H3K4me3 and H3K27me3 bivalent promoter methylation profiles in hematopoietic stem cells, early progenitors and T cells. (A) Total H3K4me3 (green) and H3K27me3 (orange) enriched promoters in HSCs, MPPs, PreMegEs, and T cells (left panel). Promoters associated with both H3K4me3 and H3K27me3 (black) were assessed for overlapping peaks (FDR ≤ 0.05) within a 5-kb region of TSS, and bivalent promoter methylation was defined as presence of concurrent H3K4me3 and H3K27me3 peaks within the −2.5- to +2.5-kb region surrounding TSS (right panel). (B) Comparison of the number of bivalent promoters in the different cell types according to the above criteria. Note that many promoters comprised both modifications but were not overlapping within the 5-kb region (dark gray). The H3K4me3 and H3K27me3 modifications present at tiled intervals outside the 5-kb region are also indicated (light gray). (C) Venn diagram showing the overlap of bivalent promoters in HSCs, MPPs, PreMegEs, and T cells. (D) The bivalent histone modification profiles at the Rhpn2 (chr7), Zfp580 (chr7), and Rassf6 (chr5) promoters in HSCs, MPPs, PreMegEs, and T cells. All figures showing the bivalent profile are labeled in the same way. Peaks of H3K4me3 (green) and H3K27me3 (orange) across tiled promoter regions (−8.2 to +3 kb) are indicated in each box diagram. TSS is shown as green vertical lines, and arrows near gene names show the direction of transcription. The x-axis shows the chromosomal coordinates, and the y-axis shows the log₂ enrichment for peaks. The gene expression values are indicated below for each gene and the different cell types are given below. (E) Percentage of bivalent promoters associated with H3K9me3, H3K79me2, H3ac, and PolII in HSCs, MPPs, PreMegEs, or T cells.