Figure 3
H3K27me3 is lost from Polycomb target gene promoters in DNA hypomethylated somatic cells. (A) Scatter plot showing the relationship between H3K27me3 enrichment in Dnmt1+/+ MEFs (x-axis) and the difference in H3K27me3 enrichments between Dnmt1+/+ and Dnmt1-/- MEFs (y-axis) at all promoter regions by ChIP-chip. A llocally weighted scatterplot smoothing line (black) is plotted. The R2 value (Pearson's) is shown alongside the P-value from a Pearson's correlation test. Hox gene promoters are plotted as red points. (B) H3K27me3 ChIP-seq data for regions surrounding Polycomb target genes. Polycomb target genes were defined as the top 10% of gene promoters as ranked by H3K27me3 enrichment (by ChIP-chip) in Dnmt1+/+ MEFs. (C) Top 10 Gene Ontology terms (Biological Process) found to be significantly enriched among H3K27me3 down genes using all genes covered on the microarray as background. The q-value for enrichment of each term is plotted as -log10(q-value). (D, E) ChIP-qPCR for H3K27me3 (D) and Ezh2 (E) in Dnmt1+/+ and Dnmt1-/- MEFs using primers for the promoters of the indicated genes. Enrichment for each immunoprecipitation (IP) is expressed as percentage of DNA in input. Non-specific IgG IP and the Actb promoter are shown as negative controls and the Chdh promoter is shown as a positive control. Error bars indicate ± standard error of the mean of two experiments.