TADs are largely conserved, with cell type–specific differences.

(A) Violin plots for distributions of insulation scores computed on pooled Hi-C datasets at 10 kb resolution, using a 150-kb (15 bin) window, on ESCs (green), DN3 (blue), and DP (red) cells. Whether analysis is restricted to the region targeted in the Capture Hi-C (top) or applied to the whole genome (bottom), ESCs have apparently more homogeneous insulation scores than thymocytes. (B) Scatter plots comparing insulation scores from pooled Hi-C data at 10 kb resolution. Top: comparing DN3 and DP cells using a 150-kb (15 bin) window; bottom: comparing ESCs and DP cells using a 70-kb (7 bin) window. SCC values are given on the graph. (C) Plots of first 2 principal components for insulation scores computed on biological replicates of Capture Hi-C datasets at 5 kb resolution, using a 25-kb (5 bin) window (left) or a 75-kb (15 bin) window (right) for DN3 (blue), DP (red), untreated ESCs (green), and ESCs after either homozygous deletion of the major CTCF site at the Bcl6 promoter (yellow) or CRISPRa ectopic induction of Bcl6 (black), Nfatc3 (gray), or Il17rb (cyan). (D) Pairwise Venn diagrams for overlap of called TAD boundaries from the pooled Capture Hi-C data of ESCs (green), DN3 (blue), and DP (red) cells. Source data available in S1 Data. CRISPRa, CRISPR activation; DN3, double negative; DP, double positive; ESC, embryonic stem cell; TAD, topologically associated domain. (PDF)