EHMT2 directs DNA methylation for efficient gene silencing in mouse embryos

Abstract

The extent to which histone modifying enzymes contribute to DNA methylation in mammals remains unclear. Previous studies suggested a link between the lysine methyltransferase EHMT2 (also known as G9A and KMT1C) and DNA methylation in the mouse. Here, we used a model of knockout mice to explore the role of EHMT2 in DNA methylation during mouse embryogenesis. The Ehmt2 gene is expressed in epiblast cells but is dispensable for global DNA methylation in embryogenesis. In contrast, EHMT2 regulates DNA methylation at specific sequences that include CpG-rich promoters of germline-specific genes. These loci are bound by EHMT2 in embryonic cells, are marked by H3K9 dimethylation, and have strongly reduced DNA methylation in Ehmt2 −/− embryos. EHMT2 also plays a role in the maintenance of germline-derived DNA methylation at one imprinted locus, the Slc38a4 gene. Finally, we show that DNA methylation is instrumental for EHMT2-mediated gene silencing in embryogenesis. Our findings identify EHMT2 as a critical factor that facilitates repressive DNA methylation at specific genomic loci during mammalian development.

Targeting the histone methyltransferase G9a activates imprinted genes and improves survival of a mouse model of Prader–Willi syndrome

“…9b). This suggests that the inhibition of G9a affects gene expression in a locus-selective manner, and this is consistent with the study reporting that only 1 of 16 imprinted loci are selectively affected in G9a −/− embryos 18 .…”

“…In addition, the inactivation of histone H3K9 methyltransferase G9a in mouse embryonic stem (ES) cells in vitro can induce the biallelic expression of Snprn that occurs with reduced DNA methylation 17 . Of note, DNA methylation of Snrpn is not affected in embryonic day 9.5 (E9.5) G9a −/− mouse embryos 17,18 , yet the allele-specific expression of Snrpn in the absence of G9a is not known in vivo . Thus, we envisioned that epigenetic manipulation of the PWS imprinting domain could enable the maternal chromosome to express PWS-associated genes that normally show paternal-specific expression, and thus provide a therapeutic strategy for PWS.…”

Loss of Kdm5c Causes Spurious Transcription and Prevents the Fine-Tuning of Activity-Regulated Enhancers in Neurons

“…Particularly interesting is our discovery that Kdm5c plays an essential role in the repression of germ line genes. Intriguingly, some of these genes are also upregulated in mouse embryos deficient for enzymes that introduce repressive marks in the chromatin, such as the methyltransferase of H3K9 Ehmt2 and the DNA methyltransferase Dnmt3b (Auclair et al, 2016), underscoring the interplay between DNA methylation, and H3K9 and H3K4 methylation (Du et al, 2015). Dnmt3b silences this class of genes by recruiting the transcriptional repressor E2F6 (Velasco et al, 2010).…”

Heterochromatin and the molecular mechanisms of ‘parent-of-origin’ effects in animals

“…This was to some extent foreshadowed by the observation that despite global demethylation the number of maternal gDMRs retaining more than 40% methylation was nonetheless around 15% at the blastocyst stage (Smallwood et al 2011), which is somewhat higher than the 150 predicted imprinted loci (Williamson et al 2013) and noticeably greater than the 81 sites in the ES cell genome where ZFP57-KAP1-SETDB1 col o c a l i z e w i t h t h e T G C C G C h e x a -n u c l e o t i d e (Quenneville et al 2011). There is also the observation that the gDMR of the imprinted Scl38a4 gene does not contain the canonical ZFP57 hexa-nucleotide binding site (Auclair et al 2015;Strogantsev et al 2015). Notably, there is partial loss of methylation at the imprinted Scl38a4 gDMR in embryos that are homozygous for a null mutation in the gene encoding the G9a HMTase (Auclair et al 2015).…”

“…There is also the observation that the gDMR of the imprinted Scl38a4 gene does not contain the canonical ZFP57 hexa-nucleotide binding site (Auclair et al 2015;Strogantsev et al 2015). Notably, there is partial loss of methylation at the imprinted Scl38a4 gDMR in embryos that are homozygous for a null mutation in the gene encoding the G9a HMTase (Auclair et al 2015). One possibility is that the G9a mutation affects the nucleation of an alternative heterochromatin-like complex at the Scl38a4 gDMR, whose replication is further compromised because G9a is a constituent of the SMARCAD1 complex ( Figure 5).…”