A modified protocol of Capture-C allows affordable and flexible high-resolution promoter interactome analysis

Large-scale epigenomic projects have mapped hundreds of thousands of potential regulatory sites in the human genome, but only a small proportion of these elements are proximal to transcription start sites. It is believed that the majority of these sequences are remote promoter-activating genomic sites scattered within several hundreds of kilobases from their cognate promoters and referred to as enhancers. It is still unclear what principles, aside from relative closeness in the linear genome, determine which promoter(s) is controlled by a given enhancer; however, this understanding is of great fundamental and clinical relevance. In recent years, C-methods have become a powerful tool for the identification of enhancer-promoter spatial contacts that, in most cases, reflect their functional link. Here, we present data on spatial interactions of 867 promoters in HeLa cells. This data is obtained with a new hybridization-based promoter Capture-C protocol that makes use of biotinylated dsDNA probes and allows high-resolution promoter interactome description. Spatial interactome of 867 promoters in HeLa cells was probed with PCHi-C technique. Two alternative PCHi-C protocols were used. Raw data: Due to patient privacy concerns, raw fastq files were submitted to SRA via dbGAP (study phs000640, substudy phs002014). Third-party reanalysis: Four Rao samples from dbGAP study phs001010.