Comparison of pause predictions of two sequence-dependent transcription models

Lu Bai, Michelle D. Wang

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Two recent theoretical models, Bai et al (2004, 2007) and Tadigotla et al (2006), formulated thermodynamic explanations of sequence-dependent transcription pausing by RNA polymerase (RNAP). The two models differ in some basic assumptions and therefore make different yet overlapping predictions for pause locations, and different predictions on pause kinetics and mechanisms. Here we present a comprehensive comparison of the two models. We show that while they have comparable predictive power of pause locations at low NTP concentrations, the Bai et al model is more accurate than Tadigotla et al at higher NTP concentrations. The pausing kinetics predicted by Bai et al is also consistent with time-course transcription reactions, while Tadigotla et al is unsuited for this type of kinetic prediction. More importantly, the two models in general predict different pausing mechanisms even for the same pausing sites, and the Bai et al model provides an explanation more consistent with recent single molecule observations.

Original languageEnglish (US)
Article numberP12007
JournalJournal of Statistical Mechanics: Theory and Experiment
Volume2010
Issue number12
DOIs
StatePublished - Dec 1 2010

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Transcription
Dependent
Prediction
predictions
Kinetics
kinetics
Model
Theoretical Model
Overlapping
Thermodynamics
low concentrations
Predict
thermodynamics
molecules

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Statistical and Nonlinear Physics
  • Statistics, Probability and Uncertainty

Cite this

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title = "Comparison of pause predictions of two sequence-dependent transcription models",
abstract = "Two recent theoretical models, Bai et al (2004, 2007) and Tadigotla et al (2006), formulated thermodynamic explanations of sequence-dependent transcription pausing by RNA polymerase (RNAP). The two models differ in some basic assumptions and therefore make different yet overlapping predictions for pause locations, and different predictions on pause kinetics and mechanisms. Here we present a comprehensive comparison of the two models. We show that while they have comparable predictive power of pause locations at low NTP concentrations, the Bai et al model is more accurate than Tadigotla et al at higher NTP concentrations. The pausing kinetics predicted by Bai et al is also consistent with time-course transcription reactions, while Tadigotla et al is unsuited for this type of kinetic prediction. More importantly, the two models in general predict different pausing mechanisms even for the same pausing sites, and the Bai et al model provides an explanation more consistent with recent single molecule observations.",
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Comparison of pause predictions of two sequence-dependent transcription models. / Bai, Lu; Wang, Michelle D.

In: Journal of Statistical Mechanics: Theory and Experiment, Vol. 2010, No. 12, P12007, 01.12.2010.

Research output: Contribution to journalArticle

TY - JOUR

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