Figure 5.

Bivalency Safeguarding Developmental Genes in Ground State Pluripotency Is Characterized by Low H3K4me3 and High H3K27me3

(A) Relative levels of H3K27me3 and H3K4me3 at bivalent, non-transcribed (low) and highly active (high) promoters, as well as Hox genes (Hox). y axis is normalized to RPGC in serum. RNA-seq expression levels and CpG methylation (% methylation of all CpGs in the region) levels at the same promoters (right) are shown. Wilcoxon signed rank test; ^∗∗∗∗p < 0.0001; not significant (n.s.), p > 0.05.

(B) Heatmap across promoters of the bivalent genes as in (A) and Figure 3D.

(C) Average profiles of H3K27me3 and H3K27me1 across 1,969 bivalent genes. SE is rendered as shaded area around lines. Additional H3K27me3 antibody replicates are shown in Figure S5A.

(D) Number of bivalent promoters that changed H3K27me3 levels more than 1.5-fold between 2i and serum, consistent across the three different H3K27me3 antibody and biological replicates. 126 bivalent promoters gained H3K27me3 (“up”), 177 bivalent promoters lost H3K27me3 in 2i (“down”), and the remaining did not change consistently. Promoters that changed H3K27me3 more than two-fold are also shown individually in Figure S5C. For each of the three groups, up, down, and “unchanged,” the average expression level from triplicate RNA-seq in serum and 2i (Finley et al., 2018) is shown. Wilcoxon signed rank test.

(E) Hypothesis for transitions in bivalency: ground state bivalency (H3K4me4 low/H3K27me3 high) is refractory to activation (“naive”). For developmental genes to be activated upon lineage commitment, bivalent promoter needs to acquire H3K4me3 first (“primed”).

See also Figure S5.