Article | Published:

Cyclin-dependent kinase control of the initiation-to-elongation switch of RNA polymerase II

Nature Structural & Molecular Biology volume 19, pages 11081115 (2012) | Download Citation

Abstract

Promoter-proximal pausing by RNA polymerase II (Pol II) ensures gene-specific regulation and RNA quality control. Structural considerations suggested a requirement for initiation-factor eviction in elongation-factor engagement and pausing of transcription complexes. Here we show that selective inhibition of Cdk7—part of TFIIH—increases TFIIE retention, prevents DRB sensitivity–inducing factor (DSIF) recruitment and attenuates pausing in human cells. Pause release depends on Cdk9–cyclin T1 (P-TEFb); Cdk7 is also required for Cdk9-activating phosphorylation and Cdk9-dependent downstream events—Pol II C-terminal domain Ser2 phosphorylation and histone H2B ubiquitylation—in vivo. Cdk7 inhibition, moreover, impairs Pol II transcript 3′-end formation. Cdk7 thus acts through TFIIE and DSIF to establish, and through P-TEFb to relieve, barriers to elongation: incoherent feedforward that might create a window to recruit RNA-processing machinery. Therefore, cyclin-dependent kinases govern Pol II handoff from initiation to elongation factors and cotranscriptional RNA maturation.

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Acknowledgements

We thank Y. Ramanathan, N. Barboza, N. Downing, A.D. Kostic and A. Searleman for assistance in the early phases of this project and Z. F. Burton (Michigan State University, East Lansing, Michigan, USA) for the TFIIE expression constructs. R.A. was supported by a Beatriu de Pinos fellowship of the Generalitat de Catalunya. This work was supported by the US National Institutes of Health grants GM056985 to R.P.F., GM063873 to D.L.B. and EB001987 to K.M.S.

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Affiliations

  1. Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, USA.

    • Stéphane Larochelle
    • , Ramon Amat
    • , Miriam Sansó
    •  & Robert P Fisher
  2. Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA.

    • Kira Glover-Cutter
    •  & David L Bentley
  3. Department of Chemistry, University of Southern California, Los Angeles, Los Angeles, California, USA.

    • Chao Zhang
  4. Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA.

    • Jasmina J Allen
    •  & Kevan M Shokat
  5. Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California, USA.

    • Jasmina J Allen
    •  & Kevan M Shokat

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Contributions

S.L., D.L.B. and R.P.F. designed the research and interpreted data. S.L., R.A., K.G.-C. and M.S. performed experiments and analyzed data. J.J.A., C.Z. and K.M.S. provided reagents. S.L. and R.P.F. wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Robert P Fisher.

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DOI

https://doi.org/10.1038/nsmb.2399

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