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Regulation of expression of the CFTR gene is poorly understood. Elements within the basal promoter of the gene do not fully explain CFTR expression patterns, suggesting that cis-regulatory elements are located elsewhere, either within the locus or in adjacent chromatin. We previously mapped DNase I hypersensitive sites (DHS) in 400 kb spanning the CFTR locus including a cluster of sites close to the 3'-end of the gene. Here we focus on a DHS at +6.8 kb from the CFTR translation end-point to evaluate its potential role in regulating expression of the gene. This DHS, which encompasses a consensus CTCF-binding site, was evident in primary human epididymis cells that express abundant CFTR mRNA. We show by DNase I footprinting and electophoretic mobility shift assays that the cis-regulatory element within this DHS binds CTCF in vitro. We further demonstrate that the element functions as an enhancer blocker in a well-established in vivo assay, and by using chromatin immunoprecipitation that it recruits CTCF in vivo. Moreover, we reveal that in primary epididymis cells, the +6.8 kb DHS interacts closely with the CFTR promoter, suggesting that the CFTR locus exists in a looped conformation, characteristic of an active chromatin hub.

Original publication

DOI

10.1093/nar/gkn1056

Type

Journal article

Journal

Nucleic Acids Res

Publication Date

03/2009

Volume

37

Pages

1086 - 1094

Keywords

3' Flanking Region, Binding Sites, CCCTC-Binding Factor, Cells, Cultured, Chromatin, Cystic Fibrosis Transmembrane Conductance Regulator, DNA Footprinting, DNA-Binding Proteins, Deoxyribonuclease I, Enhancer Elements, Genetic, Epididymis, Humans, Insulator Elements, Male, Repressor Proteins