RNA polymerase II dynamics shape enhancer–promoter interactions

How enhancers control target gene expression over long genomic distances remains an important unsolved problem. Here we investigated enhancer–promoter communication by integrating data from nucleosome-resolution genomic contact maps, nascent transcription and perturbations affecting either RNA polymerase II (Pol II) dynamics or the activity of thousands of candidate enhancers. Integration of new Micro-C experiments with published CRISPRi data demonstrated that enhancers spend more time in close proximity to their target promoters in functional enhancer–promoter pairs compared to nonfunctional pairs, which can be attributed in part to factors unrelated to genomic position. Manipulation of the transcription cycle demonstrated a key role for Pol II in enhancer–promoter interactions. Notably, promoter-proximal paused Pol II itself partially stabilized interactions. We propose an updated model in which elements of transcriptional dynamics shape the duration or frequency of interactions to facilitate enhancer–promoter communication. Perturbation of RNA polymerase II (Pol II) via chemical inhibition or dTAG-induced degradation and analysis using Micro-C and run-on sequencing show that enhancer–promoter contacts are dependent on transcription and stabilized by paused RNA Pol II.