The Birth of the 3D Genome during Early Embryonic Development

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. 3D chromatin architecture, including topologically associating domains and compartments, are weakened during germline development. Re-establishment of topologically associating domains and compartments occurs during zygotic genome activation. Transcription is associated with domain boundaries, but is neither necessary nor sufficient for their emergence. Several independent mechanisms may have evolved to structure the 3D genome.