Sequential verification of transcription by Integrator and Restrictor

Abstract

The decision between productive elongation and premature termination of promoter-proximal RNA polymerase II (RNAPII) is fundamental to metazoan gene regulation. Integrator and Restrictor complexes are implicated in promoter-proximal termination, but why metazoans utilize two complexes and how they are coordinated remains unknown. Here, we show that Integrator and Restrictor act sequentially to monitor distinct stages of transcription. Integrator predominantly engages with promoter-proximally paused RNAPII to trigger premature termination, which is prevented by cyclin-dependent kinase 7/9 activity. After pause release, RNAPII enters a “restriction zone”—universally imposed by Restrictor. Unproductive RNAPII terminates within this zone, while progression through it is promoted by U1 small nuclear ribonucleoprotein particles (snRNPs), which antagonize Integrator and Restrictor in a U1-70K-dependent manner. These findings reveal the principles of a sequential verification mechanism governing the balance between productive and attenuated transcription, rationalizing the necessity of Integrator and Restrictor complexes in metazoans.