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

Julien Richard Albert, Wan Kin Au Yeung, Keisuke Toriyama, Hisato Kobayashi, Ryutaro Hirasawa, Julie Brind’Amour, Aaron Bogutz, Hiroyuki Sasaki, Matthew Lorincz

Research output: Contribution to journalArticlepeer-review

12 Citations (Scopus)


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. While the paternal genome undergoes widespread DNAme loss before the first S-phase following fertilization, recent mass spectrometry analysis revealed that the zygotic paternal genome is paradoxically also subject to a low level of de novo DNAme. However, the loci involved, and impact on transcription were not addressed. Here, we employ allele-specific analysis of whole-genome bisulphite sequencing data and show that a number of genomic regions, including several dozen CGI promoters, are de novo methylated on the paternal genome by the 2-cell stage. A subset of these promoters maintains DNAme through development to the blastocyst stage. Consistent with paternal DNAme acquisition, many of these loci are hypermethylated in androgenetic blastocysts but hypomethylated in parthenogenetic blastocysts. Paternal DNAme acquisition is lost following maternal deletion of Dnmt3a, with a subset of promoters, which are normally transcribed from the paternal allele in blastocysts, being prematurely transcribed at the 4-cell stage in maternal Dnmt3a knockout embryos. These observations uncover a role for maternal DNMT3A activity in post-fertilization epigenetic reprogramming and transcriptional silencing of the paternal genome.

Original languageEnglish
Article number5417
JournalNature communications
Issue number1
Publication statusPublished - Dec 1 2020

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)


Dive into the research topics of 'Maternal DNMT3A-dependent de novo methylation of the paternal genome inhibits gene expression in the early embryo'. Together they form a unique fingerprint.

Cite this