The Birth of the 3D Genome during Early Embryonic Development

Trends Genet. 2018 Dec;34(12):903-914. doi: 10.1016/j.tig.2018.09.002. Epub 2018 Oct 3.


The 3D structure of chromatin in the nucleus is important for the regulation of gene expression and the correct deployment of developmental programs. The differentiation of germ cells and early embryonic development (when the zygotic genome is activated and transcription is taking place for the first time) are accompanied by dramatic changes in gene expression and the epigenetic landscape. Recent studies used Hi-C to investigate the 3D chromatin organization during these developmental transitions, uncovering remarkable remodeling of the 3D genome. Here, we highlight the changes described so far and discuss some of the implications that these findings have for our understanding of the mechanisms and functionality of 3D chromatin architecture.

Keywords: 3D chromatin architecture; TAD; maternal-to-zygotic transition; oocyte; sperm; zygotic genome activation.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Animals
  • Chromatin / genetics
  • Chromatin / ultrastructure*
  • Drosophila melanogaster / genetics
  • Drosophila melanogaster / growth & development
  • Embryonic Development / genetics*
  • Epigenesis, Genetic / genetics*
  • Female
  • Gene Expression Regulation, Developmental
  • Male
  • Mice
  • Molecular Conformation
  • Oocytes / growth & development
  • Oocytes / ultrastructure
  • Spermatozoa / growth & development
  • Spermatozoa / ultrastructure
  • Zygote / growth & development
  • Zygote / ultrastructure*


  • Chromatin