CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single-cells

Chromatin interactions are important for gene regulation and cellular specialization. Emerging evidence suggests many-body spatial interactions can play important roles in condensing super-enhancer regions into a cohesive transcriptional apparatus. Chromosome conformation studies using Hi-C are limited to pairwise, population-averaged interactions; therefore, not suitable for direct assessment of many-body interactions. We describe a computational model, CHROMATIX, that reconstructs structural ensembles based on Hi-C data and identifies significant many-body interactions. For a diverse set of highly-active transcriptional loci with at least 2 super-enhancers, we detail the many-body functional landscape and show DNase-accessibility, POLR2A binding, and decreased H3K27me3 are predictive of interaction-enriched regions.