A role for cohesin in T-cell-receptor rearrangement and thymocyte differentiation

Cohesin enables post-replicative DNA repair and chromosome segregation by holding sister chromatids together from the time of DNA replication in S phase until mitosis(1). There is growing evidence that cohesin also forms long-range chromosomal cis-interactions(2-4) and may regulate gene expression(2-10) in association with CTCF8,9, mediator(4) or tissue-specific transcription factors(10). Human cohesinopathies such as Cornelia de Lange syndrome are thought to result from impaired non-canonical cohesin functions(7), but a clear distinction between the cell-division-related and cell-division-independent functions of cohesion-as exemplified in Drosophila(11-13)-has not been demonstrated in vertebrate systems. To address this, here we deleted the cohesin locus Rad21 in mouse thymocytes at a time in development when these cells stop cycling and rearrange their T-cell receptor (TCR) a locus (Tcra). Rad21-deficient thymocytes had a normal lifespan and retained the ability to differentiate, albeit with reduced efficiency. Loss of Rad21 led to defective chromatin architecture at the Tcra locus, where cohesion-binding sites flank the TEA promoter and the Ea enhancer, and demarcate Tcra from interspersed Tcrd elements and neighbouring housekeeping genes. Cohesin was required for long-range promoter-enhancer interactions, Tcra transcription, H3K4me3 histone modifications that recruit the recombination machinery(14,15) and Tcra rearrangement. Provision of pre-rearranged TCR transgenes largely rescued thymocyte differentiation, demonstrating that among thousands of potential target genes across the genome(4,8-10), defective Tcra rearrangement was limiting for the differentiation of cohesin-deficient thymocytes. These findings firmly establish a cell-division-independent role for cohesin in Tcra locus rearrangement and provide a comprehensive account of the mechanisms by which cohesin enables cellular differentiation in a well-characterized mammalian system.