Transcriptional Dysregulation in NIPBL and Cohesin Mutant Human Cells

Abstract

Cohesin regulates sister chromatid cohesion during the mitotic cell cycle with Nipped-B-Like (NIPBL) facilitating its loading and unloading. In addition to this canonical role, cohesin has also been demonstrated to play a critical role in regulation of gene expression in nondividing cells. Heterozygous mutations in the cohesin regulator NIPBL or cohesin structural components SMC1A and SMC3 result in the multisystem developmental disorder Cornelia de Lange Syndrome (CdLS). Genome-wide assessment of transcription in 16 mutant cell lines from severely affected CdLS probands has identified a unique profile of dysregulated gene expression that was validated in an additional 101 samples and correlates with phenotypic severity. This profile could serve as a diagnostic and classification tool. Cohesin binding analysis demonstrates a preference for intergenic regions suggesting a cis-regulatory function mimicking that of a boundary/insulator interacting protein. However, the binding sites are enriched within the promoter regions of the dysregulated genes and are significantly decreased in CdLS proband, indicating an alternative role of cohesin as a transcription factor. Appropriate segregation of chromosomes to daughter cells depends upon proper cohesion of sister chromatids during mitosis. The multiprotein cohesin complex and its regulators are key factors in this process. Intriguingly, recent work has shown that the cohesin complex also has other cellular roles, including a role in regulating gene expression. Additionally, mutations in cohesin structural and regulatory components have been linked to human multisystem developmental disorders such as Cornelia de Lange Syndrome (CdLS), but the role cohesin is playing in the pathogenesis of this disorder is unknown. To define the role that cohesin plays in regulating gene expression in human cells, we analyzed gene expression and genome-wide cohesin binding patterns in cells from normal subjects and from CdLS probands with mutations in the cohesin regulator NIPBL or in the cohesin structural component SMC1A. We found a strikingly conserved pattern of gene dysregulation in these different cell lines that correlates with disease severity and a significant correlation between gene dysregulation and cohesin binding around misexpressed genes. The observed pattern of binding and misexpression is consistent with cohesin having a putative role as a boundary/insulator interacting protein or transcription factor, the activity of which is disrupted in CdLS probands.