Cohesin acts as a transcriptional gatekeeper by restraining pause–release to promote processive elongation

Cohesin organizes 3D chromatin architecture, including promoter–enhancer loops, yet its loss causes surprisingly modest changes in steady-state gene expression. We resolve this paradox by demonstrating that cohesin performs two opposing but balancing functions through genome-wide analyses and in vitro transcription complex reconstitution. First, it promotes transcription initiation by facilitating enhancer– promoter communication that maintains active promoter chromatin. Second, it acts as a transient gate that delays pause release by briefly associating with the transcriptional machinery during the pause–release transition. This gating occurs downstream of CDK9 and is relieved by cohesin’s ATPase-dependent turnover. Kinetic modelling shows that minimal changes in steady-state gene expression result from the counterbalance between reduced initiation and enhanced pause release. In contrast, cohesin depletion impairs robust transcriptional induction in response to external stimuli. Moreover, the cohesin-mediated delay in pause release serves as a quality-control-like step by promoting elongation complex assembly and transcription processivity. These insights have important implications for cohesin-related diseases, including cancers and cohesinopathies, and broader principles of transcriptional regulation.