MChIPC: genome-wide measurement of enhancer-promoter spatial interactions at sub-kilobase resolution

Mammalian genomes are littered with hundreds of thousands of distal regulatory sequences which provide robust and precise spatiotemporal control of expression for around 20,000 genes. These genomic sequences are usually scattered around their target genes but can be as far as several megabases away from them, oftentimes skipping the closest active promoters to regulate more remote ones. Therefore it is hardly possible to predict functional enhancer-promoter (E-P) interactions based solely on 1D epigenomic datasets. At the same time such predictions are extremely important for both basic and applied science. CRISPR/Cas based functional screening techniques have become useful tools for experimental identification of E-P regulatory interactions. However such approaches apparently are not able to detect a significant proportion of E-P interactions due to regulatory buffering effects. Physical E-P interactions are arguably mechanistically necessary for regulatory activity. Hence development of proximity-ligation based biochemical techniques, often regarded as C-methods, has a great potential to improve prediction of functional E-P pairs. Here we present a novel C-method – MChIPC – for genome-wide E-P proximity assessment with single nucleosome resolution. MChIPC is based on the recently described MCC protocol which exploits MNase digestion of mildly lysed cells to achieve superior resolution of interaction profiles. MChIPC also borrows chromatin immunoprecipitation step with anti-H3K4me3 antibodies from HiChIP protocol to enrich proximity ligation libraries with ligation products originating from active promoters. We applied MChIPC to the K562 erythroleukemia cells and discovered thousands of E-P loops of potential regulatory importance.