CDK7 kinase activity promotes RNA polymerase II promoter escape by facilitating initiation factor release

Cyclin-dependent kinase 7 (CDK7), part of the general transcription factor TFIIH, promotes gene transcription by phosphorylating the C-terminal domain of RNA polymerase II (RNA Pol II). Here, we combine rapid CDK7 kinase inhibition with multi-omics analysis to unravel the direct functions of CDK7 in human cells. CDK7 inhibition causes RNA Pol II retention at promoters, leading to decreased RNA Pol II initiation and immediate global downregulation of transcript synthesis. Elongation, termination, and recruitment of co-transcriptional factors are not directly affected. Although RNA Pol II, initiation factors, and Mediator accumulate at promoters, RNA Pol II complexes can also proceed into gene bodies without promoter-proximal pausing while retaining initiation factors and Mediator. Further downstream, RNA Pol II phosphorylation increases and initiation factors and Mediator are released, allowing recruitment of elongation factors and an increase in RNA Pol II elongation velocity. Collectively, CDK7 kinase activity promotes the release of initiation factors and Mediator from RNA Pol II, facilitating RNA Pol II escape from the promoter. [Display omitted] •CDK7 inhibition leads to an immediate global decrease in RNA Pol II transcript synthesis•RNA Pol II, initiation factors, and Mediator accumulate at promoters•Elongation, termination, and co-transcriptional factor recruitment remain unaffected•CDK7 promotes RNA Pol II promoter escape by releasing initiation factors and Mediator Velychko et al. show that CDK7 kinase activity is required for the efficient release of initiation factors and Mediator from RNA polymerase II (RNA Pol II), facilitating RNA Pol II release from the promoter region. This step is crucial for robust RNA synthesis of all genes and thus cellular activity.