Coordinate Regulation of DNA Methylation and H3K27me3 in Mouse Embryonic Stem Cells
Figure 1
Loss of PRC2 activity leads to changes in DNA methylation. a,
Relative fluorescence ratios for each probe from three independent MeDIP-chip experiments across the Nkx2-1 promoter. The peak of increased DNA methylation is indicated under the probes (grey bar) and the first 1 kb of the gene is indicated on the bottom. b, Validation of the peak of increased DNA methylation by bisulfite PCR. Each line represents an individual clone. Methylated CpGs are indicated by filled-in circles. c, A Fisher’s exact test was conducted for each CpG in (b) (** p<.01, *** p<.001). d, Profile of average DNA methylation relative to TSS calculated in 100 bp bins. e, Hierarchical clustering was performed on MeDIP-chip enrichment profiles to identify genes with similar profiles. 1,282 genes that passed the filtering step of the clustering software are on the y-axis. The x-axis is based on average fluorescent ratios in 100 bp bins from −3 kb (left) to +1 kb (right). Red indicates increased DNA methylation and green indicates decreased DNA methylation while black indicates unchanged DNA methylation. f, Gene ontology classifications for genes with increased (red) or decreased (green) DNAme. g, Gene ontology classifications for genes with increased DNAme upstream of the TSS (cluster 1, white) or across the entire promoter (cluster 2, grey). h, Classification of promoters based on CpG content. HCP, ICP & LCP, High-, Intermediate- & low CpG content promoter. i, Classification of promoters based on presence of H3K27me3 & H3K4me3. CpG and bivalent data used in (h) and (i) from [5] j, Boxplot of expression level change for genes enriched or depleted for DNAme in Eed−/− cells as well as for each of the two clusters described in (e).