Mapping Promoter CpG Methylation in mESCs

DNA methylation and histone modifications influence gene activities in a variety of mammalian cells. We report here the large scale mapping of DNA methylation patterns at proximal promoter regions in mouse embryonic stem cells (mESCs). A majority of methylated genes represent cell differentiation-associated genes that are repressed in mESCs. In contrast, unmethylated genes include many housekeeping and pluripotency genes such as STAT3 and Oct4/Nanog/Sox2, which are essential for ESC self-renewal. By comparing methylation patterns to the binding domains of Oct4/Nanog, Polycomb proteins, and histone H3 lysine (K) 4/27 trimethylation on gene promoters, we found that promoter DNA methylation is frequently the only epigenetic marker associated with a subset of silenced genes in mESCs that do not possess H3 K4/K27 trimethylation marks and are free from the binding of Polycomb proteins and the Oct4/Nanog transcription factors. Gene expression profiling of demethylated mESCs showed that a majority of up-regulated genes, including a subset of X-linked genes and many development genes, represent a distinct population of genes that are neither targeted by Polycomb and Oct4/Nanog, nor carry H3 K4/K27 trimethylation marks. Our data suggest that promoter methylation patterns in mESCs represent a unique epigenetic program that complements other regulatory mechanisms to allow the expression of pluripotency genes, but represses a subset of genes that will only be activated in specific cell lineages upon cell differentiation. Keywords: DNA Methylation, methylated DNA immunoprecipitation We compared DNA methylation patterns in Wildtype (J1) and DNA methylation deficient (TKO) mouse ES cells. We performed 7 replicates using different passages of mouse ES cells. For gene expression analysis, we used the same cultures and performed 3 replicates. The supplied table is the average log ratio for the 3 replicates and takes into account the dye swap of replicate 2.