Fig. 5

Identification of H3K4me3-enriched super-enhancers. a Distribution of histone mark H3K4me3 in different genome element according to the location of their significant peaks. Promoter-TSS, “− 1kb to + 100bp” of the transcription start sites. TES, “− 100bp to + 1Kb” of transcription termination sites. b Sketch of two methods identifying the H3K4me3 peaks away from the TSS region. c Distribution of H3K27ac ChIP-seq signal (normalize by ratio to highest H3K27ac reads number of enhancer) across the 4048 tumor H3K4me3-enriched enhancers. d Metagene analysis of mean histone marks H3K4me3, H3K27ac, H4K8ac, and H3K27me3 ChIP-seq density across tumor H3K4me3-enriched super and typical enhancers. Metagene plot is centered on the enhancer region. The number and mean size of super and typical enhancers are shown. e Box plot of expression (FPKM) from tumor H3K4me3-enriched typical and super-enhancer adjacent genes in both normal tissue and tumor. f Box plot of expression (FPKM) from traditional and H3K4me3-enriched super-enhancer adjacent genes in tumor. *p < 0.05, **p < 0.01. g UCSC browser view showing the ChIP-seq density of H3K4me3, H3K27ac, H4K8ac, H3K27me3, and RNA-seq signal in both normal tissue and tumor located in Epcam gene locus