Cohesin-based chromatin interactions enable regulated gene expression within pre-existing architectural compartments.
Chromosome conformation capture approaches have shown that interphase chromatin is organized into an architectural framework of Mb-sized compartments and sub-Mb-sized topological domains. Cohesin controls chromosome topology to facilitate DNA repair and chromosome segregation in cycling cells, and also associates with active enhancers and promoters and with CTCF to form long-range interactions important for gene regulation. We find that architectural compartments - a major feature of interphase chromatin organization – are maintained in non-cycling mouse thymocytes after genetic depletion of cohesin in vivo. Cohesin was however required for specific long-range interactions within permissive (A-type) compartments, where cohesin-regulated genes reside. Cohesin depletion diminished interactions between cohesin-bound sites, while alternative interactions between chromatin features associated with transcriptional activation and repression became more prominent, with corresponding changes in gene expression. Our findings indicate that cohesin-mediated long-range interactions facilitate discrete gene expression states within pre-existing chromosomal compartments. Overall design: The chromatin binding of cohesin, the cohesin-loading loading complex and Mediator was analysed by ChIP-sequencing in thymocytes for the respective subunits Rad21, NIPBL and Med1. The role of the cohesin complex in transcriptional regulation was investigated using RNA-sequencing in wild type and Rad21 KO thymocytes, while the global role of cohesin in chromatin organisation was investigated by Hi-C in wild type and Rad21 KO thymocytes. This approach allowed us to integrate the binding of cohesin and its associated factors with changes in transcription and chromatin organisation upon cohesin depletion.