Epigenetic regulation by DNA methylation during mammalian embryogenesis

Abstract

DNA methylation plays important roles in repressing gene expression and transmitting the silenced state to daughter cells. During embryogenesis, DNA methylation of the mammalian genome is dynamically regulated in stage-, sequence- and lineage-dependent manners. Loss of DNA methylation by inactivation of DNA methyltransferase genes resulted in developmental arrest in mice. These observations suggest that DNA methylation controls developmental gene regulation during embryogenesis, but its regulatory mechanisms remain largely unclear. Here we show that CpG islands associated with the X-linked homeobox gene cluster Rhox, which is highly expressed in the extraembryonic trophectoderm, are differentially methylated in a stage- and lineage-specific manner during the post-implantation development of mice. Inactivation of both Dnmt3a and Dnmt3b, DNA methyltransferases essential for the initiation of de novo DNA methylation, abolished the establishment of DNA methylation and the silencing of Rhox cluster genes in the embryo proper. The Dnmt3-dependent CpG island methylation at the Rhox locus extended for a large genomic region (about 1 Mb) containing the Rhox cluster and its surrounding genes. Complementation experiments using ES cells deficient in the DNA methyltransferases suggested that the regulation of Dnmt3a and Dnmt3b was restricted within this large genomic region, and did not affect the neighboring genes outside it, implicating the existence of region-specific boundaries. Our results suggest that DNA methylation plays important roles in both long-range gene silencing and lineage-specific silencing in embryogenesis.