Figure 5. Increased DNA methylation upon loss of PRC2 does not lead to target gene repression.

(A) Regions with significantly enriched H3K27me3 in wild-type (wt) ESCs were considered. All CpGs in these regions with 10x coverage via RRBS in both wt and Suz12^GT ESCs, and ≥.1 FPKM in at least one of these cell types, were used in the analysis. Of these 257 CpGs, 41 lose ≥10% DNA methylation, 75 gain ≥10% DNA methylation, and 141 do not change. The distribution of change in expression in Suz12^GT ESCs with respect to wt ESCs of the genes associated with these CpGs is plotted on the y-axis. No association between change in DNA methylation and gene expression is observed. (B) Same as in (A) except in day 5 SMNs. Of these 15993 CpGs, 767 lose ≥10% DNA methylation, 2816 gain ≥10% DNA methylation, and 12410 do not change. The distribution of change in expression in Suz12^GT cells with respect to wt cells of the genes associated with these CpGs is plotted on the y-axis. No association between change in DNA methylation and gene expression is observed. (C) Two example genes, Gata3 and Bmp2, are shown here. Change in H3K27me3 signal between wt and Suz12^GT cells is plotted on the left y-axis; gain in Suz12^GT is shown in yellow, and loss is shown in blue. Change in DNA methylation for each CpG with 10x coverage in both cell types is plotted in maroon on the right y-axis. Change in gene expression (log₂ of the ratio of the FPKMs (Suz12^GT/wt)) is shown in horizontal bar graphs to the right of the panel.