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

Abstract

Highlights d Mediator kinases CDK8 and CDK19 are distinct transcription regulators in the IFN-g pathway d CDK8 acts as a kinase while CDK19 functions as a scaffold in driving IFN-g gene profiles d CDK8 and CDK19 activate distinct gene sets d Mediator kinase CDK8 promotes polymerase II pause release during the IFN-g response

Structure and mechanism of the RNA polymerase II transcription machinery

“…Although Mediator binds Pol II within the PIC (Bernecky et al 2011;Plaschka et al 2015;Robinson et al 2016;Schilbach et al 2017), Mediator association with the kinase module prevents this interaction (Elmlund et al 2006;Knuesel et al 2009a;Ebmeier and Taatjes 2010). These results suggest that the Mediator kinase module may function at postinitiation stages of Pol II transcription, and this is supported by cellular and biochemical data (Donner et al 2010;Galbraith et al 2013;Steinparzer et al 2019). Furthermore, SILAC-MS experiments reveal several postinitiation regulatory factors as high-confidence Mediator kinase substrates (Poss et al 2016), including NELFA.…”

“…Furthermore, SILAC-MS experiments reveal several postinitiation regulatory factors as high-confidence Mediator kinase substrates (Poss et al 2016), including NELFA. In support, inhibition of CDK8 kinase activity increases Pol II promoter-proximal pausing in mouse and human cells (Steinparzer et al 2019). In addition to their enzymatic functions, it appears that CDK8 and its paralog CDK19 have key structural/scaffolding roles in mammals, although molecular details remain unclear.…”

“…In addition to their enzymatic functions, it appears that CDK8 and its paralog CDK19 have key structural/scaffolding roles in mammals, although molecular details remain unclear. Gene expression changes are markedly different upon CDK8 kinase inhibition compared with subunit knockdown (Poss et al 2016), and CDK19 in particular appears to function as a structural scaffold, whereas its kinase activity is less consequential (Audetat et al 2017;Steinparzer et al 2019).…”

Manipulating the Mediator complex to induce naïve pluripotency

“…Later in the transcription cycle, following recruitment of RNA Pol II to Mediator, the pre-initiation complex is completed, and CDK8/19-Mediator undergoes further structural re-arrangements to participate in the release of RNA Pol II into productive elongation [ 8 , 9 , 18 , 19 ]. CDK8/19 has been reported to phosphorylate RNA Pol II directly in vitro [ 36 , 37 ], and to affect Pol II-CTD phosphorylation in vivo [ [40] , [41] , [42] , [43] , [44] , [45] ]. Also, CDK8/19 is reported to phosphorylate and orchestrate the function of positive and negative elongations factors including NELF, DSIF, TFIIH and the super-elongation complex [ 8 , 9 ].…”

“…However, we suggest that these reported roles of CDK8/19-mediated phosphorylation in elongation may be to some extent redundant, gene-specific, and/or compensated by other kinases such as CDK7 and CDK9. In this regard, we and others have used potent CDK8/19 small molecule inhibitors where transcription is modulated but can still proceed and cells are viable [ 10 , 30 , 35 , [43] , [44] , [45] , [46] ]. Here, it is notable that while the other transcriptional CDKs, namely CDK7 and CDK9, play general roles positively promoting transcriptional elongation, the role of CDK8/19 appears more nuanced.…”