DNA methylation regulates long-range gene silencing of an X-linked homeobox gene cluster in a lineage-specific manner

Abstract

DNA methylation is a major epigenetic mechanism that has been suggested to control developmental gene regulation during embryogenesis, but its regulatory mechanisms remain unclear. In this report, 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 (∼1 Mb) containing the Rhox cluster and surrounding genes. Complementation experiments using embryonic stem (ES) cells deficient in the DNA methyltransferases suggested that the CpG-island methylation by 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.[Keywords: DNA methylation; Dnmt3a; Dnmt3b; Rhox] Supplemental material is available at http://www.genesdev.org.

Multiple layers of complexity in cis‐regulatory regions of developmental genes

“…Besides its role in imprinting, DNA methylation regulates gene expression in lineages of somatic cells during embryogenesis (Oda et al, 2006;Illingworth et al, 2008). Methylation of cytosines in CpG dinucleotides is a common epigenetic mark in vertebrate cis-regulatory regions (Deaton and Bird, 2011).…”

Finding the fifth base: Genome-wide sequencing of cytosine methylation

“…Increases in sequence read length will not only aid unambiguous alignment of sequences but will dramatically improve the ability to study allelic variation in DNA methylation through colocalization of genetic and epigenetic polymorphisms within a single read. Moreover, while cells within an organism possess the same genome sequence, numerous studies have reported differential cytosine methylation in distinct cell types, indicating that an organism's cells may display high variability, akin to its diverse transcriptomes (Futscher et al 2002;Ching et al 2005;Bibikova et al 2006;Feldman et al 2006;Oda et al 2006;Weber and Schübeler 2007). Thus, with advances in sequencing technology it will be possible to explore this concept of a dynamic cytosine methylome via recording of this mark in each different cell type within an organism throughout development, under normal and disease states and in response to a variety of environmental influences.…”

The humanRHOXgene cluster: target genes and functional analysis of gene variants in infertile men

“…This is further supported by studies examining RHOX regulation. Both mouse and human RHOX family members have been demonstrated to be strongly regulated by DNA methylation (25)(26)(27) and there is an association between RHOX hypermethylation and abnormal sperm in idiopathic infertile patients (14).…”