Oral Presentation 46th Lorne Genome Conference 2025

CDK11-dependent control of RNA polymerase II pausing at a new transcription cycle checkpoint (114341)

Jennifer Devlin 1 2 , Ben Martin 1 , Nenad Bartonicek 1 2 , Keziah Ting 2 3 , Zheng Fan 4 , Izabela Todorovski 5 , Peter Fraser 3 , Andrea Newbold 1 , Kaylene J Simpson 2 3 , Matthias Geyer 6 , Stephin J Vervoort 7 , Ricky W Johnstone 1 2
  1. Gene Regulation Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
  2. The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
  3. Laboratory Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
  4. The Institute of Cancer Research, Sutton, UK
  5. Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
  6. Institute of Structural Biology, University of Bonn, Bonn, Germany
  7. The Walter and Eliza Hall Institute, Parkville, VIC, Australia

RNA polymerase II (Pol II) transcription is a highly regulated process ensuring controlled gene expression and normal cellular homeostasis. Transcriptional dysregulation, which can arise through an array of molecular mechanisms, underpins all human disease including cancer [1,2]. A family of transcriptional cyclin-dependent-kinases (tCDKs) modulate Pol II progression through distinct phases of ‘Transcription Cycles’, including Pol II recruitment, transcriptional initiation, pausing and pause-release, elongation, and termination. The ability of Pol II to progress through each of these transcription cycle checkpoints has been linked to the catalytic activity of distinct tCDKs. While the critical contribution of CDK9 for Pol II release from pausing is well established, the requirement for other tCDKs at this rate-limiting transcription cycle checkpoint has not been fully explored [1,3,4]. 

We have identified a new role for CDK11, a comparatively understudied tCDK, for the control of Pol II pausing-to-elongation transition at a novel checkpoint that precedes the CDK9 regulatory site. Using complementary pharmacological and chemical-genetic approaches in combination with steady-state and nascent next-generation-sequencing approaches, we demonstrate that acute disruption of CDK11 activity results in rapid and robust ablation of RNA synthesis near the beginning of transcriptional units, and genome-wide stalling of Pol II at transcription-start-site (TSS) proximal regions. High-resolution Pol II chromatin immunoprecipitation and precision-nuclear-run-on transcriptomic assays reveal significant spatial differences between CDK11- and CDK9-dependent Pol II pause sites, with CDK11 regulating Pol II upstream of the CDK9 checkpoint within the pausing zone. Cancer cells exhibit profound reliance on functional CDK11, with selective CDK11 inhibition providing therapeutic efficacy in pre-clinical in vivo models of leukaemia and lymphoma, demonstrating the importance of CDK11-dependent Pol II regulation for aggressive haematological malignancies.

This study thus reveals an additional regulatory layer within the already complex molecular landscape governing Pol II dependent gene-expression that may be strategically targeted for therapeutic benefit.

  1. [1] Targeting transcription cycles in cancer S. J. Vervoort, J. R. Devlin, N. Kwiatkowski, M. Teng, N. S. Gray and R. W. Johnstone Nature Reviews Cancer 2022 Vol. 22 Issue 1 Pages 5-24
  2. [2] Transcriptional Addiction in Cancer J. E. Bradner, D. Hnisz and R. A. Young Cell 2017 Vol. 168 Issue 4 Pages 629-643
  3. [3] Dissecting the Pol II transcription cycle and derailing cancer with CDK inhibitors P. K. Parua and R. P. Fisher Nat Chem Biol 2020 Vol. 16 Issue 7 Pages 716-724
  4. [4]The PP2A-Integrator-CDK9 axis fine-tunes transcription and can be targeted therapeutically in cancer S. J. Vervoort, S. A. Welsh, J. R. Devlin, E. Barbieri, D. A. Knight, S. Offley, et al. Cell 2021 Vol. 184 Issue 12 Pages 3143-3162.e32