Analog-sensitive cell line identifies cellular substrates of CDK9
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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
Keywords: CDK9; protein kinase; transcription; RNA splicing; phosphoproteomics
Received: September 12, 2019 Accepted: November 07, 2019 Published: December 10, 2019
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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