Fig. 4

Polycomb is required for maintenance of hypomethylation in DMVs. a Heatmaps representing the corresponding level of DNA methylation and binding intensity of EED, EZH2, and RING1B [45] for large K27me3 peaks (> 5 kb, the minimal length of DMVs). Peaks were sorted by the DNA methylation levels in DMVs. An analysis of all H3K27me3 peaks yielded similar results (data not shown). b The epigenetic landscape is shown for Polycomb-bound DMV gene Foxa1 and H3K27me3-marked non-DMV gene Lyrm9. Regions with elevated DNA methylation in Eed ^-/- mESCs are shaded. c Heatmaps representing the level of DNA methylation, H3K27me3, H3K27ac, H3K4me3, H3K36me3 within DMVs, and RNA level for DMV genes in WT and Eed ^-/- mESCs. DNA methylation level in Ezh2 ^-/- mESCs is also shown. All DMVs are normalized to the same length. Levels of chromatin marks were Z-score-normalized. Fragments per kilobase per million mapped reads (FPKMs) of RNA level for WT and Eed ^-/- mESCs were quantile-normalized and log-transformed. EED-bound DMVs were defined as Polycomb DMVs. d Boxplots showing the DNA methylation level of Polycomb DMVs and other DMVs in WT and Eed ^-/- mESCs. P values (two-sided t test) are shown. e Boxplots showing the DNA methylation change (knockout (KO)-WT) for CpG islands (CGI) and non-CpG island (non-CGI) regions within Polycomb DMVs. P value (two-sided t test) is shown. f Boxplot showing DNA methylation level in Polycomb DMVs for regions with different CG densities in WT and Eed ^-/- mESC lines