Dnmt3a2 expression during embryonic development is required for phenotypic stability

Proper function and switching of regulatory elements are essential for the development of vertebrates and is known to be controlled by DNA methylation. We used isoform-specific knockouts of the de novo methyltransferase Dnmt3a, namely Dnmt3a1 and Dnmt3a2, to probe their roles in regulatory element methylation during embryogenesis and postnatal development. Mouse embryos lacking Dnmt3a1 showed minimal loss of methylation, suggesting limited involvement in embryonic development. However, they were smaller than their littermates and died about 4 weeks after birth with considerable postnatal demethylation as previously reported. In contrast, embryos lacking Dnmt3a2 showed widespread hypomethylation particularly at enhancers, CTCF sites and imprinted genes. These methylation deficits were largely repaired after birth, presumably by Dnmt3a1. The mice lacking Dnmt3a2 were viable; however, they showed an increased prevalence of sporadic abnormalities previously observed at a low frequency in laboratory mice, including anophthalmia, hydrocephalus, hydronephrosis and male infertility. Interestingly, hypomethylation of several imprinted genes was observed in sperm which might explain the infertility phenotype. Therefore, the interaction between the two isoforms is developmentally regulated, with Dnmt3a2 playing a key role in ensuring the methylation states of enhancers, CTCF sites and imprinted genes, thereby reducing the likelihood of stochastic phenotypes emerging after birth.