Abstract
The Mediator complex, which in humans is 1.4 MDa in size and includes 26 subunits, controls many aspects of RNA polymerase II (Pol II) function. Apart from its size, a defining feature of Mediator is its intrinsic disorder and conformational flexibility, which contributes to its ability to undergo phase separation and to interact with a myriad of regulatory factors. In this Review, we discuss Mediator structure and function, with emphasis on recent cryogenic electron microscopy data of the 4.0-MDa transcription preinitiation complex. We further discuss how Mediator and sequence-specific DNA-binding transcription factors enable enhancer-dependent regulation of Pol II function at distal gene promoters, through the formation of molecular condensates (or transcription hubs) and chromatin loops. Mediator regulation of Pol II reinitiation is also discussed, in the context of transcription bursting. We propose a working model for Mediator function that combines experimental results and theoretical considerations related to enhancer–promoter interactions, which reconciles contradictory data regarding whether enhancer–promoter communication is direct or indirect. We conclude with a discussion of Mediator’s potential as a therapeutic target and of future research directions.
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Acknowledgements
Due to space and citation limitations, the authors regret that they were unable to cite all relevant articles or to discuss all aspects of Mediator function in biology. The Taatjes laboratory is funded in part by the NIH (R35 GM139550 to D.J.T.) and the NSF (MCB-1818147 to D.J.T.); the Iwasa laboratory is funded in part by the NSF (MCB-190330 to J.I.).
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D.J.T. and W.F.R. wrote the article; W.F.R., S.N. and J.I. helped research data for the article.
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D.J.T. is a member of the scientific advisory board of Dewpoint Therapeutics. All the other authors declare no competing interests.
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Glossary
- Mediator complex
-
In humans, a 26-subunit complex that lacks the Mediator kinase module.
- Mediator kinase module
-
(MKM). A four-subunit complex that includes cyclin-dependent kinase 8 (CDK8), cyclin C, MED12 and MED13; vertebrates express also the paralogues CDK19, MED12L and MED13L.
- Cyclin-dependent kinase (CDK)–Mediator complex
-
Mediator bound to the Mediator kinase module (MKM), which may contain CDK8 or CDK19; because MED26 is mutually exclusive with MKM, CDK–Mediator consists of 29 subunits.
- Carboxy-terminal domain
-
(CTD). The disordered carboxyl terminus of the RNA polymerase II (Pol II) subunit RPB1, composed of heptad repeats of the general sequence YSPTSPS, which are differentially phosphorylated during Pol II transcription initiation, pausing, elongation and termination.
- Pol II jaw
-
RNA polymerase II domain composed of subunits RBP1 and RBP5 that contacts DNA downstream of the transcription start site.
- Hook domain
-
A region within the Mediator middle module, at the opposite end of the tail, which is formed by MED10, MED19 and the amino-terminal portion of MED14.
- Stalk
-
Composed of the RNA polymerase II subunits RPB4 and RPB7, the stalk serves as an interaction hub within the preinitiation complex.
- Bridge helix
-
An α-helix that spans the RNA polymerase II (Pol II) active site and undergoes structural changes in coordination with the trigger loop during nucleotide incorporation and Pol II translocation.
- Trigger loop
-
A domain near the RNA polymerase II active site that transitions between an open state and a closed state with each nucleoside triphosphate added to the nascent RNA; helps to detect base pair mismatches.
- TF activation domains
-
Regions of transcription factors (TFs) that interact with other proteins, such as chromatin remodellers or Mediator; activation domains are typically disordered with low-complexity sequences and may phase separate at physiological concentrations.
- Hysteresis
-
In the context of Mediator and transcription, hysteresis could involve a structural isomerization to achieve a more active state, triggered by transcription factor–Mediator binding and/or Mediator–preinitiation complex association. These interaction-induced structural changes may persist, rendering Mediator activity dependent on prior protein–protein interactions.
- Proteolysis-targeting chimaeras
-
Bivalent small molecules that bind a protein of interest and target it to an E3 ubiquitin ligase, thereby promoting its ubiquitylation and degradation.
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Richter, W.F., Nayak, S., Iwasa, J. et al. The Mediator complex as a master regulator of transcription by RNA polymerase II. Nat Rev Mol Cell Biol 23, 732–749 (2022). https://doi.org/10.1038/s41580-022-00498-3
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DOI: https://doi.org/10.1038/s41580-022-00498-3
