The establishment of the 3D genome structure during zygotic genome activation

Abstract

During zygotic genome activation (ZGA) and early development, hierarchical levels of chromatin structure undergo remarkable perturbations: changes in the nuclear-to-cytoplasmic ratio of various components; changes in chromatin accessibility; histone exchange; and the formation of 3D structures such as loops, topologically associated domains, and compartments. Here, we review the peculiarities, variability, and emergence of the chromatin structural features during ZGA in different organisms. Focusing on newly found structures called fountains, we describe the prerequisites for cohesin loading on DNA and possible mechanisms of genome organization in early development. Fountains resulting from asymmetric bidirectional cohesin extrusion spread from cohesin-loading points in a CTCF-independent manner. We discuss that fountains may not possess specific functions, unlike conventional chromatin structures, and could be found in other biological processes where cohesin loading occurs.