Figure 5

KDM5B controls enhancer activity by regulating H3K4 methylation. (A) KDM5B binding at p300 enhancer sites sorted by enrichment level of acetylated H3K27 (H3K27ac). (B) Heat map density profiles of H3K4me3/2/1 around intergenic p300 binding sites, sorted by H3K27ac levels. (C) Top: average profile of H3K4me3/2/1 density at intergenic p300 sites in shLuc and shKdm5b ES cells. Bottom: log2 fold change normalized tag density ratios (shKdm5b/shLuc) of H3K4me3, H3K4me2, and H3K4me1 at p300 enhancers. RPBM, reads per base pair per million reads. (D) Average profiles of H3K27ac tag densities around H3K27ac peaks in shLuc and shKdm5b ES cells. (E) Average profiles of H3K27ac tag densities of H3K27ac around p300 binding sites (proxies of enhancers) in shLuc and shKdm5b ES cells. (F) Scatter plot of H3K27ac tag densities in shLuc and shKdm5b ES cells. (G) Heat map density profiles of H3K27ac peaks, sorted by H3K27ac levels. (H) Spreading of H3K4 methylation into enhancer shores in Kdm5b knockdown ES cells is associated with a decrease in H3K27ac levels. Shown are empirical cumulative distributions for the change in H3K27ac (shKdm5b/shLuc) across two groups of enhancers sorted by changes in spreading indices, calculated independently for H3K4me3 (left panel), H3K4me2 (middle panel) or H3K4me1 (right panel). Y-axis shows the percentage of enhancers that exhibit a change in H3K27ac density less than the value specified by the x-axis. A line shifted to the left means a systematic decrease in H3K27ac levels. P-value for all <1E-5 (Kolmogorov-Smirnov test).