Structure and mechanism of the RNA polymerase II transcription machinery

Schier, Allison C.; Taatjes, Dylan J.

doi:10.1101/gad.335679.119

Cited by 182 publications

(156 citation statements)

References 247 publications

(389 reference statements)

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“…Transcription initiation is a complex process that comprises chromatin opening, assembly of a pre-initiation complex (PIC), polymerase recruitment and finally its maturation into an elongation-competent form (see 1 for review). In Drosophila and mammals, this last step is highly regulated and appears to be a key point in the control of gene expression ( 2 for review).…”

Section: Introductionmentioning

confidence: 99%

“…Using a deconvolution method and high resolution movies, we generate a time map of transcription events indicating, for each cell, the moments when different RNAP molecules start producing mRNA. This direct readout of transcriptional events in a cell population, represents a unique feature of our method, not available in other methods that fit directly a particular transcription model to the MS2 data such as methods based on the autocorrelation function [2, 5, 4], or maximal likelihood estimate [1] or on Bayesian inference [7, 6]. The map can be used for direct characterisation of transcription features, such as polymerase convoys and various statistics of inter-event times.…”

Section: Introductionmentioning

confidence: 99%

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Stochastic pausing at latent HIV-1 promoters generates transcriptional bursting

Tantale

Garcia-Olivier

L'Hostis

et al. 2020

Preprint

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Promoter-proximal polymerase pausing is a key process regulating gene expression. In latent HIV-1 cells, it prevents viral transcription and is essential for latency maintenance, while in acutely infected cells the viral factor Tat releases paused polymerase to induce viral expression. Pausing is fundamental for HIV-1, but how it contributes to bursting and stochastic viral reactivation is unclear. Here, we performed single molecule imaging of HIV-1 transcription, and we developed a quantitative analysis method that manages multiple time scales from seconds to days, and that rapidly fits many models of promoter dynamics. We found that RNA polymerases enter a long-lived pause at latent HIV-1 promoters (>20 minutes), thereby effectively limiting viral transcription. Surprisingly and in contrast to current models, pausing appears stochastic and not obligatory, with only a small fraction of the polymerases undergoing long-lived pausing in absence of Tat. One consequence of stochastic pausing is that HIV-1 transcription occurs in bursts in latent cells, thereby facilitating latency exit and providing a rationale for the stochasticity of viral rebounds.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Stochastic pausing at latent HIV-1 promoters generates transcriptional bursting

Tantale

Garcia-Olivier

L'Hostis

et al. 2020

Preprint

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“…Transcription of protein-coding genes in eukaryotes is a complex process involving recruitment of coactivators, assembly of the pre-initiation complex (PIC), including RNA polymerase II (Pol II), and transition from promoter melting and transcription initiation to productive transcriptional elongation (Schier and Taatjes 2020). The Mediator complex, a large, multi-subunit complex present in plants, animals, and single-celled eukaryotes, is central to this process (Jeronimo and Robert 2017;Soutourina 2018).…”

Section: Introductionmentioning

confidence: 99%

Altered Mediator dynamics during heat shock in budding yeast

Sarkar

Zhu

Paul

et al. 2020

Preprint

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The Mediator complex is central to transcription by RNA polymerase II (Pol II) in eukaryotes. In yeast, Mediator is recruited by activators via its tail module and then facilitates assembly of the pre-initiation complex (PIC), including Pol II, setting the stage for productive transcription. Mediator occupies proximal promoter regions only transiently prior to Pol II escape; interruption of the transcription cycle by inactivation or depletion of Kin28 inhibits Pol II escape and stabilizes Mediator occupancy at promoters. However, whether Mediator occupancy and dynamics differ for gene cohorts induced by stress or alternative growth conditions has not been examined on a genome-wide scale. Here we investigate Mediator occupancy following heat shock or CdCl2 induction, with or without depletion of Kin28. We find that Pol II occupancy exhibits similar dependence on Mediator under normal and heat shock conditions; however, Mediator occupancy does not increase upon Kin28 depletion at most genes active during heat shock, indicating altered dynamics. Furthermore, Mediator occupancy persists at genes repressed by heat shock or CdCl2 induction and exhibits peaks upstream of the proximal promoter whether or not Kin28 is depleted, suggesting that Mediator is recruited by activators but is unable to engage PIC components at these repressed targets. Finally, we show a reduced dependence on PIC components for Mediator occupancy at promoters after heat shock, further supporting an altered dynamics or stronger engagement with activators under these conditions.

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“…The general transcription factor TFIIH plays a pivotal role in both RNA polymerase II (Pol II) transcription initiation and DNA repair [1][2][3]. The core TFIIH complex from H. sapiens and other metazoans has seven subunits: XPB, XPD, p62, p52, p44, p34, and p8.…”

Section: Introductionmentioning

confidence: 99%

The role of XPB/Ssl2 dsDNA translocation processivity in transcription-start-site scanning

Tomko

Luyties

Rimel

et al. 2020

Preprint

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The general transcription factor TFIIH contains three ATP-dependent catalytic activities. TFIIH functions in nucleotide excision repair primarily as a DNA helicase and in Pol II transcription initiation as a dsDNA translocase and protein kinase. During initiation, the XPB/Ssl2 subunit of TFIIH couples ATP hydrolysis to dsDNA translocation facilitating promoter opening and the kinase module phosphorylates the C-terminal domain to facilitate the transition to elongation. These functions are conserved between metazoans and yeast; however, yeast TFIIH also drives transcription start-site scanning in which Pol II scans downstream DNA to locate productive start-sites. The ten-subunit holo-TFIIH from S. cerevisiae has a processive dsDNA translocase activity required for scanning and a structural role in scanning has been ascribed to the three-subunit TFIIH kinase module. Here, we assess the dsDNA translocase activity of ten-subunit holo- and core-TFIIH complexes (i.e. seven subunits, lacking the kinase module) from both S. cerevisiae and H. sapiens. We find that neither holo nor core human TFIIH exhibit processive translocation, consistent with the lack of start-site scanning in humans. Furthermore, in contrast to holo-TFIIH, the S. cerevisiae core-TFIIH also lacks processive translocation and its dsDNA-stimulated ATPase activity was reduced ~5-fold to a level comparable to the human complexes, potentially explaining the reported upstream shift in start-site observed in the absence of the S. cerevisiae kinase module. These results suggest that neither human nor S. cerevisiae core-TFIIH can translocate efficiently, and that the S. cerevisiae kinase module functions as a processivity factor to allow for robust transcription start-site scanning.

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Structure and mechanism of the RNA polymerase II transcription machinery

Cited by 182 publications

References 247 publications

Stochastic pausing at latent HIV-1 promoters generates transcriptional bursting

Stochastic pausing at latent HIV-1 promoters generates transcriptional bursting

Altered Mediator dynamics during heat shock in budding yeast

The role of XPB/Ssl2 dsDNA translocation processivity in transcription-start-site scanning

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