2. Academic Validation
  3. Selective inhibition of CDK7 reveals high-confidence targets and new models for TFIIH function in transcription

Selective inhibition of CDK7 reveals high-confidence targets and new models for TFIIH function in transcription

  • Genes Dev. 2020 Nov 1;34(21-22):1452-1473. doi: 10.1101/gad.341545.120.
Jenna K Rimel # 1,  Zachary C Poss # 2,  Benjamin Erickson 3 4,  Zachary L Maas 1 2 5,  Christopher C Ebmeier 2,  Jared L Johnson 6,  Tim-Michael Decker 1,  Tomer M Yaron 6 7 8 9,  Michael J Bradley 10,  Kristin B Hamman 10,  Shanhu Hu 10,  Goran Malojcic 10,  Jason J Marineau 10,  Peter W White 11,  Martine Brault 11,  Limei Tao 11,  Patrick DeRoy 11,  Christian Clavette 11,  Shraddha Nayak 12,  Leah J Damon 1 5,  Ines H Kaltheuner 13,  Heeyoun Bunch 14,  Lewis C Cantley 6,  Matthias Geyer 13,  Janet Iwasa 12,  Robin D Dowell 2 5,  David L Bentley 3 4,  William M Old 2,  Dylan J Taatjes 1
Affiliations

Affiliations

  • 1 Department of Biochemistry, University of Colorado, Boulder, Colorado 80303, USA.
  • 2 Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA.
  • 3 Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA.
  • 4 UC-Denver RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA.
  • 5 BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA.
  • 6 Meyer Cancer Center, Weill Cornell Medicine, New York, New York 10065, USA.
  • 7 Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York 10065, USA.
  • 8 Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York 10065, USA.
  • 9 Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York 10065, USA.
  • 10 Syros Pharmaceuticals, Massachusetts 02140 USA.
  • 11 Paraza Pharma, Inc., Montreal, Quebec H4S 1Z9, Canada.
  • 12 Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, USA.
  • 13 Institute of Structural Biology, University of Bonn, Bonn 53127, Germany.
  • 14 School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea.
  • # Contributed equally.
PMID: 33060135 DOI: 10.1101/gad.341545.120
Abstract

CDK7 associates with the 10-subunit TFIIH complex and regulates transcription by phosphorylating the C-terminal domain (CTD) of RNA polymerase II (RNAPII). Few additional CDK7 substrates are known. Here, using the covalent inhibitor SY-351 and quantitative phosphoproteomics, we identified CDK7 kinase substrates in human cells. Among hundreds of high-confidence targets, the vast majority are unique to CDK7 (i.e., distinct from Other transcription-associated kinases), with a subset that suggest novel cellular functions. Transcription-associated factors were predominant CDK7 substrates, including SF3B1, U2AF2, and Other splicing components. Accordingly, widespread and diverse splicing defects, such as alternative exon inclusion and intron retention, were characterized in CDK7-inhibited cells. Combined with biochemical assays, we establish that CDK7 directly activates Other transcription-associated kinases CDK9, CDK12, and CDK13, invoking a "master regulator" role in transcription. We further demonstrate that TFIIH restricts CDK7 kinase function to the RNAPII CTD, whereas Other substrates (e.g., SPT5 and SF3B1) are phosphorylated by the three-subunit CDK-activating kinase (CAK; CCNH, MAT1, and CDK7). These results suggest new models for CDK7 function in transcription and implicate CAK dissociation from TFIIH as essential for kinase activation. This straightforward regulatory strategy ensures CDK7 activation is spatially and temporally linked to transcription, and may apply toward Other transcription-associated kinases.

Keywords

CDK12; CDK13; CDK7; CDK9; SF3B1; SILAC-MS; TFIIH; kinase inhibitor; splicing; transcription.

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