Supplementary Figure 3: MLL2 knockout induces minor changes in TADs and CTCF occupancy, while reshaping local interactions of bivalent promoters.

a, Left, percentage of TAD border conservation with two bins between Mll2^WT and Mll2^KO mESCs (n = 23 TAD conservation values per chromosome; the box extends from lower to upper quartiles, with a line at the median; outliers are shown as individual points). Middle, TAD border strength distributions (n = 2,885 aligned TAD borders; the bar plot shows the mean and 90% confidence interval). Right, relative TAD size distributions (n = 2,803 TAD borders for Mll2^WT and n = 3,004 TAD borders for Mll2^KO; the bar plot shows the mean and 90% confidence interval). b, CTCF peak enrichment in Mll2^WT and Mll2^KO mESCs. c, Boxplot of expression levels of genes within A (yellow) or B (blue) compartments in Mll2^WT. A 0.1 pseudocount was added to total RNA RPKM values. The bottom and top of the boxes are the first and third quartiles, and the line is the median (n = 2 independent cell cultures). Whiskers correspond to 1.5 times the IQR from the median. P values were computed using the Wilcoxon test (two-sided). d, As in c for 148 bivalent genes within regions switching from A to B compartments in Mll2^KO ESCs. P values were computed using the Wilcoxon test (two-sided). e, Hi-C Z-score interaction maps (2-kb resolution) with 500 bins upstream and downstream of the TSS of the indicated genes in wild-type or Mll2^KO ESCs. Z scores were calculated by correcting interaction frequencies with genomic distance⁷⁰. Gene locations are indicated with a circle; red arrows highlight interaction scores that were stronger in wild-type than Mll2^KO. f, 3D interaction meta-plots (10-kb resolution) depicting observed versus expected interaction frequencies between bivalent TSS. Hubs visualize inter-TAD (2–10 Mb) crosstalk between TSSs. Areas are centered on the respective TSS (±150 kb).