Cohesin exists in two variants carrying either STAG/SA1 or SA2. Here we have addressed their specific contributions to the unique spatial organization of the mouse embryonic stem cell genome, which ensures super-enhancer-dependent transcription of pluripotency factors and repression of lineage-specification genes within Polycomb domains. We find that cohesin-SA2 facilitates Polycomb domain compaction through Polycomb repressing complex 1 (PRC1) recruitment and promotes the establishment of long-range interaction networks between distant Polycomb-bound promoters that are important for gene repression. Cohesin-SA1, in contrast, disrupts these networks, while preserving topologically associating domain (TAD) borders. The diverse effects of both complexes on genome topology may reflect two modes of action of cohesin. One, likely involving loop extrusion, establishes overall genome arrangement in TADs together with CTCF and prevents excessive segregation of same-class compartment regions. The other is required for organization of local transcriptional hubs such as Polycomb domains and super-enhancers, which define cell identity.

This work was funded by the Spanish Ministry of Economy and Competitiveness and the European Regional Development Fund (FEDER) (grant BFU2016-79841-R to A.L.), Comunidad de Madrid (contract PEJD-2016/BMD-3190 to G.M.-S.), Centro de Excelencia Severo Ochoa to CNIO (SEV-2015-0510), and the National Institute of Health Carlos III (ISCIII). The work of Y.C. and M.A.M.-R. was partially supported by the European Research Council (ERC) under the Seventh Framework Programme FP7/2007–2013 (ERC grant agreement 609989) and the European Union’s Horizon 2020 research and innovation program (grant agreement 676556). M.A.M.-R. also acknowledges support from the Spanish Ministry of Economy and Competitiveness (BFU2017-85926-P and the Centro de Excelencia Severo Ochoa to Center for Genomic Regulation), and the Generalitat de Catalunya (AGAUR grant SGR468 and CERCA Programme).