Browsing by Author "Heberling, Tamra"

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Data for DNA Transcription and Pausing with Torque [dataset]
(Montana State University ScholarWorks, 2015-10) Heberling, Tamra
Data for two stochastic models describing DNA transcription with short frequent pauses is available. The TASEP data is for the basic stochastic model without torque. The Elongation with Torque Assisted Motion (ETAM) model, includes torque in the simulation. This dataset is associated with the article Heberling T, Davis L, Gedeon J, Morgan C, Gedeon T (2016) A Mechanistic Model for Cooperative Behavior of Co-transcribing RNA Polymerases. PLoS Computational Biology 12(8): e1005069. http://doi.org/10.1371/journal.pcbi.1005069
A Mechanistic Model for Cooperative Behavior of Co-transcribing RNA Polymerases
(2016-08) Davis, Lisa; Gedeon, Tomas; Heberling, Tamra; Gedeon, Jakub; Morgan, Charles
In fast-transcribing prokaryotic genes, such as an rrn gene in Escherichia coli, many RNA polymerases (RNAPs) transcribe the DNA simultaneously. Active elongation of RNAPs is often interrupted by pauses, which has been observed to cause RNAP traffic jams; yet some studies indicate that elongation seems to be faster in the presence of multiple RNAPs than elongation by a single RNAP. We propose that an interaction between RNAPs via the torque produced by RNAP motion on helically twisted DNA can explain this apparent paradox. We have incorporated the torque mechanism into a stochastic model and simulated transcription both with and without torque. Simulation results illustrate that the torque causes shorter pause durations and fewer collisions between polymerases. Our results suggest that the torsional interaction of RNAPs is an important mechanism in maintaining fast transcription times, and that transcription should be viewed as a cooperative group effort by multiple polymerases.