Genome-wide analysis of DNA methylation dynamics during early human development

PLoS Genet. 2014 Dec 11;10(12):e1004868. doi: 10.1371/journal.pgen.1004868. eCollection 2014 Dec.


DNA methylation is globally reprogrammed during mammalian preimplantation development, which is critical for normal development. Recent reduced representation bisulfite sequencing (RRBS) studies suggest that the methylome dynamics are essentially conserved between human and mouse early embryos. RRBS is known to cover 5-10% of all genomic CpGs, favoring those contained within CpG-rich regions. To obtain an unbiased and more complete representation of the methylome during early human development, we performed whole genome bisulfite sequencing of human gametes and blastocysts that covered>70% of all genomic CpGs. We found that the maternal genome was demethylated to a much lesser extent in human blastocysts than in mouse blastocysts, which could contribute to an increased number of imprinted differentially methylated regions in the human genome. Global demethylation of the paternal genome was confirmed, but SINE-VNTR-Alu elements and some other tandem repeat-containing regions were found to be specifically protected from this global demethylation. Furthermore, centromeric satellite repeats were hypermethylated in human oocytes but not in mouse oocytes, which might be explained by differential expression of de novo DNA methyltransferases. These data highlight both conserved and species-specific regulation of DNA methylation during early mammalian development. Our work provides further information critical for understanding the epigenetic processes underlying differentiation and pluripotency during early human development.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Blastocyst / physiology
  • CpG Islands
  • DNA Methylation*
  • Embryo Culture Techniques
  • Female
  • Gene Expression Regulation, Developmental
  • Genome-Wide Association Study
  • Genomic Imprinting
  • Humans
  • Oocytes / physiology
  • Sequence Analysis, DNA
  • Tandem Repeat Sequences

Grant support

This work was supported by Grants-in-Aid for Scientific Research (KAKENHI) (2567091), Health and Labour Sciences Research Grant (H25-Jisedai-Ippan-001) and the Takeda Science Foundation (TA) and KAKENHI (26112502, 24613001) (HO). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.