Analog-sensitive cell line identifies cellular substrates of CDK9

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

Research output: Contribution to journalArticlepeer-review

18 Scopus citations


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.

Original languageEnglish
Pages (from-to)6934-6943
Number of pages10
Issue number65
StatePublished - 2019
Externally publishedYes


  • CDK9
  • Phosphoproteomics
  • Protein kinase
  • RNA splicing
  • Transcription


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