Fig. 6

Relationship between TOP2B/CTCF/RAD21 sites and Hi-C structure. a TOP2B, CTCF, and RAD21 co-bound sites localize to chromosomal domain borders. ChIP-seq tracks for TOP2B, CTCF, and RAD21 as well as binding sites classified as co-occupied for all three proteins are shown alongside a Hi-C matrix of intra-chromosomal interactions from mouse liver at an example region on chromosome 1 (left panel). The genome-wide relative position of TOP2B/CTCF/RAD21 triple sites (blue) and CTCF/RAD21 double sites (red) within mouse Hi-C domains (right panel). b Average contact insulation profiles of CTCF/RAD21 sites with (top panels) and without (bottom panels) TOP2B in mouse Hi-C data. The profiles are also shown after separation based on CTCF motif orientation in the genome (last two columns, the CTCF motif is shown above the corresponding column). c Binding sites classified as co-occupied for TOP2B/CTCF/RAD21 are shown after separation based on CTCF motif orientation (G-rich orientation, “- strand,” light blue; C-rich orientation, “+ strand,” dark blue) relative to an example Hi-C region on chromosome 12 (left panel). Genome-wide analysis of co-occupied sites, separated based on CTCF motif orientation and their relative position within domains (right panel). ChIP-exo profiles centered on CTCF motifs at sites close to domain borders (within 10 % of the full domain size) are also shown