Multi-omics and biochemical reconstitution reveal CDK7-dependent mechanisms controlling RNA polymerase II function at gene 5′- and 3′ ends
Olivia Luyties,
Lynn Sanford,
Jessica Rodino,
Michael Nagel,
Taylor Jones,
Jenna K. Rimel,
Christopher C. Ebmeier,
Megan Palacio,
Grace S. Shelby,
Kira Cozzolino,
Finn Brennan,
Axel Hartzog,
Mirzam B. Saucedo,
Lotte P. Watts,
Sabrina Spencer,
Jennifer F. Kugel,
Robin D. Dowell,
Dylan J. Taatjes
Affiliations
Olivia Luyties
Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
Lynn Sanford
Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA
Jessica Rodino
Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
Michael Nagel
Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
Taylor Jones
Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
Jenna K. Rimel
Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
Christopher C. Ebmeier
Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
Megan Palacio
Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
Grace S. Shelby
Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
Kira Cozzolino
Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
Finn Brennan
Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
Axel Hartzog
Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
Mirzam B. Saucedo
Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
Lotte P. Watts
Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA
Sabrina Spencer
Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA
Jennifer F. Kugel
Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
Robin D. Dowell
Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA
Dylan J. Taatjes
Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA; Corresponding author
Summary: CDK7 regulates RNA polymerase II (RNAPII) initiation, elongation, and termination through incompletely understood mechanisms. Because contaminating kinases prevent reliable CDK7 analysis with nuclear extracts, we reconstitute RNAPII transcription with purified factors. We show that CDK7 inhibition slows and/or pauses RNAPII promoter-proximal transcription and suppresses re-initiation, and these effects are Mediator and TFIID dependent. Similarly in human cells, CDK7 inhibition reduces transcriptional output by suppressing RNAPII initiation and/or re-initiation. Moreover, widespread 3′ end readthrough transcription occurs in CDK7-inhibited cells; mechanistically, this results from rapid nuclear depletion of RNAPII elongation and termination factors (e.g., DSIF, Integrator, NELF, SPT6, PPP1R10/PNUTS, and SCAF8), including high-confidence CDK7 kinase targets. Collectively, these results define how CDK7 governs RNAPII function at gene 5′ ends and 3′ ends and reveal that nuclear abundance of elongation and termination factors is kinase dependent. Because 3′-readthrough transcription is commonly induced during stress, our results further suggest that regulated suppression of CDK7 activity enables this transcriptional response.
