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Regulation of the RNA polymerase II pre-initiation complex by its associated coactivators

Nature Reviews Genetics volume 24, pages 767–782 (2023)Cite this article

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Abstract

The RNA polymerase II (Pol II) pre-initiation complex (PIC) is a critical node in eukaryotic transcription regulation, and its formation is the major rate-limiting step in transcriptional activation. Diverse cellular signals borne by transcriptional activators converge on this large, multiprotein assembly and are transduced via intermediary factors termed coactivators. Cryogenic electron microscopy, multi-omics and single-molecule approaches have recently offered unprecedented insights into both the structure and cellular functions of the PIC and two key PIC-associated coactivators, Mediator and TFIID. Here, we review advances in our understanding of how Mediator and TFIID interact with activators and affect PIC formation and function. We also discuss how their functions are influenced by their chromatin environment and selected cofactors. We consider how, through its multifarious interactions and functionalities, a Mediator-containing and TFIID-containing PIC can yield an integrated signal processing system with the flexibility to determine the unique temporal and spatial expression pattern of a given gene.

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Fig. 1: A paradigmatic TBP-nucleated PIC assembly pathway.
Fig. 2: General principles of coactivator-dependent PIC recruitment and function.
Fig. 3: Modular structure of metazoan Mediator.
Fig. 4: TFIID structure and dynamics.
Fig. 5: TFIID recruitment to promoters in the context of a nucleosome-depleted region.
Fig. 6: Pathways for delivery of Mediator from distal enhancers to the PIC.
Fig. 7: A TFIID-containing and Mediator-containing PIC.

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Acknowledgements

The authors apologize to colleagues whose work could not be cited directly owing to space constraints. The authors thank past and current members of their laboratory for their many contributions to the authors’ understanding of the pre-initiation complex (PIC) and its coactivators. The authors are thankful to M. Gnädig, K. Ito and T. Onikubo for critical reading of the manuscript. The authors’ work was supported by National Institutes of Health (NIH) grants CA234575, CA273709 and AI148387.

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  1. Laboratory of Biochemistry & Molecular Biology, The Rockefeller University, New York, NY, USA

    Sohail Malik & Robert G. Roeder

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  1. Sohail Malik
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Correspondence to Sohail Malik.

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Glossary

+1 Nucleosome

A precisely positioned nucleosome located just downstream from the core promoter. Together with an upstream localized −1 nucleosome, it delimits the boundaries of a nucleosome-depleted region. It is not to be confused with the transcription start site (TSS), which is sometimes also referred to as the +1 site.

Basal transcription

Baseline levels of transcription that might occur in the absence of activation signals.

Bromodomain

A conserved protein domain that can recognize acetylated lysine residues. It is found in many chromatin readers, as well as BET (bromodomain and extra-terminal) family members such as BRD4.

Core promoter

A regulatory region within a transcriptional locus that consists of numerous elements that collectively or singly specify the transcription start site (TSS) by recruiting and orienting the pre-initiation complex (PIC). Elements include the TATA box, initiator (Inr), motif ten element (MTE) and downstream promoter element (DPE), among others.

Enhancers

Regulatory elements that carry binding sites for multiple transcriptional activators. Typically, enhancers are found at distal locations relative to the transcription start site (TSS), although some are located more proximally. Variants include super-enhancers, which are characterized by a large number of activator binding sites. In yeast, the upstream activator binding site (UAS) serves the same purpose.

Initiation

The formation of the first phosphodiester bond by pre-initiation complex (PIC)-associated RNA polymerase II (Pol II) following ATP hydrolysis-dependent promoter melting.

Intrinsically disordered regions

(IDRs). Regions in a protein that lack any defined three-dimensional structure, at least in the absence of an interacting protein. They have a high propensity to form higher-order structures through weak multivalent interactions.

Pausing

Transient stalling of transcribing RNA polymerase II (Pol II) soon after promoter clearance that is regulated by a combination of pause-inducing and pause-release factors.

Phase separation

A tendency of two immiscible liquids to separate into distinct phases. In the transcription field, the term largely refers to the tendency of some activators and coactivators that contain intrinsically disordered regions (IDRs) to form condensates when forced into situations where they can cluster, for example on super-enhancers.

Pol II stalk

A prominent feature of RNA polymerase II (Pol II) composed mainly of RPB4 and RPB7 subunits. It can regulate other Pol II elements (for example, the clamp) and acts as a hub for the interaction of multiple pre-initiation complex (PIC) components.

Promoter escape

A series of post-initiation events that occur as a prelude to RNA polymerase II (Pol II) entry into the elongation mode and result in relinquishing of stabilizing interactions that anchor the pre-initiation complex (PIC). This process is closely related to promoter clearance.

RPB1 CTD

The large unstructured carboxy-terminal domain (CTD) of the largest RNA polymerase II (Pol II) subunit. In human, it consists of 52 heptapeptide repeats with the consensus sequence YSPTSPS. The repeat units are subject to phosphorylation at multiple residues. In the context of the pre-initiation complex (PIC), Ser5 is the predominant target of the cyclin-dependent kinase (CDK)-activating kinase (CAK) module of TFIIH.

YEATS domain

One of several domains that can recognize acylated lysine residues. So called because of its original identification in the chromatin reading modules of Yaf9, ENL, AF9, TAF1 and Sas5.

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Malik, S., Roeder, R.G. Regulation of the RNA polymerase II pre-initiation complex by its associated coactivators. Nat Rev Genet 24, 767–782 (2023). https://doi.org/10.1038/s41576-023-00630-9

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