Functional association of Gdown1 with RNA polymerase II poised on human genes

The Mediator complex and transcription elongation

BACKGROUND

Mediator is an evolutionarily conserved multisubunit RNA polymerase II (Pol II) coregulatory complex. Although Mediator was initially found to play a critical role in the regulation of the initiation of Pol II transcription, recent studies have brought to light an expanded role for Mediator at post-initiation stages of transcription.

SCOPE OF REVIEW

We provide a brief description of the structure of Mediator and its function in the regulation of Pol II transcription initiation, and we summarize recent findings implicating Mediator in the regulation of various stages of Pol II transcription elongation.

MAJOR CONCLUSIONS

Emerging evidence is revealing new roles for Mediator in nearly all stages of Pol II transcription, including initiation, promoter escape, elongation, pre-mRNA processing, and termination.

GENERAL SIGNIFICANCE

Mediator plays a central role in the regulation of gene expression by impacting nearly all stages of mRNA synthesis. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.

Promoter clearance by RNA polymerase II

Many changes must occur to the RNA polymerase II (pol II) transcription complex as it makes the transition from initiation into transcript elongation. During this intermediate phase of transcription, contact with initiation factors is lost and stable association with the nascent transcript is established. These changes collectively comprise promoter clearance. Once the transcript elongation complex has reached a point where its properties are indistinguishable from those of complexes with much longer transcripts, promoter clearance is complete. The clearance process for pol II consists of a number of steps and it extends for a surprisingly long distance downstream of transcription start. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.

The Spt4-Spt5 complex: a multi-faceted regulator of transcription elongation

In all domains of life, elongating RNA polymerases require the assistance of accessory factors to maintain their processivity and regulate their rate. Among these elongation factors, the Spt5/NusG factors stand out. Members of this protein family appear to be the only transcription accessory proteins that are universally conserved across all domains of life. In archaea and eukaryotes, Spt5 associates with a second protein, Spt4. In addition to regulating elongation, the eukaryotic Spt4-Spt5 complex appears to couple chromatin modification states and RNA processing to transcription elongation. This review discusses the experimental bases for our current understanding of Spt4-Spt5 function and recent studies that are beginning to elucidate the structure of Spt4-Spt5/RNA polymerase complexes and mechanism of Spt4-Spt5 action. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.

Regulation of mammalian transcription by Gdown1 through a novel steric crosstalk revealed by cryo-EM

In mammals, a distinct RNA polymerase II form, RNAPII(G) contains a novel subunit Gdown1 (encoded by POLR2M), which represses gene activation, only to be reversed by the multisubunit Mediator co-activator. Here, we employed single-particle cryo-electron microscopy (cryo-EM) to disclose the architectures of RNAPII(G), RNAPII and RNAPII in complex with the transcription initiation factor TFIIF, all to ~19 Å. Difference analysis mapped Gdown1 mostly to the RNAPII Rpb5 shelf-Rpb1 jaw, supported by antibody labelling experiments. These structural features correlate with the moderate increase in the efficiency of RNA chain elongation by RNAP II(G). In addition, our updated RNAPII-TFIIF map showed that TFIIF tethers multiple regions surrounding the DNA-binding cleft, in agreement with cross-linking and biochemical mapping. Gdown1's binding sites overlap extensively with those of TFIIF, with Gdown1 sterically excluding TFIIF from RNAPII, herein demonstrated by competition assays using size exclusion chromatography. In summary, our work establishes a structural basis for Gdown1 impeding initiation at promoters, by obstruction of TFIIF, accounting for an additional dependent role of Mediator in activated transcription.

Gdown1: making a link between mediator and RNA polymerase II elongation control

Gdown1 is a substoichiometric RNA polymerase II subunit that modulates effects of both Mediator and elongation factors in vitro and is broadly distributed across the human genome. Here we assemble the existing information on Gdown1, provide additional bioinformatics analyses, and propose a working model for Gdown1 function.

Rethinking the role of TFIIF in transcript initiation by RNA polymerase II

TFIIF is considered to be a general transcription factor, based on the fact that it is essential for assembly of RNA polymerase II preinitiation complexes on fully double-stranded templates in vitro. Existing models assign various tasks to TFIIF during preinitiation complex formation and transcript initiation. Recent results do not support all aspects of those models but they do emphasize the significance of the interaction of TFIIF and TFIIB. Other recent findings raise the possibility that a fraction of RNA polymerase II transcription complex assembly proceeds through a pathway that is independent of TFIIF.

Get back TFIIF, don't let me Gdown1

In this issue of Molecular Cell, papers by the Price and Roeder labs reveal how the Gdown1 protein antagonizes the general transcription factor TFIIF during RNAPII initiation and elongation and how the Mediator complex intervenes in this molecular tug-of-war to activate RNAPII.