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Nucleosome positioning on the chromatin strand plays a critical role in regulating accessibility of DNA to transcription factors and chromatin modifying enzymes. Hence, detailed information on nucleosome depletion or movement at cis-acting regulatory elements has the potential to identify predicted binding sites for trans-acting factors. Using a novel method based on enrichment of mononucleosomal DNA by bacterial artificial chromosome hybridization, we mapped nucleosome positions by deep sequencing across 250 kb, encompassing the cystic fibrosis transmembrane conductance regulator (CFTR) gene. CFTR shows tight tissue-specific regulation of expression, which is largely determined by cis-regulatory elements that lie outside the gene promoter. Although multiple elements are known, the repertoire of transcription factors that interact with these sites to activate or repress CFTR expression remains incomplete. Here, we show that specific nucleosome depletion corresponds to well-characterized binding sites for known trans-acting factors, including hepatocyte nuclear factor 1, Forkhead box A1 and CCCTC-binding factor. Moreover, the cell-type selective nucleosome positioning is effective in predicting binding sites for novel interacting factors, such as BAF155. Finally, we identify transcription factor binding sites that are overrepresented in regions where nucleosomes are depleted in a cell-specific manner. This approach recognizes the glucocorticoid receptor as a novel trans-acting factor that regulates CFTR expression in vivo.

Original publication

DOI

10.1093/nar/gks1462

Type

Journal article

Journal

Nucleic Acids Res

Publication Date

01/03/2013

Volume

41

Pages

2857 - 2868

Keywords

Binding Sites, CCCTC-Binding Factor, Caco-2 Cells, Chromatin Immunoprecipitation, Chromosome Mapping, Cystic Fibrosis Transmembrane Conductance Regulator, Dexamethasone, Gene Silencing, Genetic Loci, Glucocorticoids, Hepatocyte Nuclear Factor 3-alpha, Humans, Nucleosomes, Protein Binding, Receptors, Glucocorticoid, Repressor Proteins, Response Elements, Sequence Analysis, DNA, Transcription Factors