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. 2015 Nov 17;44(5):2110–2124. doi: 10.1093/nar/gkv1214

Figure 2.

Figure 2.

Well-positioned nucleosomes primarily localize to regulatory regions and display sequence-driven rotational positioning. (A) Screenshot displaying coverage plots of sub + mono-, sub-, mono-, supra-, inter- and di-nucleosomal range MNase-seq fragments as well as sub + mono range H4-ChIP-seq fragments corrected by matching gDNA control. Region shown is chr6:92 500–106 500. Blue gene: forward strand; Red gene: reverse strand; Green blocks: 10 000 most positioned nucleosomes as identified by DANPOS (B) Pie charts displaying the distribution of gDNA (left), all nucleosomes identified by DANPOS (middle) or the 10 000 most positioned nucleosomes (right) in various genomic regions (single-exon genes, multi-exon genes, 5′ intergenic regions, 3′ intergenic regions), respectively (C) Dinucleotide frequency profiles in and around 147 bp gDNA fragments (left), or MNase-seq fragments overlapping all (middle) or the 10 000 most positioned (right) nucleosomes called by DANPOS. Note: this analysis was performed exclusively on 147 bp long fragments selected based on paired-end mapping. Grey vertical lines are positioned in 10.5 bp intervals starting 4 bp inwards from the fragment ends. Note: the tri-nucleotide frequency observable in the middle panel is likely caused by codon bias in nucleosomes originating from coding sequences.