Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C.

ABSTRACT: Genome-wide association studies have identified more than 70 common variants that are associated with breast cancer risk. Most of these variants map to non-protein-coding regions and several map to gene deserts, regions of several hundred kilobases lacking protein-coding genes. We hypothesized that gene deserts harbor long-range regulatory elements that can physically interact with target genes to influence their expression. To test this, we developed Capture Hi-C (CHi-C), which, by incorporating a sequence capture step into a Hi-C protocol, allows high-resolution analysis of targeted regions of the genome. We used CHi-C to investigate long-range interactions at three breast cancer gene deserts mapping to 2q35, 8q24.21, and 9q31.2. We identified interaction peaks between putative regulator

SUBMITTER: Dryden NH 

PROVIDER: S-EPMC4216926 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature