Promoter DNA methylation couples genome-defence mechanisms to epigenetic reprogramming in the mouse germline

Abstract

SUMMARYMouse primordial germ cells (PGCs) erase global DNA methylation (5mC) as part of the comprehensive epigenetic reprogramming that occurs during PGC development. 5mC plays an important role in maintaining stable gene silencing and repression of transposable elements (TE) but it is not clear how the extensive loss of DNA methylation impacts on gene expression and TE repression in developing PGCs. Using a novel epigenetic disruption and recovery screen and genetic analyses, we identified a core set of germline-specific genes that are dependent exclusively on promoter DNA methylation for initiation and maintenance of developmental silencing. These gene promoters appear to possess a specialised chromatin environment that does not acquire any of the repressive H3K27me3, H3K9me2, H3K9me3 or H4K20me3 histone modifications when silenced by DNA methylation. Intriguingly, this methylation-dependent subset is highly enriched in genes with roles in suppressing TE activity in germ cells. We show that the mechanism for developmental regulation of the germline genome-defence genes involves DNMT3B-dependent de novo DNA methylation. These genes are then activated by lineage-specific promoter demethylation during distinct global epigenetic reprogramming events in migratory (~E8.5) and post-migratory (E10.5-11.5) PGCs. We propose that genes involved in genome defence are developmentally regulated primarily by promoter DNA methylation as a sensory mechanism that is coupled to the potential for TE activation during global 5mC erasure, thereby acting as a failsafe to ensure TE suppression and maintain genomic integrity in the germline.

Ontogeny of CpG island methylation and specificity of DNMT3 methyltransferases during embryonic development in the mouse

“…In accordance with previous data [7,11], promoter CGI methylation is enriched at genes involved in gamete functions ( Figure 2G; Figure S4A in Additional file 1). Using our custom CGI annotation, we identified 87 CGI promoters with more than 50% methylation in E8.5 embryos and found that 79% (69/87) are associated with germline genes (Additional file 3).…”

The mammalian germline as a pluripotency cycle

“…However, the regulatory elements of naive pluripotency genes escape DNA methylation in the postimplantation epiblast, only becoming fully methylated later in development (Bao et al, 2009;Li et al, 2007;Osorno et al, 2012). Conversely, CpG islands associated with late germline genes, such as Dazl and Sycp3, are specifically targeted for methylation and gene silencing (Borgel et al, 2010;Hackett et al, 2012). Preventing inappropriate expression of these genes in somatic tissues may be important to avoid tumorigenesis (Simpson et al, 2005).…”

Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing

“…It is highly desirable to develop a single-cell epigenome analysis technique, ideally one that provides single-base resolution. As one of the most important epigenetic modifications, DNA methylation is critical for a wide variety of biological processes, including the regulation of genomic imprinting and X-chromosome inactivation, as well as the repression of transposable elements within the genome (Bird 2002;Lister et al 2009;Hackett et al 2012). DNA is methylated at the carbon atom occupying the fifth position of the cytosine ring (5mC) and is catalyzed by the DNA cytosine methyltransferases, Dnmt1, Dnmt3a, and Dnmt3b (Reik 2007).…”