Cohesin bridging as a physical principle of enhancer-promoter communication

Abstract

Central to genome function, enhancers are non-coding sequences that can control transcription from promoters hundreds of kilobases away. Yet the physical basis of this long-range communication remains unclear. A prevalent view is that enhancers activate promoters when the two elements come into spatial proximity through the 3D folding of chromatin. However, activation by spatial proximity alone has struggled to explain several core features of enhancer function. Here, we propose that the molecular motor cohesin transmits long-range enhancer action by forming bridges between enhancers and promoters during loop extrusion. In this view, rare and transient bridges carry regulatory communication, rather than mere spatial proximity. We develop a quantitative model that predicts transcriptional output from cohesin-bridging dynamics and validate it by engineering cells in which strategically positioned CTCF sites rewire loop extrusion trajectories. The model explains how enhancer action scales with genomic distance, and how it can be either facilitated or insulated by CTCF sites across two orders of magnitude-behaviors incompatible with proximity-based models. Finally, our framework reveals that CTCF sites can block enhancers bidirectionally, by either blocking or releasing cohesin loops, resolving longstanding paradoxes between their effects on transcriptional regulation and genome folding. Together, our results establish cohesin bridging as a mode of enhancer-promoter communication that can be modulated by genomic context to achieve selective and tunable transcriptional control over long genomic distances.