Intronic enhancers coordinate epithelial-specific looping of the active CFTR locus

Christopher J. Ott, Neil P. Blackledge, Jenny L. Kerschner, Shih Hsing Leir, Gregory E. Crawford, Calvin U. Cotton, Ann Harris*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

90 Scopus citations


The regulated expression of large human genes can depend on long-range interactions to establish appropriate three-dimensional structures across the locus. The cystic fibrosis transmembrane conductance regulator (CFTR) gene, which encompasses 189 kb of genomic DNA, shows a complex pattern of expression with both spatial and temporal regulation. The flanking loci, ASZ1 and CTTNBP2, show very different tissue-specific expression. The mechanisms governing control of CFTR expression remain poorly understood, although they are known to involve intronic regulatory elements. Here, we show a complex looped structure of the CFTR locus in cells that express the gene, which is absent from cells in which the gene is inactive. By using chromatin conformation capture (3C) with a bait probe at the CFTR promoter, we demonstrate close interaction of this region with sequences in the middle of the gene about 100 kb from the promoter and with regions 3′ to the locus that are about 200 kb away. We show that these interacting regions correspond to prominent DNase I hypersensitive sites within the locus. Moreover, these sequences act cooperatively in reporter gene constructs and recruit proteins that modify chromatin structure. The model for CFTR gene expression that is revealed by our data provides a paradigm for other large genes with multiple regulatory elements lying within both introns and intergenic regions. We anticipate that these observations will enable original approaches to designing regulated transgenes for tissue-specific gene therapy protocols.

Original languageEnglish (US)
Pages (from-to)19934-19939
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number47
StatePublished - Nov 24 2009


  • Cis-acting elements
  • Cystic fibrosis transmembrane conductance regulator
  • Enhancer:promoter interactions
  • Regulation of expression

ASJC Scopus subject areas

  • General


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