CRL3ARMC5 ubiquitin ligase and Integrator phosphatase form parallel mechanisms to control early stages of RNA Pol II transcription

Control of RNA polymerase II (RNA Pol II) through ubiquitylation is essential for the DNA-damage response. Here, we reveal a distinct ubiquitylation pathway in human cells, mediated by CRL3 ARMC5 , that targets excessive and defective RNA Pol II molecules at the initial stages of the transcription cycle. Upon ARMC5 loss, RNA Pol II accumulates in the free pool and in the promoter-proximal zone but is not permitted into elongation. We identify Integrator subunit 8 (INTS8) as a gatekeeper preventing the release of excess RNA Pol II molecules into gene bodies. Combined loss of ARMC5 and INTS8 has detrimental effects on cell growth and results in the uncontrolled release of excessive RNA Pol II complexes into early elongation, many of which are transcriptionally incompetent and fail to reach the ends of genes. These findings uncover CRL3 ARMC5 and Integrator as two distinct pathways acting in parallel to monitor the quantity and quality of transcription complexes before they are licensed into elongation. • CRL3 ARMC5 ubiquitylates RNA Pol II to regulate its levels off-DNA and at gene starts • CRL3 ARMC5 targets perturbed, incompetent RNA Pol II complexes • Integrator phosphatase compensates for the loss of ARMC5 • ARMC5 and Integrator prevent the release of incompetent RNA Pol II into late elongation Cacioppo, Gillis, Shlamovitz, Zeller, et al. show that CRL3 ARMC5 ubiquitylates RNA Pol II at early stages of transcription as part of a major homeostatic RNA Pol II turnover mechanism. CRL3 ARMC5 and the Integrator phosphatase act as complementary pathways, monitoring the quantity and quality of RNA Pol II complexes before they are licensed into elongation.