A Cohesin Cancer Mutation Reveals a Role for the Hinge Domain in Genome Organization and Gene Expression

The cohesin complex functions in the spatial organization of the genome into DNA loop structures. While cohesin is known to occupy enhancers, promoters and CTCF sites, the molecular mechanisms through which cohesin is loaded onto chromatin, localizes to these specific genomic sites, then forms and maintains loops are not fully understood. In yeast, targeted mutagenesis and suppressor screens identified the hinge domains of Smc1 and Smc3 as being required for cohesin loading onto chromatin and the topological entrapment of sister chromatids during DNA replication. It is not known whether the cohesin hinge also regulates these functions in mammalian cells or participates in metazoan-specific functions in interphase chromatin organization. Investigation of cancer sequencing databases revealed a hotspot mutation in the SMC1A hinge at amino acid residue arginine (R) 586 in leukemia. We used CRISPR/Cas9 genome editing to generate murine embryonic stem cell (ESC) lines with an endogenous tryptophan (W) mutation at amino acid 586, as seen in cancers. Transcriptomic analysis of SMC1A-R586W ESCs reveals global dysregulation of the transcriptional programs, with reduced expression of pluripotency-controlling TFs, activation of differentiation programs, and misexpression of oncogenes. Strikingly, RAD21 ChIP-seq indicates that SMC1A-R586W reduces cohesin enrichment at promoters and enhancers, but not at CTCF sites. Hi-C analysis reveals altered genome organization, including a reduction in short-range, intra-domain DNA contacts. This work indicates that the cohesin hinge participates in the cohesin loading reaction at promoters and enhancers, and/or promotes the localization of cohesin to these elements. These findings further suggest that cohesin mutations can contribute to oncogenesis through selective loss of cohesin at transcriptional regulatory elements.