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

Journal Article

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.CFTR occupies a TAD bordered by CTCF/cohesin binding sites within which are cell-type-selective cis-regulatory elements for the locus. We showed previously that intronic and extragenic enhancers, when occupied by specific transcription factors, are recruited to the CFTR promoter by a looping mechanism to drive gene expression. Here we use a combination of CRISPR/Cas9 editing of cis-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 the CFTR locus. We found the boundaries of the CFTRTAD 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 on CFTR expression. Within the TAD, intronic enhancers recruit cell-type selective transcription factors and deletion of a pivotal enhancer element dramatically decreases CFTR expression, but has minor effect on its 3D structure.

Full Text

Duke Authors

Cited Authors

  • Yang, R; Kerschner, JL; Gosalia, N; Neems, D; Gorsic, LK; Safi, A; Crawford, GE; Kosak, ST; Leir, S-H; Harris, A

Published Date

  • April 2016

Published In

Volume / Issue

  • 44 / 7

Start / End Page

  • 3082 - 3094

PubMed ID

  • 26673704

Electronic International Standard Serial Number (EISSN)

  • 1362-4962

International Standard Serial Number (ISSN)

  • 0305-1048

Digital Object Identifier (DOI)

  • 10.1093/nar/gkv1358

Language

  • eng