Specific contributions of cohesin-SA1 and cohesin-SA2 to TADs and Polycomb domains in embryonic stem cells.

Cohesin complex, a main organizer of mammalian genomes, exists in two versions that differ in the identity of the STAG/SA subunit, which can be SA1 or SA2. Mouse embryonic stem cell (mESC) provide a useful system to address the specific contributions of each variant to genome architecture and gene expression, since 3D organization of super- enhancers and Polycomb domains is essential to achieve transcription of pluripotency factors and repression of lineage specification genes, respectively. Hi-C analyses reveal That cohesin-SA1 preserves the integrity of topological associating domains (TAD) boundaries together with CTCF and prevents excessive segregation of same-class Compartment regions. Cohesin-SA2 is enriched within super-enhancers and Polycomb domains. Moreover, it contributes to establishment and compaction of Polycomb domains through PRC1 recruitment thereby promoting interchromosomal interactions among Hox gene promoters and favoring gene repression. In contrast, these interactions are counteracted by cohesin-SA1. The opposite effects of the two complexes on genome topology explain the distinct consequences of their ablation for the mESCs Transcriptome. Overall design: ChIP-seq for cohesin subunits was performed in mES cells growing under serum/LIF (SA1, SA2 and SMC1) or serum/LIF/2i (SA1 and SA2) conditions, and peak calling was done against the corresponding input sample. Suz12 and Ring1B ChIP-seq was performed in duplicates in serum/LIF growing mES control and depleted from SA1 or SA2 by means of Dharmacon SMART pool siRNAs. RNA-seq was performed in triplicates in serum/LIF growing mES control and depleted from SA1, and in duplicates from SA2 depleted cells by means of Dharmacon SMART pool siRNAs. HiC-seq was performed in two independent biological replicates in mES cells growing under serum/LIF/2i or serum/LIF mES cells control and depleted from SA1 and SA2 by means of Dharmacon SMART pool siRNAs.