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

Author(s)

Nakajima, Rafael Takahiro ^[1] ; Costa, Pedro Rafael ^[1] ; Lemke, Ney ^[1]

Affiliation

^[1] Univ Estadual Paulista, Inst Biosci, Dept Phys & Biophys, UNESP, BR-18618689 Botucatu, SP - Brazil

• Document type: Journal article
• Source: Journal of Theoretical Biology; v. 488, MAR 7 2020.
• Web of Science Citations: 0

Abstract

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. (C) 2019 Elsevier Ltd. All rights reserved. (AU)

• FAPESP's process: 13/06683-2 - Cooperative transcription of ribosomal genes in Escherichia coli using a stochastic model sequence-dependet
• Grantee: Rafael Takahiro Nakajima
• Support Opportunities: Scholarships in Brazil - Master