Figure 1: Global analysis of CTCF-binding sites.

A total of 26,232 CTCF-binding sites were identified by ChIP-seq of mammary tissue from lactating mice, by peak calling and overlapping three CTCF ChIP-seq samples (a) Ninety-eight per cent (25,644) of the sites were shared between mammary tissue, adipose tissue, cerebellum, heart, kidney and Th17 cells (GSE29218, GSE40918, GSE74189, GSE74826). Out of those, 65% (16,733) have been identified in all tissues and 35% (8,911) in distinct subsets. Two per cent (588) of the sites appeared to be mammary-specific. (b) Read coverage of CTCF-binding sites shared between tissues (height 37) was approximately 1.6 times higher than the mammary-specific ones (height 23). (c) The CCCTC motif was the highest ranked motif in both peak sets (±200 bp). Seventy-four per cent (19,057) of CTCF-binding sites shared between tissues had an underlying CCCTC-binding motif and 57% (337) of the mammary-specific binding sites had one. (d) A total of 370 CTCF-binding sites were detected within the 440 mammary super-enhancers. Ninety-six per cent (355) of them were shared CTCF-binding sites and 4% (15) were mammary-specific. (e) The read coverage of CTCF-binding sites shared between tissues (height 40) was approximately 2.5 times higher than those of mammary-specific ones (height 16). (f) Sixty-nine per cent (246) of the shared CTCF-binding sites and one site (7%) of the mammary-specific ones had an underlying CTCF motif. (g) CTCF-binding sites associated with 440 mammary super-enhancer boundaries. Ninety-seven per cent (854) were shared between tissues and 3% (26) were mammary-specific. (h) Read coverage of CTCF-binding sites shared between tissues (height 41) was approximately two times higher than that of mammary-specific ones (height 19). (i) Seventy-one per cent (610) of shared CTCF-binding sites, and 35% (nine) of mammary-specific ones had an underlying CTCF motif.