Genomics

Dataset Information

302

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


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. 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 CFTR TAD 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. Examination of open chromatin region in Caco2 (colorectal adenocarcinoma cells), HBE (primary human bronchial epithelial cells), and primary adult human epididymis cells

ORGANISM(S): Homo sapiens  

SUBMITTER: Rui Yang   Ann Harris 

PROVIDER: E-GEOD-74709 | ArrayExpress | 2016-01-07

SECONDARY ACCESSION(S): SRP065832GSE74709PRJNA301216

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

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

Yang Rui R   Kerschner Jenny L JL   Gosalia Nehal N   Neems Daniel D   Gorsic Lidija K LK   Safi Alexias A   Crawford Gregory E GE   Kosak Steven T ST   Leir Shih-Hsing SH   Harris Ann A  

Nucleic acids research 20151215 7


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  ...[more]

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