Genome-wide nucleosome-resolution map of promoter-centered interactions in human cells corroborates the enhancer-promoter looping model

The enhancer-promoter looping model, in which enhancers activate their target genes via physical contact, has been the dominant hypothesis in the field for decades. However, a systematic testing of this hypothesis has not been conducted, primarily due to the absence of suitable experimental techniques. In this study, we present a new MNase-based proximity ligation method called MChIP-C, allowing for the measurement of protein-mediated chromatin interactions at single-nucleosome resolution on a genome-wide scale. By applying MChIP-C to study H3K4me3 promoter-centered interactions in K562 cells, we found that it had greatly improved resolution and sensitivity compared to restriction endonuclease-based C-methods. This allowed us to identify EP300 histone acetyltransferase and the SWI/SNF remodelling complex as potential candidates for establishing and/or maintaining enhancer-promoter interactions. Finally, leveraging data from published CRISPRi screens, we found that most functionally-verified enhancers do physically interact with their cognate promoters, supporting the enhancer-promoter looping model. Crosslinked K562 cells were subjected to MNase digestion, proximity ligation, chromatin immunoprecipitation with H3K4me3 antibodies (Active motif, 39016) and deep sequencing, the whole procedure was dubbed MChIP-C. MChIP-C was performed in 4 biological replicates. Conventional H3K4me3 (Active motif, 39016) ChIP-seq was performed in one replicate.