Enhancer-promoter compatibility is mediated by the promoter-proximal region

Abstract Gene promoters induce transcription in response to distal enhancers. How enhancers specifically activate their target promoter while bypassing other promoters remains unclear. Here, we find that the promoter-proximal region is critical for cell-type specific enhancer-promoter compatibility. Using high-throughput genome-engineering in mouse embryonic stem cells (mESC), we systematically replace the endogenous Sox9 promoter with different libraries of core and extended (i.e. full) promoters and assess their response to long-range regulatory elements in mESCs and neural progenitor cells. We find that only a subset of full promoters is activated by distal neuronal enhancers and that the promoter-proximal region is necessary for this enhancer-promoter compatibility. Core promoters alone are insufficient to respond to distal enhancers but modulate the transcriptional output of responsive promoters. Our results suggest that within multipartite regulatory domains, the promoter-proximal region fulfills a facilitator-like function that filters and transmits signal from distal enhancers, ultimaltely conferring enhancer-promoter compatibility.