Multiplexed analysis of chromosome conformation at vastly improved sensitivity

Pooling barcoded 3C libraries and simultaneously capturing interactions at many loci of interest generates reproducible cis - and trans -interaction maps at high resolution from low amounts of input material. This allows for the comparison of interactions in different cell types using common software designed for differential analysis of sequence count data, rather than requiring software specifically designed for 3C experiments. Methods for analyzing chromosome conformation in mammalian cells are either low resolution or low throughput and are technically challenging. In next-generation (NG) Capture-C, we have redesigned the Capture-C method to achieve unprecedented levels of sensitivity and reproducibility. NG Capture-C can be used to analyze many genetic loci and samples simultaneously. High-resolution data can be produced with as few as 100,000 cells, and single-nucleotide polymorphisms can be used to generate allele-specific tracks. The method is straightforward to perform and should greatly facilitate the investigation of many questions related to gene regulation as well as the functional dissection of traits examined in genome-wide association studies.