GSE206131
RNA polymerase II and PARP1 shape enhancer-promoter contacts [Micro-C]
What controls enhancer-promoter communication to allow for cis-transcriptional regulation remains a mystery. Here we studied how transcriptional dynamics shapes enhancer-promoter contacts. We demonstrate that enhancer function is reflected in enhancer-promoter contacts frequency which highly depend on active transcription. Pol II pausing, which is widespread across metazoan enhancers and promoters, has a direct effect on focal enhancer-promoter contacts. We confirmed this effect by depleting NELFB, a subunit of the negative elongation factor complex and a pivotal factor in Pol II pausing. Moreover, the catalytic activity of PARP1, a regulator of transcription and chromatin condensation, stabilizes enhancer-promoter contacts globally, but can destabilize contacts by promoting Pol II escape from pausing. Based on these findings, we propose an updated model that couples transcription and enhancer-promoter contacts. Overall design: Micro-C libraries were prepared for K562 and Jurkat human cell lines, with at least one replicate per cell line. Two biological replicates with two technical replicates each were prepared for each condition of K562 cells treated for 90 minutes with either Olaparib to inhibit PARP1 function and the DMSO control. Two biological replicates with two technical replicates each were also prepared for each time point of dTAG-13 incubation for mECSs harboring a homozygous endogenous NELFB-FKBP12F36V fusion protein (0, 30 and 60 minutes) as well as for 8 hours and 24 hours after dTAG-13 washout.