Cooperative and sequence-dependent model for RNAP dynamics: Application to ribosomal gene transcription.

Autor: Nakajima RT; Institute of Biosciences, UNESP - Univ Estadual Paulista, Department of Physics and Biophysics, Botucatu, 18618-689, Brazil. Electronic address: takahiro.nakajima@unesp.br., Costa PR; Institute of Biosciences, UNESP - Univ Estadual Paulista, Department of Physics and Biophysics, Botucatu, 18618-689, Brazil. Electronic address: costapr@ibb.unesp.br., Lemke N; Institute of Biosciences, UNESP - Univ Estadual Paulista, Department of Physics and Biophysics, Botucatu, 18618-689, Brazil. Electronic address: ney.lemke@unesp.br.
Jazyk: angličtina
Zdroj: Journal of theoretical biology [J Theor Biol] 2020 Mar 07; Vol. 488, pp. 110134. Date of Electronic Publication: 2019 Dec 23.
DOI: 10.1016/j.jtbi.2019.110134
Abstrakt: Escherichia coli ribosomal genes are a well-established experimental model used to investigate the transcription process. These genes are essential to cell physiology and are therefore strongly expressed. Multiple transcription units collaborate in rrn expression. Experiments involving electron microscopy have shown the non-uniform density of the RNA polymerases transcribing these ribosomal operons. Here, we investigate RNAP collaborative transcription in E. coli ribosomal genes using a stochastic sequence-dependent model that included interactions among the RNAPs. We achieved results consistent with experimental data using a model with variable parametrization for genic and intergenic regions, compared with previous attempts that used uniform parameters for genic and intergenic regions. Our model also showed that cooperative behaviour reduced the dwell times in pause sites predicted by the single-round approach but induced a new pausing event at an upstream position. This work may stimulate new experimental research and provide other scenarios to test our model predictions.
Competing Interests: Declaration of Competing Interest Competing financial interests: The authors declare no competing financial interests.
(Copyright © 2019. Published by Elsevier Ltd.)
Databáze: MEDLINE
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