The DNMT3A ADD domain is required for efficient de novo DNA methylation and maternal imprinting in mouse oocytes

Author summaryEpigenetic modifications of histones and DNA play important roles in gene regulation and embryonic development. We herein examine the role of histone-tail recognition by DNMT3A, the major DNA methyltransferase expressed in mammalian oocytes, in mediating de novo DNA methylation in this cell-type. The ADD domain is known to interact with histone H3 tail unmethylated at lysine 4. We found that amino-acid substitutions in the DNMT3A ADD domain disrupting the histone-tail recognition cause mosaic loss of DNA methylation in mouse oocytes, suggesting that this domain plays an important role in efficient, and likely processive, DNA methylation. Furthermore, the mosaic loss of DNA methylation in oocytes resulted in lethality of derived embryos during mid-to-late gestation, with stochastic multi-locus imprinting defects. The ADD mutant mice pose a model to study stochastic inheritance of epigenetic perturbations in germ cells to the next generation. Establishment of a proper DNA methylation landscape in mammalian oocytes is important for maternal imprinting and embryonic development. De novo DNA methylation in oocytes is mediated by the DNA methyltransferase DNMT3A, which has an ATRX-DNMT3-DNMT3L (ADD) domain that interacts with histone H3 tail unmethylated at lysine-4 (H3K4me0). The domain normally blocks the methyltransferase domain via intramolecular interaction and binding to histone H3K4me0 releases the autoinhibition. However, H3K4me0 is widespread in chromatin and the role of the ADD-histone interaction has not been studied in vivo. We herein show that amino-acid substitutions in the ADD domain of mouse DNMT3A cause dwarfism. Oocytes derived from homozygous females show mosaic loss of CG methylation and almost complete loss of non-CG methylation. Embryos derived from such oocytes die in mid-to-late gestation, with stochastic and often all-or-none-type CG-methylation loss at imprinting control regions and misexpression of the linked genes. The stochastic loss is a two-step process, with loss occurring in cleavage-stage embryos and regaining occurring after implantation. These results highlight an important role for the ADD domain in efficient, and likely processive, de novo CG methylation and pose a model for stochastic inheritance of epigenetic perturbations in germ cells to the next generation.

Automated summary

This study investigates the role of histone-tail recognition by DNMT3A in mediating de novo DNA methylation in mammalian oocytes. It shows that disruption of the interaction between the ADD domain of DNMT3A and histone H3 tail leads to mosaic loss of DNA methylation, resulting in lethality of derived embryos during mid-to-late gestation and stochastic multi-locus imprinting defects. These findings highlight the importance of the ADD domain in efficient de novo DNA methylation and provide a model for studying the stochastic inheritance of epigenetic perturbations in germ cells.