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Regulatory Functions of the Mediator Kinases CDK8 and CDK19 Charli B

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Regulatory Functions of the Mediator Kinases CDK8 and CDK19 Charli B TRANSCRIPTION 2019, VOL. 10, NO. 2, 76–90 https://doi.org/10.1080/21541264.2018.1556915 REVIEW Regulatory functions of the Mediator kinases CDK8 and CDK19 Charli B. Fant and Dylan J. Taatjes Department of Biochemistry, University of Colorado, Boulder, CO, USA ABSTRACT ARTICLE HISTORY The Mediator-associated kinases CDK8 and CDK19 function in the context of three additional Received 19 September 2018 proteins: CCNC and MED12, which activate CDK8/CDK19 kinase function, and MED13, which Revised 13 November 2018 enables their association with the Mediator complex. The Mediator kinases affect RNA polymerase Accepted 20 November 2018 II (pol II) transcription indirectly, through phosphorylation of transcription factors and by control- KEYWORDS ling Mediator structure and function. In this review, we discuss cellular roles of the Mediator Mediator kinase; enhancer; kinases and mechanisms that enable their biological functions. We focus on sequence-specific, transcription; RNA DNA-binding transcription factors and other Mediator kinase substrates, and how CDK8 or CDK19 polymerase II; chromatin may enable metabolic and transcriptional reprogramming through enhancers and chromatin looping. We also summarize Mediator kinase inhibitors and their therapeutic potential. Throughout, we note conserved and divergent functions between yeast and mammalian CDK8, and highlight many aspects of kinase module function that remain enigmatic, ranging from potential roles in pol II promoter-proximal pausing to liquid-liquid phase separation. Introduction and MED13L associate in a mutually exclusive fash- ion with MED12 and MED13 [12], and their poten- The CDK8 kinase exists in a 600 kDa complex tial functional distinctions remain unclear. known as the CDK8 module, which consists of four CDK8 is considered both an oncogene [13–15] proteins (CDK8, CCNC, MED12, MED13). The and a tumor suppressor[16], indicative of its cell- CDK8 module associates with regulatory sites on type and context-specific roles. Through mechan- a genome-wide scale [1–3], and global targeting of isms that remain incompletely understood, human the CDK8 module appears to reflect its association CDK8 promotes cell growth via the serum with the 26-subunit Mediator complex[4]. CDK8 response pathway [17] and also functions to main- module–Mediator association is reversible [5–7] tain both tumors and embryonic stem cells in an but stable, and distinct populations of “CDK8- undifferentiated state[18]. Further highlighting the Mediator” complexes can be biochemically purified basic role for CDK8 in cell proliferation and devel- [8,9]. The Mediator–CDK8 module interaction opment, knockout of CDK8 in flies or mice is occurs via MED13 [10,11] and an undefined set of embryonic lethal [19,20]. Mediator subunits. A paralog of CDK8, called In this review, we describe the functional roles of CDK19, emerged in vertebrates and has high the Mediator kinases CDK8 and CDK19 and propose sequence similarity to CDK8, including near- speculative models for how they might regulate pol II identical cyclin binding and kinase domains. transcription in various contexts. We start with tran- Comparatively little is known about CDK19; how- scriptional reprogramming and enhancer-promoter ever, it appears to assemble into an analogous looping and then transition to metabolism. Next, we “CDK19 module” (i.e. CDK19, CCNC, MED12, discuss small molecule inhibitors, which have yielded MED13)[12]. In addition to CDK19, paralogs for valuable insights about CDK8 and CDK19 function. MED12 and MED13 (MED12L and MED13L) We conclude with sections devoted to the mechanism emerged in vertebrates. Unlike CDK19, the MED12 of action of Mediator kinases, in the context of the and MED13 paralogs are more divergent in four-subunit kinase module and the 29-subunit sequence, with only 59% and 53% sequence identity, CDK8-Mediator complex. respectively. The kinase module paralogs MED12L CONTACT Dylan J. Taatjes [email protected] © 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives License (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited, and is not altered, transformed, or built upon in any way. TRANSCRIPTION 77 Mediator kinases, enhancers, and CDK19 protein levels [1,17] or inhibition of transcriptional reprogramming CDK8 and CDK19 kinase activity [46,48,49] does Sequence-specific, DNA-binding transcription fac- not globally affect steady-state mRNA levels; tors (TFs) are major drivers of cell physiology and rather, only subsets of genes are affected that cell state[21]. As examples of their biological influ- vary with context (e.g. hypoxia) or cell type. ence, fibroblasts can be converted into myotubes How can these results be reconciled? Although upon expression of a single TF, MyoD[22], and the mechanistic roles of Mediator kinases remain various combinations of TFs can reprogram enigmatic (see below), we speculate that CDK8 and somatic cells to a pluripotent state [23–27]. CDK19 regulate pol II transcription, in part, Consistent with these themes, specific sets of TFs through enhancers and enhancer-promoter com- define each cell type and enforce expression of cell munication (Figure 1). Whereas the human gen- type-specific genes [28–32]. Current models of ome contains an estimated fifty- to sixty-thousand “ ” how TFs establish and maintain cell type-specific enhancers[50], only a subset of these will be active gene expression patterns involve TF binding to in any given cell type[51], and this is dependent clustered sites at enhancer and promoter regions. upon chromatin structure and TF binding[52]. This concentrated, localized TF binding recruits Enhancers are cell type-specific and active enhan- factors such as Mediator and cohesin to help cers reflect the lineage-specific TFs that bind form and stabilize enhancer-promoter loops [2,3]; enhancer sequences [38,53]. Although the process these loops, in turn, promote high-level expression of enhancer activation remains incompletely of cell type-specific genes [33,34], many of which understood, it coincides with TF binding and bidir- include the lineage-specific TFs required to initiate ectional transcription of enhancer RNAs (eRNAs) the feed-forward cascade[35]. The importance of [54]. Accordingly, bidirectional eRNA transcrip- enhancer-promoter interactions (via formation of tion is cell type-specific[55]. Interestingly, changes stable chromatin loops) is underscored by the fact in eRNA transcription appear to be a seminal event – that looped architectures change during develop- in response to signaling cascades [56 58]. This mental transitions [36–38] and their disruption is rapid, bidirectional eRNA transcriptional response, pathogenic [39,40]. ChIP-Seq data suggest which is triggered by stimulus-specific TFs[55], can Mediator occupies promoter and enhancer regions occur within minutes of a stimulus, and correlates genome-wide, and is especially abundant at super- with a re-organization of enhancer-promoter con- “ ” enhancers [41,42]. In fact, occupancy of the tacts and a reprogramming of gene expression Mediator subunit MED1 is considered a marker networks [59,60]. for super-enhancers, along with H3K27Ac and The CDK8 module may be an essential compo- BRD4 [43]. Super-enhancers represent clusters of nent of this rapid enhancer response, based upon enhancers that form interconnected hubs with a number of observations [61]. CDK8 occupies other enhancer and promoter sequences to sup- enhancer elements genome-wide[48], and CDK8 port high levels of gene expression[44]. (and/or CDK19) phosphorylates TFs that bind The Mediator kinases CDK8 and CDK19 regu- enhancer elements[62]. TF phosphorylation by late TF function through phosphorylation [45,46]; Mediator kinases has been shown to alter TF activity in addition, Mediator appears to be required for [45,46]; TF activity, in turn, correlates with expres- expression of most, if not all, pol II transcripts in sion of bidirectional, enhancer-associated eRNAs mammalian genomes, and ChIP-Seq experiments [54,55,57]. The expression of eRNAs also correlates indicate that the CDK8 module co-localizes with with formation of enhancer-promoter loops[63], Mediator genome-wide [2,3], including at super- and may function, at least in part, through direct enhancers [41,47,48]. Based upon these observa- interactions with the CDK8-Mediator complex[64]. tions, a reasonable expectation is that disruption of Each of these activities (formation of enhancer- CDK8 and/or CDK19 function would markedly promoter loops, eRNA transcription, TF phosphor- impact global gene expression patterns. Contrary ylation) can contribute to the establishment of new to these expectations, knockdown of CDK8 or gene expression programs, whether during cellular differentiation or in response to signaling cascades. 78 C. B. FANT AND D. J. TAATJES (a) (b) I I gene B RNA gene D POL II CTD MED PIC POL II K POL II K PIC RNA MED POL II MED CTD PIC CTD ENHANCER POL II RNA ENHANCER CTD POL II POL II RNA gene A PIC MED bursting/ gene C I re-initiation I Figure 1. Speculative models for CDK8 or CDK19 module function at mammalian enhancers. a) CDK8 or CDK19 module (“K”) association with an enhancer (e.g. via TF binding) enables its interaction with promoters that are juxtaposed via chromatin loops. This
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