Low tolerance for transcriptional variation at cohesin genes is accompanied by functional links to disease-relevant pathways.

Abstract

The cohesin complex plays an essential role in genome organisation and cell division. A full complement of the cohesin complex and its regulators is important for normal development, since heterozygous mutations in genes encoding these components can be sufficient to produce a disease phenotype. The implication that genes encoding the cohesin subunits or cohesin regulators must be tightly controlled and resistant to variability in expression has not yet been formally tested. Here, we identify spatial-regulatory connections with potential to regulate expression of cohesin loci (Mitotic: <i>SMC1A</i>, <i>SMC3</i>, <i>STAG1</i>, <i>STAG2</i>, <i>RAD21</i>/<i>RAD21-AS</i>; Meiotic: <i>SMC1B</i>, <i>STAG3</i>, <i>REC8</i>, <i>RAD21L1</i>), cohesin-ring support genes (<i>NIPBL</i>, <i>MAU2</i>, <i>WAPL</i>, <i>PDS5A</i>, <i>PDS5B</i>) and <i>CTCF</i>, including linking their expression to that of other genes. We searched the genome-wide association studies (GWAS) catalogue for SNPs mapped or attributed to cohesin genes by GWAS (GWAS-attributed) and the GTEx catalogue for SNPs mapped to cohesin genes by <i>cis</i>-regulatory variants in one or more of 44 tissues across the human body (expression quantitative trail locus-attributed). Connections that centre on the cohesin ring subunits provide evidence of coordinated regulation that has little tolerance for perturbation. We used the CoDeS3D SNP-gene attribution methodology to identify transcriptional changes across a set of genes coregulated with the cohesin loci that include biological pathways such as extracellular matrix production and proteasome-mediated protein degradation. Remarkably, many of the genes that are coregulated with cohesin loci are themselves intolerant to loss-of-function. The results highlight the importance of robust regulation of cohesin genes and implicate novel pathways that may be important in the human cohesinopathy disorders.