Figure 4

Bivalent priming of TSSs is prevalent and its resolution varies during differentiation. (A) Resolution and formation of bivalency during differentiation. Each column represents a gene bivalent in any of our cell types and is colored in the cell types in which it is bivalent. Columns/genes were grouped by their bivalency across cell types. (B) Bottom panels represent genes bivalently marked outside the HSPC stage. The number of genes possessing H3K4me3 but lacking H3K27me3 in HSPCs (red), possessing H3K27me3 but lacking H3K4me3 in HSPCs (green), and possessing neither in HSPCs (black) are shown. (C) The T-cell regulator GATA3 shows bivalent priming and resolution. In ESCs (black), HSPCs (grey) and B-cells (blue) the GATA3 promoter (TSS +/− 0.5kbp) is enriched with H3K4me3 and H3K27me3 and is not transcribed. In pRBCs (red), only H3K27me3 is found. In T-cells (green), GATA3 is bound by PolII and is transcribed. (D) The B-cell master regulator PAX5 is bivalently marked in ESCs (black), HSPCs (grey) and T-cells (green). It is bound by PolII in HSPCs as well. In pRBCs (red), H3K4me3 is lost, leaving only H3K27me3. In B-cells (blue), PAX5 is enriched in H3K4me3, bound by PolII, and uniquely expressed. (E) Genes specifically expressed in downstream lineages are bivalently prepared in HSPC and ESC.