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.

Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins

“…Our results are, however, consistent with several other studies which were deposited on bioRxiv or published in peer‐reviewed journals during preparation or after submission of our manuscript (Gassler et al , ; Haarhuis et al , ; Nora et al , ; Rao et al , 2017; Schwarzer et al , ). In these studies, chromatin structure was analyzed by Hi‐C experiments following inactivation of either cohesin (Rao et al , 2017), the cohesin loading complex (Schwarzer et al , ), CTCF (Nora et al , ), or WAPL (Haarhuis et al , ).…”

“…Cohesin, CTCF and WAPL, but not PDS5 proteins, have also been inactivated in other recent Hi‐C studies which were deposited on bioRxiv (Kubo et al , ) or published in peer‐reviewed journals during preparation or after submission of our manuscript (Gassler et al , ; Haarhuis et al , ; Rao et al , 2017; Schwarzer et al , ). We compare and contrast the results of these as well as the earlier studies (Seitan et al , ; Sofueva et al , ; Zuin et al , ) with ours in the Discussion.…”

Cohesin: building loops, but not compartments

“…SCC1‐deficient cells lacked virtually all loops genomewide (Fig A). Cohesin therefore is essential for the formation and/or maintenance of loops (Gassler et al , ; Rao et al , ; Wutz et al , ). Re‐introduction of SCC1 in depleted cells led to the re‐appearance of loops within an hour (Rao et al , ).…”

“…If cohesin were to form loops through a processive mechanism, the duration with which it entraps DNA may well determine how far loops can be enlarged. Three studies have now tested this hypothesis in different ways (Gassler et al , ; Haarhuis et al , ; Wutz et al , ). WAPL deficiency led to a far longer residence time of cohesin on the DNA.…”

“…They show that CTCF is required for the formation of loops between CTCF sites (Fig A; Nora et al , ; Wutz et al , ). The formation of loops per se is not affected by CTCF depletion, as this rather is cohesin dependent (Gassler et al , ; Rao et al , ; Wutz et al , ). The available data would support the model that cohesin forms loops until it encounters an inwards‐pointing CTCF site.…”