Multiplexed analysis of chromosome conformation at vastly improved sensitivity

Current methods for analysing chromosome conformation in mammalian cells are either insensitive and low resolution or low throughput. Since available methods are both expensive and relatively difficult to perform and analyse they are not widely used outside of specialised laboratories. Here we have redesigned the Capture-C method producing a new approach, called next generation (NG) Capture-C. This produces unprecedented levels of sensitivity and reproducibility, which can be used to analyse any number of genetic loci and/or many samples in a single experiment. NG Capture-C is straightforward to perform, requiring only standard reagents and access to conventional next generation sequencing platforms. Importantly, high-resolution data can be produced on as few as 100,000 cells and SNPs can be used to generate allele specific tracks. The method should therefore greatly facilitate the task of linking SNPs identified by genome wide association studies with the genes they influence. The complete and detailed protocol presented here, with new publicly available tools for library design and data analysis, will allow most laboratories to analyse chromatin conformation at levels of sensitivity and throughput that were previously impossible.