Figure 4. PRC2 is antagonistic to DNA methylation in cis.

Through RRBS, percent methylation at each CpG with ≥10-fold coverage was calculated in wild-type (wt), Suz12^GT, Suz12^Δ, and Eed^null ESCs and day 5 differentiated cells. (A) Distribution of methylation at all CpGs is shown. Low: ≤15% methylated; high: ≥80%. (B) This panel is an explanatory example of the data analysis and visualizations used in Figures 4C–D, using the lower-left heatmap of 4C as an example. (left) CpGs were binned according to % methylation in wt (y-axis) and Suz12^GT (x-axis) ESCs. Thus, the matrix displays the number of CpGs in each 2-D bin. The data is largely along the x = y line (CpGs with the same % methylation in Suz12^GT as wild-type), shifting towards the top right (more methylation in Suz12^GT). (right) Fold enrichment over the overall distribution of the data was determined for each bin using a replicate-based background model (see Methods). In this example, high statistical enrichment over background in Suz12^GT cells (yellow) is visible for CpGs with little methylation in wt cells (C) CpGs in wt H3K27me3-enriched regions are used to analyze changes in DNA methylation in ESCs (left panel) and day 5 SMN (right panel). The enrichment in the lower heatmaps shows CpGs with low methylation in wt (y-axis) gaining methylation in Suz12^GT (x-axis). (D) (Top) H3K27me3-enriched regions in wt ESCs that lose enrichment in Suz12^GT. (Bottom) Regions maintaining H3K27me3 enrichment in Suz12^GT ESCs. Regions losing H3K27me3 in Suz12^GT cells gain overall more DNA methylation than those maintaining significant H3K27me3.