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

Jenna K. Rimel, Zachary C. Poss, Benjamin Erickson, Zachary L. Maas, Christopher C. Ebmeier, Jared L. Johnson, Tim Michael Decker, Tomer M. Yaron, Michael J. Bradley, Kristin B. Hamman, Shanhu Hu, Goran Malojcic, Jason J. Marineau, Peter W. White, Martine Brault, Limei Tao, Patrick DeRoy, Christian Clavette, Shraddha Nayak, Leah J. DamonInes H. Kaltheuner, Heeyoun Bunch, Lewis C. Cantley, Matthias Geyer, Janet Iwasa, Robin D. Dowell, David L. Bentley, William M. Old, Dylan J. Taatjes

Research output: Contribution to journalArticlepeer-review

47 Scopus citations

Abstract

CDK7 associates with the 10-subunit TFIIH complex and regulates transcription by phosphorylating the C-terminal domain (CTD) ofRNApolymerase II (RNAPII). Fewadditional 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 newmodels for CDK7 function in transcription and implicateCAKdissociation fromTFIIH 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.

Original languageEnglish
Pages (from-to)1452-1473
Number of pages22
JournalGenes and Development
Volume34
Issue number21-22
DOIs
StatePublished - 1 Nov 2020
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2020 Rimel et al.

Funding

We thank R. Tjian for ERCC3 antibodies, W.L. Kraus for NELF expression plasmids, R. Fisher for SPT4 and SPT5 expression plasmid, and the UC-Boulder BioFrontiers Computing Core (National Institutes of Health [NIH] OD12300). Funding support was provided by the NIH (GM118051 to D.L.B., GM110064 to D.J.T., and T32GM065103 to L.J.D.), the National Cancer Institute (R21CA205912 to W.M.O. and D.J.T., and F31CA250432 to J.K.R.), the German Research Foundation (DFG; DE 3069/1-1 to T.M.D., and GE 976/9-2 to M.G.), and the National Science Foundation (MCB1818147 to D.J.T., ABI1759949 to R.D.D., and MCB1903300 to J.I.). D.J.T. is a member of the SAB at Dewpoint Therapeutics. The laboratory of D.J.T. receives some support from Syros Pharmaceuticals. L.C.C. is a founder and member of the SAB of Agios Pharmaceuticals and of Petra Pharmaceuticals. These companies are developing novel therapies for cancer. L.C.C.’s laboratory also receives some financial support from Petra Pharmaceuticals. J.L.J. reports consultant activities for Petra Pharmaceuticals. T.M.Y. is a stockholder and on the board of directors of Destroke, Inc., an early-stage start-up developing mobile technology for automated clinical stroke detection. M.J.B., K.B.H., S.H., G.M., and J.J.M. have or had an equity position in Syros Pharmaceuticals, Inc.

FundersFunder number
Petra Pharmaceuticals
UC-Boulder BioFrontiers Computing Core
National Science FoundationMCB1818147, MCB1903300, ABI1759949
National Institutes of HealthGM118051, T32GM065103, GM110064
NIH Office of the DirectorS10OD012300
National Cancer InstituteF31CA250432, R21CA205912
Deutsche ForschungsgemeinschaftGE 976/9-2, DE 3069/1-1

    Keywords

    • CDK12
    • CDK13
    • CDK7
    • CDK9
    • Kinase inhibitor
    • SF3B1
    • SILAC-MS
    • Splicing
    • TFIIH
    • Transcription

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