Maternal DNMT3A-dependent de novo methylation of the zygotic paternal genome inhibits gene expression in the early embryo

Abstract

De novo DNA methylation (DNAme) during mammalian spermatogenesis yields a densely methylated genome, with the exception of CpG islands (CGIs), which are hypomethylated in sperm. Following fertilization, the paternal genome undergoes widespread DNAme loss before the first S-phase. Paradoxically, recent mass spectrometry analysis revealed that a low level of de novo DNAme occurs exclusively on the zygotic paternal genome. However, the loci involved and impact on genic transcription was not addressed. Here, we employ allele-specific analysis of wholegenome bisulphite sequencing (WGBS) data and show that a number of genomic regions, including several dozen CGI promoters, are de novo methylated on the paternal genome in 2-cell embryos. A subset of these promoters maintains DNAme through development to the blastocyst stage. Consistent with zygotic paternal DNAme acquisition (PDA), many of these loci are hypermethylated in androgenetic blastocysts but hypomethylated in parthenogenetic blastocysts. Strikingly, PDA is lost following maternal deletion of Dnmt3a. Furthermore, a subset of promoters showing PDA which are normally transcribed from the paternal allele in blastocysts show premature transcription at the 4-cell stage in maternal Dnmt3a knockout embryos. These observations uncover an unexpected role for maternal DNMT3A activity in postfertilization epigenetic reprogramming and transcriptional silencing of the paternal genome.

Can We Use Gene-Editing to Induce Apomixis in Sexual Plants?

“…However, the zygotic transition postfertilization is initiated by asymmetric activation of parental genomes, with most genes playing major roles in the early development of plant embryos being maternally expressed [129,130]. Yet, de novo post-fertilization epigenetic reprogramming and transcriptional silencing of the paternal genome is controlled by DNMT3A in mice, a DNA methyltransferase highly expressed in oocytes [131]. Dnmt3a maternal knockout embryos die during post-implantation development [131].…”

“…Yet, de novo post-fertilization epigenetic reprogramming and transcriptional silencing of the paternal genome is controlled by DNMT3A in mice, a DNA methyltransferase highly expressed in oocytes [131]. Dnmt3a maternal knockout embryos die during post-implantation development [131]. Thus, using a plant ortholog of DNMT3A might help to unblock paternal gene expression in the early embryo and possibly result in zygotic embryo lethality without affecting the development of somatic embryos.…”