Multi-omics and biochemical reconstitution reveal CDK7-dependent mechanisms controlling RNA polymerase II function at gene 5′- and 3′ ends
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 inh...
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| Language: | English |
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Elsevier
2025-07-01
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| Series: | Cell Reports |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2211124725006758 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Olivia Luyties |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-e89387f543d049239ed84be19d97efa6 |
| institution | Kabale University |
| issn | 2211-1247 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Cell Reports |
| spelling | doaj-art-e89387f543d049239ed84be19d97efa62025-08-20T03:32:01ZengElsevierCell Reports2211-12472025-07-0144711590410.1016/j.celrep.2025.115904Multi-omics and biochemical reconstitution reveal CDK7-dependent mechanisms controlling RNA polymerase II function at gene 5′- and 3′ endsOlivia Luyties0Lynn Sanford1Jessica Rodino2Michael Nagel3Taylor Jones4Jenna K. Rimel5Christopher C. Ebmeier6Megan Palacio7Grace S. Shelby8Kira Cozzolino9Finn Brennan10Axel Hartzog11Mirzam B. Saucedo12Lotte P. Watts13Sabrina Spencer14Jennifer F. Kugel15Robin D. Dowell16Dylan J. Taatjes17Department of Biochemistry, University of Colorado, Boulder, CO 80303, USADepartment of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USADepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USADepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USADepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USADepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USADepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USADepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USADepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USADepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USADepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USADepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USADepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USADepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USADepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USADepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USADepartment of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USADepartment of Biochemistry, University of Colorado, Boulder, CO 80303, USA; Corresponding authorSummary: 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.http://www.sciencedirect.com/science/article/pii/S2211124725006758CP: Molecular biology |
| spellingShingle | 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 Multi-omics and biochemical reconstitution reveal CDK7-dependent mechanisms controlling RNA polymerase II function at gene 5′- and 3′ ends Cell Reports CP: Molecular biology |
| title | Multi-omics and biochemical reconstitution reveal CDK7-dependent mechanisms controlling RNA polymerase II function at gene 5′- and 3′ ends |
| title_full | Multi-omics and biochemical reconstitution reveal CDK7-dependent mechanisms controlling RNA polymerase II function at gene 5′- and 3′ ends |
| title_fullStr | Multi-omics and biochemical reconstitution reveal CDK7-dependent mechanisms controlling RNA polymerase II function at gene 5′- and 3′ ends |
| title_full_unstemmed | Multi-omics and biochemical reconstitution reveal CDK7-dependent mechanisms controlling RNA polymerase II function at gene 5′- and 3′ ends |
| title_short | Multi-omics and biochemical reconstitution reveal CDK7-dependent mechanisms controlling RNA polymerase II function at gene 5′- and 3′ ends |
| title_sort | multi omics and biochemical reconstitution reveal cdk7 dependent mechanisms controlling rna polymerase ii function at gene 5 and 3 ends |
| topic | CP: Molecular biology |
| url | http://www.sciencedirect.com/science/article/pii/S2211124725006758 |
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