Transcriptional Responses to IFN-γ Require Mediator Kinase-Dependent Pause Release and Mechanistically Distinct CDK8 and CDK19 Functions

Mol Cell. 2019 Nov 7;76(3):485-499.e8. doi: 10.1016/j.molcel.2019.07.034.

Iris Steinparzer ¹, Vitaly Sedlyarov ², Jonathan D Rubin ³, Kevin Eislmayr ¹, Matthew D Galbraith ⁴, Cecilia B Levandowski ³, Terezia Vcelkova ¹, Lucy Sneezum ¹, Florian Wascher ¹, Fabian Amman ⁵, Renata Kleinova ¹, Heather Bender ⁶, Zdenek Andrysik ⁶, Joaquin M Espinosa ⁴, Giulio Superti-Furga ⁷, Robin D Dowell ⁸, Dylan J Taatjes ⁹, Pavel Kovarik ¹⁰

Affiliations

1 Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, Vienna, Austria.
2 CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
3 Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA.
4 Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
5 Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, Vienna, Austria; Department of Theoretical Chemistry of the University of Vienna, 1090 Vienna, Austria.
6 Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
7 CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
8 BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA; Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA.
9 Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA. Electronic address: [email protected].
10 Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, Vienna, Austria. Electronic address: [email protected].

PMID: 31495563 DOI: 10.1016/j.molcel.2019.07.034

Abstract

Transcriptional responses to external stimuli remain poorly understood. Using global nuclear run-on followed by Sequencing (GRO-seq) and precision nuclear run-on Sequencing (PRO-seq), we show that CDK8 kinase activity promotes RNA polymerase II pause release in response to interferon-γ (IFN-γ), a universal cytokine involved in immunity and tumor surveillance. The Mediator kinase module contains CDK8 or CDK19, which are presumed to be functionally redundant. We implemented cortistatin A, chemical genetics, transcriptomics, and Other methods to decouple their function while assessing enzymatic versus structural roles. Unexpectedly, CDK8 and CDK19 regulated different gene sets via distinct mechanisms. CDK8-dependent regulation required its kinase activity, whereas CDK19 governed IFN-γ responses through its scaffolding function (i.e., it was kinase independent). Accordingly, CDK8, not CDK19, phosphorylates the STAT1 transcription factor (TF) during IFN-γ stimulation, and CDK8 kinase inhibition blocked activation of JAK-STAT pathway TFs. Cytokines such as IFN-γ rapidly mobilize TFs to "reprogram" cellular transcription; our results implicate CDK8 and CDK19 as essential for this transcriptional reprogramming.

Keywords

CDK19; CDK8; Mediator kinase; RNA polymerase II; STAT1; cortistatin A; eRNA; interferon; promoter-proximal pausing; transcription.

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