Mechanisms of transcription control by distal enhancers from single-gene nanoscopy

Distal enhancers activate genes over vast genomic distances, but how this communication occurs and what signals are transmitted are poorly understood. Using real-time single-gene nanoscopy and targeted perturbations, we define physical parameters and mechanisms of enhancer-promoter communication. We find that productive interactions are dynamic, occur at a proximity of ≲100 nm, and are coordinated with transcriptional bursts. Enhancers and promoters find one another not only through passive diffusion; we often directly observe them being actively brought together by cohesin-mediated loop extrusion, which is a key determinant of transcriptional burst frequency. We also discover that specific general transcription factors (GTFs) of RNA polymerase II machinery are key to initiating transcriptional bursts, and enhancer-promoter interactions activate bursting by embedding the promoter within GTF clusters that form at the enhancers. Our results resolve the molecular and biochemical signals involved in long-range gene activation and elucidate the biophysical mechanisms for their transmission from the enhancer to the promoter.