Fig. 7: Super-enhancers interact with a diverse set of genes.

a Intersection of mature erythroid super-enhancers (SE, n = 95) and non-super-enhancers (non-SE, n = 1172) with significant interacting fragments (MPPC ≥ 0.01) identified interacting genes. b Level of H3K27ac (fragment per kilobase per million mapped reads) over the promoters of significantly interacting genes interacting with SE (n = 226) and non-SE (n = 2042). For a and b, boxplots whiskers show 5–95 percentile and box shows 25th and 75th percentiles with the median, **p = 0.005, ****p < 0.0001 for a two-sided Mann–Whitney U-test. c Mean nascent expression for SE-interacting genes (n = 226 genes, each dot is the mean of three biological replicates) throughout erythroid differentiation was determined using 4sU-seq in haematopoietic stem and progenitor and burst-forming unit-erythroid cells (S0-Low), early and late colony-forming unit-erythroid cells (S0-medium and S1, respectively), and maturing terminal differentiating cells (S2, S3). Error bars show mean with 95% confidence interval. ***p = 0.0005, ****p < 0.0001 one-way ANOVA with Sidak’s multiple comparison test. d MA plot of expression in S0-Low and S3 cells with SE-interacting genes highlighted. e Percentage of total genes and SE-interacting genes with increased or decreased expression throughout differentiation. ****p < 0.0001 Chi-squared test (d.f. = 3). Source data are available in the Source Data file.