Genomic Approaches to Studying CFTR Transcriptional Regulation
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.
Key wordsCFTR DNase-chip chromosome conformation capture enhancers regulatory elements
We would like to thank Dr. Neil Blackledge (Department of Biochemistry, Oxford University) for generating data shown in Fig. 13.3b and Dr. Greg Crawford (Institute for Genome Sciences & Policy, Duke University) for assistance with the DNase-chip technique.