Epigenetic gene regulation in mouse embryonic stem cells and the developing central nervous system

DNA methylation is an important epigenetic mechanism in many eukaryotic cells. Previous work has demonstrated a necessity for the proper establishment and maintenance of DNA methylation during mammalian development. DNA methylation plays a role in X chromosome inactivation, gene imprinting, gene regulation, genome defense and genomic stability. We are interested in understanding the role of DNA methylation in embryonic stem cells as well as in the developing central nervous system.;To determine the role of DNA methylation in mouse embryonic stem cells (mESCs), we performed a methylated DNA immunoprecipitation assay coupled with hybridization to a whole genome promoter microarray. Using this methodology, we found 6127 genes promoters that are methylated and 5074 that have unmethylated promoters. When we compared our methylation data with whole genome histone H3 lysine 4 (K4) and lysine 27 (K27) trimethylation data, we found that almost one third of all genes in mESCs are only marked by DNA methylation. Our data suggest that in mESCs promoter methylation represents a unique epigenetic program that complements other regulatory mechanisms to ensure appropriate gene expression.;Since mESCs give rise to all other cell types in the body, it is also important to understand the role of DNA methylation in regulating cellular differentiation. To study the role of DNA methylation in differentiated somatic cells, we used a CNS specific conditional knockout mouse of the maintenance methyltransferase Dnmt1 in mice. Gene expression studies comparing wild type CNS to hypomethylated CNS showed a large number of immune related genes were deregulated. We found that MHC class I proximal promoters are almost completely unmethylated in wild type animals, with the exception of a few sites that exhibit significant changes compared to Dnmt1 -/- CNS. Using a conditional knockout of STAT3, the binding partner of STAT1, we find that MHC class I gene expression is decreased compared to wild type animals. These results suggest that DNA hypomethylation increases the activation of the JAK-STAT pathway and this activation is partially involved in regulating MHC class I expression in the CNS. In conclusion, my dissertation studies demonstrated that DNA methylation is an important epigenetic regulator of gene expression in both mESCs and the mammalian CNS.