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( A ) Chemically cleaved nucleosomal DNA fragments from interphase and mitotic <t>HeLa</t> <t>S3</t> cells visualized on an agarose gel. ( B ) Crick–Watson cleavage peak-to-peak distance plot showing three dominant distances (–12, –5, and +2 nucleotides), consistent with primary and secondary cleavage sites at –1 and +6, respectively. ( C ) Frequency of AA/TT/AT/TA dinucleotides within nucleosomes and their flanking regions, based on unique nucleosome maps from interphase and metaphase. ( D–F ) Representative genomic loci showing nucleosome occupancy scores from both clone 2 and clone 1-2. Distinct interphase–metaphase differences are observed at a CTCF-binding site on Chromosome 1 (D) and the TSS of AAR2 on Chromosome 20 (E), while similar patterns are found near an exon of C16orf46 on Chromosome 16 (F). Nucleosome organization is consistent across both clones.
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( A ) Chemically cleaved nucleosomal DNA fragments from interphase and mitotic <t>HeLa</t> <t>S3</t> cells visualized on an agarose gel. ( B ) Crick–Watson cleavage peak-to-peak distance plot showing three dominant distances (–12, –5, and +2 nucleotides), consistent with primary and secondary cleavage sites at –1 and +6, respectively. ( C ) Frequency of AA/TT/AT/TA dinucleotides within nucleosomes and their flanking regions, based on unique nucleosome maps from interphase and metaphase. ( D–F ) Representative genomic loci showing nucleosome occupancy scores from both clone 2 and clone 1-2. Distinct interphase–metaphase differences are observed at a CTCF-binding site on Chromosome 1 (D) and the TSS of AAR2 on Chromosome 20 (E), while similar patterns are found near an exon of C16orf46 on Chromosome 16 (F). Nucleosome organization is consistent across both clones.
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( A ) Chemically cleaved nucleosomal DNA fragments from interphase and mitotic <t>HeLa</t> <t>S3</t> cells visualized on an agarose gel. ( B ) Crick–Watson cleavage peak-to-peak distance plot showing three dominant distances (–12, –5, and +2 nucleotides), consistent with primary and secondary cleavage sites at –1 and +6, respectively. ( C ) Frequency of AA/TT/AT/TA dinucleotides within nucleosomes and their flanking regions, based on unique nucleosome maps from interphase and metaphase. ( D–F ) Representative genomic loci showing nucleosome occupancy scores from both clone 2 and clone 1-2. Distinct interphase–metaphase differences are observed at a CTCF-binding site on Chromosome 1 (D) and the TSS of AAR2 on Chromosome 20 (E), while similar patterns are found near an exon of C16orf46 on Chromosome 16 (F). Nucleosome organization is consistent across both clones.
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( A ) Chemically cleaved nucleosomal DNA fragments from interphase and mitotic <t>HeLa</t> <t>S3</t> cells visualized on an agarose gel. ( B ) Crick–Watson cleavage peak-to-peak distance plot showing three dominant distances (–12, –5, and +2 nucleotides), consistent with primary and secondary cleavage sites at –1 and +6, respectively. ( C ) Frequency of AA/TT/AT/TA dinucleotides within nucleosomes and their flanking regions, based on unique nucleosome maps from interphase and metaphase. ( D–F ) Representative genomic loci showing nucleosome occupancy scores from both clone 2 and clone 1-2. Distinct interphase–metaphase differences are observed at a CTCF-binding site on Chromosome 1 (D) and the TSS of AAR2 on Chromosome 20 (E), while similar patterns are found near an exon of C16orf46 on Chromosome 16 (F). Nucleosome organization is consistent across both clones.
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( A ) Chemically cleaved nucleosomal DNA fragments from interphase and mitotic HeLa S3 cells visualized on an agarose gel. ( B ) Crick–Watson cleavage peak-to-peak distance plot showing three dominant distances (–12, –5, and +2 nucleotides), consistent with primary and secondary cleavage sites at –1 and +6, respectively. ( C ) Frequency of AA/TT/AT/TA dinucleotides within nucleosomes and their flanking regions, based on unique nucleosome maps from interphase and metaphase. ( D–F ) Representative genomic loci showing nucleosome occupancy scores from both clone 2 and clone 1-2. Distinct interphase–metaphase differences are observed at a CTCF-binding site on Chromosome 1 (D) and the TSS of AAR2 on Chromosome 20 (E), while similar patterns are found near an exon of C16orf46 on Chromosome 16 (F). Nucleosome organization is consistent across both clones.

Journal: bioRxiv

Article Title: Differential nucleosome organization in human interphase and metaphase chromosomes

doi: 10.1101/2025.11.11.687715

Figure Lengend Snippet: ( A ) Chemically cleaved nucleosomal DNA fragments from interphase and mitotic HeLa S3 cells visualized on an agarose gel. ( B ) Crick–Watson cleavage peak-to-peak distance plot showing three dominant distances (–12, –5, and +2 nucleotides), consistent with primary and secondary cleavage sites at –1 and +6, respectively. ( C ) Frequency of AA/TT/AT/TA dinucleotides within nucleosomes and their flanking regions, based on unique nucleosome maps from interphase and metaphase. ( D–F ) Representative genomic loci showing nucleosome occupancy scores from both clone 2 and clone 1-2. Distinct interphase–metaphase differences are observed at a CTCF-binding site on Chromosome 1 (D) and the TSS of AAR2 on Chromosome 20 (E), while similar patterns are found near an exon of C16orf46 on Chromosome 16 (F). Nucleosome organization is consistent across both clones.

Article Snippet: Parental human HeLa S3 cells (ATCC CCL-2.2) were used to generate H4S47C-expressing cell lines for chemical mapping studies.

Techniques: Agarose Gel Electrophoresis, Binding Assay, Clone Assay