Fig. 6

Pol II depletion had a relatively modest effect on the promoter-associated chromatin interactions. a Aggregate H3K27ac HiChIP contact maps around pairs of either active or silent gene promoters in the mESCs grouped by intra-TAD pairs (between 200 kb and 2 Mb) or cis long-range (from 2 to 10 Mb) (upper panel). Data are represented in a violin box plot showing the means ± SD (bottom panel). Significance was calculated using two-way ANOVA with Tukey’s test. b Aggregate H3K27ac HiChIP contact maps around pairs of active gene promoters in the mESCs and separated into three equal slices (each N = 833) based on the expression level (left panel). Data are represented as in a stripe box plot showing the means ± SD (right panel). Significance was calculated using two-way ANOVA with Tukey’s test. c Aggregated H3K27ac HiChIP contact maps around pairs of either active or silent gene promoters in the mESCs, which were classified based on the presence of CTCF-binding sites within ± 5 kb (left panel). Data are represented in a violin box plot showing the means ± SD (right panel). Significance was calculated using two-way ANOVA with Tukey’s test. d Average insulation score based on the H3K27ac HiChIP data set for promoters under untreated and Pol II-degraded conditions (6 h) (left panel), and the insulation score for promoters were quantified and are illustrated in the box plot in the right panel. Significance was determined using a Wilcoxon test (*p < 0.05, **p < 0.01, ***p < 0.001). e Illustrated as d, but the promoters were classified according to the gene expression level (high/medium/low)