A Mechanism of Cohesin-Dependent Loop Extrusion Organizes Zygotic Genome Architecture

Fertilization triggers assembly of higher-order chromatin structure from a nucleosomal state to generate a totipotent embryo. Chromatin loops and domains are detected in mouse zygotes by single-nucleus Hi-C (snHi-C) but not bulk Hi-C; both are absent in Drosophila embryos. We investigated whether zygotic chromatin structures are generated by cohesin-dependent loop extrusion. Using snHi-C of mouse knockout embryos, we demonstrate the zygotic genome folds into loops and domains that critically depend on Scc1-cohesin and are regulated in size by Wapl. Remarkably, we discovered distinct effects on maternal and paternal chromatin loop sizes, likely reflecting loop extrusion dynamics and reprogramming states. Polymer simulations based on snHi-C are consistent with a model where cohesin locally compacts chromatin and restricts inter-chromosomal interactions by active loop extrusion, whose processivity is controlled by Wapl. Our simulations and experimental data provide evidence that cohesin-dependent loop extrusion organizes mammalian genomes over multiple scales from the one-cell embryo onwards. We generated 144 Hi-C libraries from pronuclei of zygotes of Scc1 and Wapl knockout mice and wild-type G2 zygotes (31 Scc1flox, 45 Scc1D(m)/+(p), 18 Waplflox, 18 WaplD(m)/+(p), 32 G2).