Cell type–specific TADs uncovered by conventional Hi-C.

(A) Venn diagram for overlaps of called TAD boundaries from the pooled Hi-C data of ESCs (green; data taken from [21]), DN3 (blue), and DP (red) cells. (B) Pairwise Venn diagrams for the overlaps, as in (A). (C) Pooled Hi-C maps shown at 10 kb resolution for an approximately 2 Mb region around the thymocyte-expressed Runx1 gene in ESCs (top; green), DN3 (middle; blue), and DP (bottom; red) cells, just above color-coded plots showing the positions and scores of called TAD boundaries, and CTCF ChIP-seq profiles (normalized by counts per million reads). Positions of genes are shown at the bottom of the plot. Red and blue bars denote the position of a thymocyte-specific domain formed around the Runx1 gene, with a thymocyte-specific boundary corresponding to increased CTCF binding denoted by an asterisk. Triangles denote the orientation of the CTCF motifs at the border of this thymocyte-specific spatial chromatin domain. Source data available in S1 Data. DN3, double negative; DP, double positive; ESC, embryonic stem cell; TAD, topologically associated domain. (PDF)