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The CFTR gene was identified over 20 years ago, and yet how the gene is transcriptionally regulated is not fully understood. Completion of the human genome sequence has encouraged a new generation of genomic techniques that can be used to identify and characterize the regulatory elements of the genome, which are often hidden in non-coding regions. In this chapter we describe two techniques that we have used to identify regulatory regions of the CFTR locus: DNase-chip, which utilizes DNase I-digested chromatin hybridized to tiled microarrays in order to locate regions of the CFTR locus that are "open" and thus likely regions of transcription factor binding; and quantitative chromosome conformation capture (q3C), which uses quantitative PCR analysis of digested and ligated, crosslinked chromosomes to measure physical interactions between distal genomic regions. When used together, these methods provide a powerful avenue to discover transcriptional regulatory elements within large genomic regions.

Original publication

DOI

10.1007/978-1-61779-117-8_13

Type

Journal article

Journal

Methods Mol Biol

Publication Date

2011

Volume

741

Pages

193 - 209

Keywords

Biotinylation, Caco-2 Cells, Chromatin, Cystic Fibrosis Transmembrane Conductance Regulator, DNA, DNA Primers, Deoxyribonuclease I, Electrophoresis, Gel, Pulsed-Field, Genetic Loci, Genomics, Humans, Molecular Conformation, Oligonucleotide Array Sequence Analysis, Polymerase Chain Reaction, Transcription, Genetic