The Mediator kinase module: an interface between cell signaling and transcription

Abstract

The Mediator complex controls RNA polymerase II (pol II) activity by coordinating the assembly of pol II regulatory factors at transcription start sites and by mediating interactions between enhancer-bound transcription factors (TFs) and the pol II enzyme. Mediator structure and function is completely altered upon binding the Mediator kinase module, a multi-subunit complex that contains CDK8 or its vertebrate-specific paralog CDK19. Here, we review the mechanisms by which the Mediator kinase module controls pol II transcription, emphasizing its impact on TF activity, pol II elongation, enhancer function, and chromatin architecture. We also highlight how the Mediator kinase module integrates signaling pathways with transcription to enable rapid, stimulus-specific responses, as well as its links to human disease.

Keywords: MED12; MED13; eRNA; enhancer-promoter loops; metabolism; pol II pausing.

Figure 1.. Structural model of the yeast (S. cerevisiae) Mediator kinase module [6].

Note the MED12 N-terminus (dark pink; at right) interacts with CDK8 and CCNC whereas the MED12 C-terminus (light pink) interacts with MED13. High-resolution data for the human complex are lacking but can be expected to show similar features. The subunit sequence similarity is 38%, 40%, 24%, and 22% for CDK8, CCNC, MED12, and MED13, respectively; also, human MED12 and MED13 each contain about 750 additional amino acids compared with yeast subunits. These additional amino acids are designated with semi-transparent ovals (right panel). PDB ID: 7KPX

Figure 2.. The Mediator kinase module coordinates signaling inputs and transcriptional outputs.

Signaling pathways such as MAPK, IFN, and WNT/β-catenin, direct transcriptional responses through transcription factors (TFs); TFs then recruit Mediator to enhancers and promoters to enable pre-initiation complex (PIC) assembly and activation of pol II transcription. The Mediator kinase module (MKM) controls TF function through phosphorylation; upon binding Mediator, the MKM blocks Mediator-pol II interaction and therefore regulates PIC assembly. The MKM also appears to influence pol II pausing and elongation via its kinase activity and through physical association with the super elongation complex (SEC). However, the molecular mechanisms remain unclear.

Figure 3.. Schematic of the RNA polymerase II Pre-initiation complex (PIC).

PIC structure is based upon cryoEM data from human complexes [41-43]. Each red X denotes Mediator kinase phosphorylation sites (MED14, MED26, TAF10, POLR2M) and their approximate location in the PIC. Because PIC structure is dynamic, specific sites may be phosphorylated only during select transcriptional stages (e.g. pol II pause release). The TFIIH-associated CDK-activating kinase module (CAK) binds Mediator at a similar site compared with the Mediator kinase module (MKM). This site would position the MKM downstream of the transcription start site, which may be important for MKM-dependent regulation of pol II pause release or elongation. IIA: TFIIA, IIB: TFIIB, IID, TFIID, IIE, TFIIE, IIF: TFIIF, IIH: TFIIH, TBP: TATA binding protein, CTD: C-terminal domain, CAK: CDK activating kinase module (CDK7, CCNH, MNAT1), part of TFIIH.

Figure 4.. Speculative models for Mediator kinase module regulation of enhancer function and pol II transcription.

(A) CDK-Mediator may prime enhancers for future activation [98] by regulating the activity of enhancer-bound TFs and nearby chromatin modifying or remodeling complexes, through phosphorylation [48]. (B) CDK8/CDK19 phosphorylation of Mediator may promote Mediator kinase module (MKM) dissociation [12], to promote Mediator-dependent enhancer-promoter looping, PIC assembly, and pol II transcription initiation. Mediator kinase activity activates eRNA transcription at enhancers [25] and the Mediator kinase module (MKM) may remain associated with the enhancer through interactions with TFs [94] or eRNA transcripts [95]. (C) This could position the MKM for downstream phosphorylation events (e.g. to regulate pause release or elongation) without requiring association with PIC-bound Mediator. Transcriptional bursting [115] may be favored through formation of transcriptional condensates [116] (green shading) that may compartmentalize initiation factors including multiple pol II enzymes for rapid re-initiation following pause release. Premature termination can also occur at promoter-proximal sites, regulated in part by XRN2 and SETX [46, 47]. The SEC, NELF, XRN2, SETX, are each phosphorylated by the MKM [48]. (D) Re-binding of the MKM to Mediator will block PIC assembly and inhibit further transcription initiation [10], which may serve as a means to shut off transcription and disassemble the PIC. Re-assembly of the PIC could occur over time, to initiate transcription from the promoter once again.

BOX 1 Figure.. Sequence conservation and domain structure of human Mediator kinase module subunits.

Regions marked “disordered” are predicted to be intrinsically disordered, and defined domains are individually labeled. Evolutionary conservation was calculated from 150 homologs of at least 35% identity, using ConSurf [120]. Sequence identity between paralogs is noted.