Oncotarget

Research Papers:

Analog-sensitive cell line identifies cellular substrates of CDK9

Tim-Michael Decker _, Ignasi Forné, Tobias Straub, Hesham Elsaman, Guoli Ma, Nilay Shah, Axel Imhof and Dirk Eick _

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Oncotarget. 2019; 10:6934-6943. https://doi.org/10.18632/oncotarget.27334

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Abstract

Tim-Michael Decker1,4, Ignasi Forné2, Tobias Straub3, Hesham Elsaman1, Guoli Ma1, Nilay Shah1,5, Axel Imhof2 and Dirk Eick1

1 Department of Molecular Epigenetics, Helmholtz Center Munich and Center for Integrated Protein Science Munich (CIPSM), Germany

2 Biomedical Center Munich, ZFP, Ludwig-Maximilian University Munich, Germany

3 Bioinformatic Unit, Biomedical Center Munich, Ludwig-Maximilian University Munich, Planegg-Martinsried, Germany

4 Present address: Department of Biochemistry, University of Colorado, Boulder, USA

5 Present address: Stowers Institute for Medical Research, Kansas City, Missouri, USA

Correspondence to:

Tim-Michael Decker,email: timmichael.decker@colorado.edu
Dirk Eick,email: eick@helmholtz-muenchen.de

Keywords: CDK9; protein kinase; transcription; RNA splicing; phosphoproteomics

Received: September 12, 2019     Accepted: November 07, 2019     Published: December 10, 2019

ABSTRACT

Transcriptional cyclin-dependent kinases regulate all phases of transcription. Cyclin-dependent kinase 9 (CDK9) has been implicated in the regulation of promoter-proximal pausing of RNA polymerase II and more recently in transcription termination. Study of the substrates of CDK9 has mostly been limited to in vitro approaches that lack a quantitative assessment of CDK9 activity. Here we analyzed the cellular phosphoproteome upon inhibition of CDK9 by combining analog-sensitive kinase technology with quantitative phosphoproteomics in Raji B-cells. Our analysis revealed the activity of CDK9 on 1102 phosphosites quantitatively, and we identified 120 potential cellular substrates. Furthermore, a substantial number of CDK9 substrates were described as splicing factors, highlighting the role of CDK9 in transcription-coupled splicing events. Based on comparison to in vitro data, our findings suggest that cellular context fundamentally impacts the activity of CDK9 and specific selection of its substrates.


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