Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus

Yang, R.; Kerschner, J. L.; Gosalia, N.; Neems, D.; Gorsic, L. K.; Safi, A.; Crawford, G. E.; Kosak, S. T.; Leir, S. H.; Harris, A.

Nucleic Acids Res. 2015 Dec 18; 44(7):3082-94

Abstract

Higher order chromatin structure establishes domains that organize the genome and coordinate gene expression. However, the molecular mechanisms controlling transcription of individual loci within a topological domain (TAD) are not fully understood. The cystic fibrosis transmembrane conductance regulator (CFTR) gene provides a paradigm for investigating these mechanisms.CFTRoccupies a TAD bordered by CTCF/cohesin binding sites within which are cell-type-selectivecis-regulatory elements for the locus. We showed previously that intronic and extragenic enhancers, when occupied by specific transcription factors, are recruited to theCFTRpromoter by a looping mechanism to drive gene expression. Here we use a combination of CRISPR/Cas9 editing ofcis-regulatory elements and siRNA-mediated depletion of architectural proteins to determine the relative contribution of structural elements and enhancers to the higher order structure and expression of theCFTRlocus. We found the boundaries of theCFTRTAD are conserved among diverse cell types and are dependent on CTCF and cohesin complex. Removal of an upstream CTCF-binding insulator alters the interaction profile, but has little effect onCFTRexpression. Within the TAD, intronic enhancers recruit cell-type selective transcription factors and deletion of a pivotal enhancer element dramatically decreasesCFTRexpression, but has minor effect on its 3D structure.

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