Highly connected enhancer communities control lineage-determining genes in human mesenchymal stem cells

Adipocyte differentiation is driven by waves of transcriptional regulators that reprogram the en-hancer landscape and change the wiring of the promoter interactome. Here, we establish enhancer-capture Hi-C to interrogate the extent and role of enhancer-to-enhancer interactions during adi-pocyte differentiation of human mesenchymal stem cells. We find that enhancers form an elaborate network that is highly dynamic during differentiation and tightly coupled to changes of enhancer activity. These interactions are important for enhancer function, since transcription factors at baited enhancers stabilize transcription factor binding at target enhancers, a phenomenon we term cross-interaction stabilization of transcription factors (CIST). Moreover, highly interconnected enhancers (HICE) act as integration hubs orchestrating differentiation by formation of insulated 3D enhancer communities, inside which, HICE, and other enhancers, converge on phenotypically important gene promoters. Collectively, these results indicate that dynamic enhancer interactions play a key role in regulation of enhancer function, and that HICE are important for both signal integration and compartmentalization of the genome. Genome-wide profiling of transcription factors using ChIP-seq, gene expression using RNA-seq and enhancer-anchored chromatin interactions using enhancer capture Hi-C during adipocyte differentiation of human mesenchymal stem cells.