Figure 2

Impact of promoter differential methylation on histone modification profiles at imprinted genes. Histone modification enrichment is compared in mouse embryonic stem cells at imprinted genes with and without a promoter differentially methylated region (DMR). Transcription start sites were assessed for enrichment of H3K4me3, H3K27me3, H3K9me3 and H4K20me3 using source data from Mikkelsen et al. [50]. The presence of one particular modification at an imprinted gene does not preclude the presence of another. A significantly different epigenetic profile for these four marks is observed at genes with a promoter DMR compared to genes without a promoter DMR (chi-square contingency test, P < 0.0001). Germline DMRs are not distinguished from somatic DMRs in this analysis. H3K9me3 and H4K20me3 are exclusively enriched at imprinted genes possessing a promoter DMR. A greater proportion of genes with promoter DMRs are developmentally expressed compared to genes without promoter DMRs (71% compared to 48% respectively); the increase in H3K4me3 and the decrease in H3K27me3 at genes with a promoter DMR likely reflects this (see Additional file 2 and Figure 4).