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

Publication ,  Journal Article
Ott, CJ; Blackledge, NP; Kerschner, JL; Leir, S-H; Crawford, GE; Cotton, CU; Harris, A
Published in: Proc Natl Acad Sci U S A
November 24, 2009

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.

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Published In

Proc Natl Acad Sci U S A

DOI

EISSN

1091-6490

Publication Date

November 24, 2009

Volume

106

Issue

47

Start / End Page

19934 / 19939

Location

United States

Related Subject Headings

  • p300-CBP Transcription Factors
  • Promoter Regions, Genetic
  • Oligonucleotide Array Sequence Analysis
  • Nucleic Acid Conformation
  • Introns
  • Humans
  • Hepatocyte Nuclear Factor 1
  • Genes, Reporter
  • Gene Expression Regulation
  • Epithelial Cells
 

Citation

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Ott, C. J., Blackledge, N. P., Kerschner, J. L., Leir, S.-H., Crawford, G. E., Cotton, C. U., & Harris, A. (2009). Intronic enhancers coordinate epithelial-specific looping of the active CFTR locus. Proc Natl Acad Sci U S A, 106(47), 19934–19939. https://doi.org/10.1073/pnas.0900946106
Ott, Christopher J., Neil P. Blackledge, Jenny L. Kerschner, Shih-Hsing Leir, Gregory E. Crawford, Calvin U. Cotton, and Ann Harris. “Intronic enhancers coordinate epithelial-specific looping of the active CFTR locus.Proc Natl Acad Sci U S A 106, no. 47 (November 24, 2009): 19934–39. https://doi.org/10.1073/pnas.0900946106.
Ott CJ, Blackledge NP, Kerschner JL, Leir S-H, Crawford GE, Cotton CU, et al. Intronic enhancers coordinate epithelial-specific looping of the active CFTR locus. Proc Natl Acad Sci U S A. 2009 Nov 24;106(47):19934–9.
Ott, Christopher J., et al. “Intronic enhancers coordinate epithelial-specific looping of the active CFTR locus.Proc Natl Acad Sci U S A, vol. 106, no. 47, Nov. 2009, pp. 19934–39. Pubmed, doi:10.1073/pnas.0900946106.
Ott CJ, Blackledge NP, Kerschner JL, Leir S-H, Crawford GE, Cotton CU, Harris A. Intronic enhancers coordinate epithelial-specific looping of the active CFTR locus. Proc Natl Acad Sci U S A. 2009 Nov 24;106(47):19934–19939.
Journal cover image

Published In

Proc Natl Acad Sci U S A

DOI

EISSN

1091-6490

Publication Date

November 24, 2009

Volume

106

Issue

47

Start / End Page

19934 / 19939

Location

United States

Related Subject Headings

  • p300-CBP Transcription Factors
  • Promoter Regions, Genetic
  • Oligonucleotide Array Sequence Analysis
  • Nucleic Acid Conformation
  • Introns
  • Humans
  • Hepatocyte Nuclear Factor 1
  • Genes, Reporter
  • Gene Expression Regulation
  • Epithelial Cells