Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci

Nat Commun. 2015 Feb 19;6:6178. doi: 10.1038/ncomms7178.

Abstract

Multiple regulatory elements distant from their targets on the linear genome can influence the expression of a single gene through chromatin looping. Chromosome conformation capture implemented in Hi-C allows for genome-wide agnostic characterization of chromatin contacts. However, detection of functional enhancer-promoter interactions is precluded by its effective resolution that is determined by both restriction fragmentation and sensitivity of the experiment. Here we develop a capture Hi-C (cHi-C) approach to allow an agnostic characterization of these physical interactions on a genome-wide scale. Single-nucleotide polymorphisms associated with complex diseases often reside within regulatory elements and exert effects through long-range regulation of gene expression. Applying this cHi-C approach to 14 colorectal cancer risk loci allows us to identify key long-range chromatin interactions in cis and trans involving these loci.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Pairing / genetics
  • Cell Line, Tumor
  • Chromatin / metabolism*
  • Chromosomes, Human, Pair 8 / genetics
  • Colorectal Neoplasms / genetics*
  • Genetic Loci*
  • Genetic Predisposition to Disease*
  • Humans
  • In Situ Hybridization, Fluorescence
  • Molecular Sequence Annotation
  • Nucleotide Motifs / genetics
  • Risk Factors
  • Statistics as Topic

Substances

  • Chromatin