Insight into promoter clearance by RNA polymerase II

Luse, Donal S.

doi:10.1073/pnas.1916582116

Cited by 5 publications

(2 citation statements)

References 21 publications

(30 reference statements)

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“…5b). Lastly, our analysis includes the minimal set of GTFs required for in vitro transcription using a naked DNA template (68)(69)(70). In future work and using methods suitable for analysis of multi-subunit complexes, it will be interesting to investigate the dynamics of TFIIH (71,72), Mediator and Pol II itself (73,74).…”

Section: Discussionmentioning

confidence: 99%

Genome-scale chromatin interaction dynamic measurements for key components of the RNA Pol II general transcription machinery

Kupkova

Shetty

Hoffman

et al. 2023

Preprint

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BackgroundA great deal of work has revealed in structural detail the components of the machinery responsible for mRNA gene transcription initiation. These include the general transcription factors (GTFs), which assemble at promoters along with RNA Polymerase II (Pol II) to form a preinitiation complex (PIC) aided by the activities of cofactors and site-specific transcription factors (TFs). However, less well understood are thein vivoPIC assembly pathways and their kinetics, an understanding of which is vital for determining on a mechanistic level how rates ofin vivoRNA synthesis are established and how cofactors and TFs impact them.ResultsWe used competition ChIP to obtain genome-scale estimates of the residence times for five GTFs: TBP, TFIIA, TFIIB, TFIIE and TFIIF in budding yeast. While many GTF-chromatin interactions were short-lived (< 1 min), there were numerous interactions with residence times in the several minutes range. Sets of genes with a shared function also shared similar patterns of GTF kinetic behavior. TFIIE, a GTF that enters the PIC late in the assembly process, had residence times correlated with RNA synthesis rates.ConclusionsThe datasets and results reported here provide kinetic information for most of the Pol II-driven genes in this organism and therefore offer a rich resource for exploring the mechanistic relationships between PIC assembly, gene regulation, and transcription. The relationships between gene function and GTF dynamics suggest that shared sets of TFs tune PIC assembly kinetics to ensure appropriate levels of expression.

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Section: Discussionmentioning

confidence: 99%

Genome-scale chromatin interaction dynamic measurements for key components of the RNA Pol II general transcription machinery

Kupkova

Shetty

Hoffman

et al. 2023

Preprint

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show abstract

“…Previous biochemical and biophysical data suggest that a bona fide ITC is long-persisting and that promoter escape occurs after synthesis of dozens of nucleotides (Fazal et al, 2015; Fujiwara et al, 2019; Luse, 2019). However this is unlikely to occur in cells as the initially transcribing pol II is thought to encounter another pol II or a nucleosome at promoter proximal regions shortly after the initiation of transcription (Ehrensberger et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

Structural visualization of de novo initiation of RNA polymerase II transcription

Yang

Fujiwara

Kim

et al. 2021

Preprint

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Structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription were previously facilitated by the use of synthetic oligonucleotides. Here we report structures of initiation complexes de novo converted from pre-initiation complex (PIC) through catalytic activities and stalled at different template positions. Contrary to previous models, the closed-to-open promoter transition was accompanied by a large positional change of the general transcription factor TFIIH which became in closer proximity to TFIIE for the active delivery of the downstream DNA to the pol II active center. The initially-transcribing complex (ITC) reeled over 80 base pairs of the downstream DNA by scrunching, while retaining the fixed upstream contact, and underwent the transition to elongation when it encountered promoter-proximal pol II from a preceding round of transcription. TFIIH is therefore conducive to promoter melting, TSS scanning, and promoter escape, extending far beyond synthesis of a short transcript.

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Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II

et al. 2022

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Insight into promoter clearance by RNA polymerase II

Cited by 5 publications

References 21 publications

Genome-scale chromatin interaction dynamic measurements for key components of the RNA Pol II general transcription machinery

Genome-scale chromatin interaction dynamic measurements for key components of the RNA Pol II general transcription machinery

Structural visualization of de novo initiation of RNA polymerase II transcription

Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II

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