Fig. 2

Distribution of bivalent nucleosomes at gene promoters. a Examples of individual genes showing the patterns of H3K4me3, H3K27me3 and bivalent nucleosomes around the TSS. Direction of gene transcription (brown arrow) and CpG islands (black bar) shown. b Schematic of distribution of H3K4me3 (black) and H3K27me3 (red) peaks called within +/−5000 bp from the TSS. Genes previously described as bivalent carry overlapping H3K4me3 and H3K27me3 (green region) peaks. c Size distribution of the H3K4me3, H3K27me3 peak calls, and the overlapping regions of these peaks. d–g Distribution of H3K4me3 d H3K27me3 e Sequential ChIP (H3K27me3 → H3K4me3)-seq reads (bivalent nucleosomes, f), and H2A.Z g around the TSS (x-axis, TSS is 0). Promoters were classified into H3K4me3-exclusive (black), H3K27me3-exclusive (red), or none (none of the marks detected), promoters based on identification of ChIP-seq enrichment peak calls using SICER in the +/−2500 bp around the TSS. Promoters with overlapping H3K4me3 and H3K27me3 enrichment peak calls in the +/−2500 bp around the TSS were defined as Bivalent promoters (green). ChIP-seq reads were binned at 10 bp intervals. Y-axis represents average ChIP-seq reads normalized to corresponding average of the input .h Gene expression ranges of the three different promoter classes