Figure 3

Positioning and modification patterns of nucleosomes around cis-acting elements in CD4⁺ T cell. (A) CTCF binding sites at promoters and (B) intergenic regions, aligned by CTCF sequence motif (if present) or by peak-center (if absent). The y-axis denotes the average number of positioned nucleosomes for each binding site. Nine active histone modifications are ordered by ChIP-Seq efficiency as in Table S1 in Additional file 1, and shown at peak locations. Inactive marks are absent in positioned nucleosomes around CTCF binding sites, DNase I HS regions, and TSSs, thus are not drawn here. Colors indicate the proportion of positioned nucleosomes carrying a particular histone mark (key on the bottom). (C) DNase I HS sites in promoters and (D) in intergenic regions. (E) TSS of expressed genes and (F) unexpressed genes.