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

Abstract Fertilization triggers assembly of higher‐order chromatin structure from a condensed maternal and a naïve paternal genome to generate a totipotent embryo. Chromatin loops and domains have been detected in mouse zygotes by single‐nucleus Hi‐C (snHi‐C), but not bulk Hi‐C. It is therefore unclear when and how embryonic chromatin conformations are assembled. Here, we investigated whether a mechanism of cohesin‐dependent loop extrusion generates higher‐order chromatin structures within the one‐cell embryo. Using snHi‐C of mouse knockout embryos, we demonstrate that the zygotic genome folds into loops and domains that critically depend on Scc1‐cohesin and that are regulated in size and linear density by Wapl. Remarkably, we discovered distinct effects on maternal and paternal chromatin loop sizes, likely reflecting differences in loop extrusion dynamics and epigenetic reprogramming. Dynamic polymer models of chromosomes reproduce changes in snHi‐C, suggesting a mechanism where cohesin locally compacts chromatin 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 onward

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

Chromatin is reprogrammed after fertilization to produce a totipotent zygote with the potential to generate a new organism1. The maternal genome inherited through the oocyte and the paternal genome provided by sperm coexist as separate haploid nuclei in the zygote. How these two epigenetically distinct genomes are spatially organized is poorly understood. Existing chromosome conformation capture-based methods2–5 are inapplicable to oocytes and zygotes due to a paucity of material. To study the 3D chromatin organization in rare cell types, we developed a single-nucleus Hi-C (snHi-C) protocol that provides >10-fold more contacts per cell than the previous method2. Here we show that chromatin architecture is uniquely reorganized during the mouse oocyte-to-zygote transition and is distinct in paternal and maternal nuclei within single-cell zygotes. Features of genomic organization including compartments, topologically associating domains (TADs) and loops are present in individual oocytes when averaged over the genome; each feature at a locus is variable between cells. At the sub-megabase level, we observe stochastic clusters of contacts that violate TAD boundaries but average into TADs. Strikingly, we found that TADs and loops but not compartments are present in zygotic maternal chromatin, suggesting that these are generated by different mechanisms. Our results demonstrate that the global chromatin organization of zygote nuclei is fundamentally different from other interphase cells. An understanding of this zygotic chromatin “ground state” has the potential to provide insights into reprogramming to totipotency