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. 2012 Jul 19;7(7):e41374. doi: 10.1371/journal.pone.0041374

Figure 5. CTCF-binding sites demarcate euchromatin and heterochromatin.

Figure 5

(A) Circos map of the whole-genome chromatin domains, associated CTCF-binding sites, DNaseI HS, and histone modifications of chromosome 11 generated using the Circos software package. Chromatin domains were identified in K562 cells using HMMSeg, with DNaseI HS and histone modifications as inputs. The outermost circle (circle 1) represents the chromosome band (scale in kb). Circles 2 and 3 represent the peaks and tag density profile of CTCF-binding sites, respectively. Circle 4 represents the DNaseI HS profile. Circles 5–11 represent the histone modifications H3K27ac, H3K27me3, H3K36me3, H3K4me1, H3K4me2, H3K4me3, and H3K9ac, respectively. Circle 12 represents the euchromatin (medium blue) and heterochromatin (light cyan) domains. Intrachromosomal interactions are drawn in the innermost ring with color intensities (from white to gray) reflecting interaction strength (low to high). (B–D) Number profiles of cell type-specific (B), common (C), and ubiquitous (D) CTCF-binding sites centered on boundaries of different chromatin domains and extended 320 kb upstream of and 320 kb downstream of the boundary at 1 kb resolution. The area to the left of the vertical dash-dot line and all negative coordinates represent heterochromatin domains; the area to the right of the vertical dash-dot line and all positive coordinates represent euchromatin domains. Plotted on the y-axis is the normalized number of CTCF-binding sites and on the x-axis is distance from the chromatin boundary. Blue lines show moving-window averages with window sizes of 16 kb. The yellow strip represents the region of 5th and 95th percentiles for the number profile of the corresponding 10,000 shuffled CTCF-binding sites. The horizontal dashed line represents the median number profile of the corresponding 10,000 shuffled CTCF-binding sites. (E) Percentage of the cell type-specific, common, and ubiquitous barrier CTCF-binding sites that overlapped with each other within all CTCF and barrier CTCF across five cell types. (F) Chromatin domains are mediated by CTCF loops. Bar chart representing the median intrachromosomal interactions across the human genome (blue bar), and the median intrachromosomal interactions between any CTCF-binding sites (cyan bar), any barrier CTCF-binding sites (yellow bar), and barriers of adjacent chromatin domains (red bar) in K562 cells.