-B binding elements and occupancy
#### Quantifying nucleosome positioning surrounding CENP-B boxes
#### Hoolock leuconedys Oxford Nanopore Technologies (ONT) sequencing
#### Hoolock leuconedys Dovetail Omni-C sequencing
#### Hoolock leuconedys CUT&RUN sequencing
#### Hoolock leuconedys genome assembly
#### Hoolock leuconedys centromere annotation
### Quantification and statistical analysis