INTS12 Bridges Integrator and NELF to Prevent the Release of Non-processive RNA Polymerase II Complexes

Summary Promoter-proximal RNA Polymerase II (RNAPII) pausing and the processivity are controlled by distinct modules of the Integrator complex, which together fine-tune transcription and protect against the accumulation of defective RNAPII complexes. Compromised activity of individual Integrator modules has been linked to human disease including cancer and developmental disorders, caused by defective transcription of protein-coding or small-nuclear RNAs. Despite extensive characterisation of the Integrator complex both genetically and structurally, the role of smallest member of the complex, INTS12, has remained enigmatic. Here, we uncover that INTS12 loss acts to stabilise the association between NELF and Integrator via its PHD domain and N-terminus, respectively, thus safeguarding against the release of defective RNAPII complexes. Acute degradation of INTS12 results in the selective dissociation of Integrator from the NELF-RNAPII complex which subsequently convert to their canonical paused form from which they can be released by CDK9. In the absence of INTS12 excess release of defective RNAPII via P-TEFb/SEC, loss of the ARMC5 salvage pathway and deletion of the catalytic and core Integrator subunits is toxic to cells. These findings demonstrate that there is interconversion between canonical paused RNAPII and paused-Integrator, and highlight the critical interplay between these processes and P-TEFb mediated pause-release to ensure that only transcription competent complexes are released into elongation. INTS12 degradation confers CDK9 inhibitor resistance and triggers cellular stress through a phosphatase module-independent mechanism. INTS12 stabilizes the Integrator-NELF complex through its N-terminus and PHD domain. Acute INTS12 degradation promotes aberrant release of promoter-proximal RNA polymerase II complexes. RNA polymerase II complexes released upon INTS12 loss exhibit defective elongation and reduced processivity. INTS12 loss removes Integrator from RNAPII resulting in aberrant paused-state from which it can be released by CDK9. Excess CDK9 activity and ARMC5 loss are synthetically lethal with INTS12 deficiency. Competing Interest Statement The authors have declared no competing interest.