The DNMT3A PWWP domain is essential for the normal DNA methylation landscape in mouse somatic cells and oocytes

Abstract

DNA methylation at CG sites is important for gene regulation and embryonic development. In mouse oocytes, de novo CG methylation requires preceding transcription-coupled histone mark H3K36me3 and is mediated by a DNA methyltransferase DNMT3A. DNMT3A has a PWWP domain, which recognizes H3K36me2/3, and heterozygous mutations in this domain, including D329A substitution, cause aberrant CG hypermethylation of regions marked by H3K27me3 in somatic cells, leading to a dwarfism phenotype. We herein demonstrate that D329A homozygous mice show greater CG hypermethylation and severer dwarfism. In oocytes, D329A substitution did not affect CG methylation of H3K36me2/3-marked regions, including maternally methylated imprinting control regions; rather, it caused aberrant hypermethylation in regions lacking H3K36me2/3, including H3K27me3-marked regions. Thus, the role of the PWWP domain in CG methylation seems similar in somatic cells and oocytes; however, there were cell-type-specific differences in affected regions. The major satellite repeat was also hypermethylated in mutant oocytes. Contrary to the CA hypomethylation in somatic cells, the mutation caused hypermethylation at CH sites, including CA sites. Surprisingly, oocytes expressing only the mutated protein could support embryonic and postnatal development. Our study reveals that the DNMT3A PWWP domain is important for suppressing aberrant CG hypermethylation in both somatic cells and oocytes but that D329A mutation has little impact on the developmental potential of oocytes.

Histone H3K36me2 and H3K36me3 form a chromatin platform essential for DNMT3A-dependent DNA methylation in mouse oocytes

“…Then, upon recruitment, the ADD domains of DNMT3A and DNMT3L recognize H3K4me0, leading to the disruption of the autoinhibitory structure of DNMT3A 5 , 40 . While the DNMT3A PWWP domain does bind to H3K36me2 and H3K36me3, we recently found that DNA methylation still occurs in H3K36me2/3-enriched regions even when a point mutation (D329A) disrupting H3K36me2/3 binding is introduced 45 . Therefore, the DNMT3A-DNMT3L complex could have an additional, uncharacterized mechanism for recognizing H3K36me2/3.…”

The UHRF protein family in epigenetics, development, and carcinogenesis

“… 57 , 69 ) In growing oocytes, transcriptionally active regions marked with lysine 36-trimethylated H3 (H3K36me3) are the primary target of methylation. 70 – 74 ) We found that UHRF1 KO showed a 25% reduction in global methylation, predominantly occurring in transcriptionally inactive regions with no H3K36me3. 61 ) This reduction is greater than that observed in DNMT1 KO oocytes.…”

KDM4C Contributes to Trophoblast-like Stem Cell Conversion from Porcine-Induced Pluripotent Stem Cells (piPSCs) via Regulating CDX2

“…Epigenetics refers to the stable and inheritable changes in gene expression without alterations in DNA sequences, and is crucially involved in gene regulation, cellular differentiation, gene imprinting, X-chromosome inactivation and other cellular processes [ 18 ]. Previous studies evaluating H3K36me2 observed inconsistent results for recruiting DNMT3A and shaping the intergenic DNA methylation landscape [ 19 ]. Moreover, H3K36me2 could demarcate PRC2-mediated H3K27me2 and H3K27me3 domains in ESCs [ 20 , 21 ].…”