Analysis of RNA Chain Elongation and Termination by Saccharomyces cerevisiae RNA Polymerase III

Matsuzaki, H.; Ga, Kassavetis; Ep, Geiduschek

doi:10.1006/jmbi.1994.1072

Cited by 109 publications

(118 citation statements)

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“…Finally, MBF reproduces the correct NTP concentration depen- dence of pausing by yeast Pol III on the SUP4 template (38). It is encouraging that (i) we predict the correct pause sites and trend in their number (the number of experimental pauses decreases from 10 at 100 M to 4 at 1 mM, whereas the corresponding predicted numbers decrease from 7 to 4) and (ii) the statistical significance increases with decreasing NTP concentration.…”

Section: Statistical Mechanics Approachsupporting

confidence: 65%

“…[Note that, as in the gel experiments used to identify transcriptional pauses (36)(37)(38), a pause site refers to the transcript length for which pausing occurs, without reference to the precise backtracked position along the template.] The cutoff parameter, (0 Ͻ Ͻ 1), is determined by optimizing the statistical significance of our predictions over all experimental templates.…”

Section: Statistical Mechanics Approachmentioning

confidence: 99%

“…In particular, progressively lower cutoff values were required to reduce the sequence coverage to or below 30% for MBF, SBF, MBNF, and SBNF, respectively. Because (i) the lower bound on the duration of experimentally defined pauses is given by the time resolution, of the order of 1 s (38), and (ii) at saturating NTP the average elongation time is one order of magnitude lower, it follows that the elongation rate at typical pause sites should be of the order of 10% of the maximum rate. This is in agreement with the cutoff found for MBF, greater (by a factor of 5) than the cutoffs for SBF and MBNF, and substantially greater than the cutoff for SBNF, pointing to MBF as the most physically reasonable of the four models.…”

Section: Statistical Mechanics Approachmentioning

confidence: 99%

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Thermodynamic and kinetic modeling of transcriptional pausing

Tadigotla

Maoiléidigh

Sengupta

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

106

185

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We present a statistical mechanics approach for the prediction of backtracked pauses in bacterial transcription elongation derived from structural models of the transcription elongation complex (EC). Our algorithm is based on the thermodynamic stability of the EC along the DNA template calculated from the sequence-dependent free energy of DNA–DNA, DNA–RNA, and RNA–RNA base pairing associated with ( i ) the translocational and size fluctuations of the transcription bubble; ( ii ) changes in the associated DNA–RNA hybrid; and ( iii ) changes in the cotranscriptional RNA secondary structure upstream of the RNA exit channel. The calculations involve no adjustable parameters except for a cutoff used to discriminate paused from nonpaused complexes. When applied to 100 experimental pauses in transcription elongation by Escherichia coli RNA polymerase on 10 DNA templates, the approach produces statistically significant results. We also present a kinetic model for the rate of recovery of backtracked paused complexes. A crucial ingredient of our model is the incorporation of kinetic barriers to backtracking resulting from steric clashes of EC with the cotranscriptionally generated RNA secondary structure, an aspect not included explicitly in previous attempts at modeling the transcription elongation process.

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Section: Statistical Mechanics Approachsupporting

confidence: 65%

Section: Statistical Mechanics Approachmentioning

confidence: 99%

Section: Statistical Mechanics Approachmentioning

confidence: 99%

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Thermodynamic and kinetic modeling of transcriptional pausing

Tadigotla

Maoiléidigh

Sengupta

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

106

185

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“…Single-molecule analyses on bacterial enzyme confirmed recently this hypothesis (28). The existence of such an unactivated state was also inferred for Pol III from detailed analyses of RNA chain elongation (29). We did not evidence, however, any difference in the proportion of ternary complexes incorporating the correct or an incorrect nucleotide.…”

Section: Mechanics Of Error Avoidance and Error Correction By Pol IIIsupporting

confidence: 78%

Selectivity and proofreading both contribute significantly to the fidelity of RNA polymerase III transcription

Alic

Ayoub²,

Landrieux³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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We examine here the mechanisms ensuring the fidelity of RNA synthesis by RNA polymerase III (Pol III). Misincorporation could only be observed by using variants of Pol III deficient in the intrinsic RNA cleavage activity. Determination of relative rates of the reactions producing correct and erroneous transcripts at a specific position on a tRNA gene, combined with computational methods, demonstrated that Pol III has a highly efficient proofreading activity increasing its transcriptional fidelity by a factor of 10 3 over the error rate determined solely by selectivity (1.8 ؋ 10 ؊4 ). We show that Pol III slows down synthesis past a misincorporation to achieve efficient proofreading. We discuss our findings in the context of transcriptional fidelity studies performed on RNA Pols, proposing that the fidelity of transcription is more crucial for Pol III than Pol II.nucleotide selectivity ͉ transcriptional fidelity

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“…In mammals, a stretch of four Ts is the most frequent terminator, and a stretch of more than five Ts is rare (Braglia et al 2005). RNAPIII pauses not only at the terminator region but also at several other T stretches during transcription (Campbell and Setzer 1992;Matsuzaki et al 1994). Campbell and Setzer (1992) proposed that RNAPIII release at the terminator is dependent on nascent RNA strand displacement during transcription elongation and can be uncoupled from termination signal recognition.…”

Section: Rnapiii: a Terminator On Its Own?mentioning

confidence: 99%

Transcription termination by nuclear RNA polymerases

Richard

Manley²

2009

Genes Dev.

291

326

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Gene transcription in the cell nucleus is a complex and highly regulated process. Transcription in eukaryotes requires three distinct RNA polymerases, each of which employs its own mechanisms for initiation, elongation, and termination. Termination mechanisms vary considerably, ranging from relatively simple to exceptionally complex. In this review, we describe the present state of knowledge on how each of the three RNA polymerases terminates and how mechanisms are conserved, or vary, from yeast to human.

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Analysis of RNA Chain Elongation and Termination by Saccharomyces cerevisiae RNA Polymerase III

Cited by 109 publications

References 0 publications

Thermodynamic and kinetic modeling of transcriptional pausing

Thermodynamic and kinetic modeling of transcriptional pausing

Selectivity and proofreading both contribute significantly to the fidelity of RNA polymerase III transcription

Transcription termination by nuclear RNA polymerases

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