Loop extrusion creates rare, long-lived encounters underlying enhancer-promoter communication

Enhancers regulate transcription from distal genomic positions, but how their spatial encounters with promoters drive activation remains unclear. Using polymer simulations and high-resolution live-cell microscopy, we identify rare but long-lived chromatin encounters arising from cohesin-mediated loop extrusion. These events occur when cohesin loads near the midpoint between two loci and extrudes them through a defined spatial radius, producing encounter durations that exceed those of random collisions. We show that such encounters explain observed nonlinear relationships between contact probability and transcription, and accurately predict transcriptional changes upon perturbation of cohesin or its cofactors. Our findings support a time-gated model of distal enhancer-promoter communication in which only rare, long-lived and mostly extrusion-driven encounters are productive, offering a unifying framework for how chromosome dynamics control transcription in single cells.