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

Autor(es)

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

Afiliação do(s) autor(es)

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

• Tipo de documento: Artigo Científico
• Fonte: Journal of Theoretical Biology; v. 488, MAR 7 2020.
• Citações Web of Science: 0

Resumo

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)

• Processo FAPESP: 13/06683-2 - Transcrição cooperativa de genes ribossomais em Escherichia coli usando um modelo estocástico e dependente de sequência
• Beneficiário: Rafael Takahiro Nakajima
• Modalidade de apoio: Bolsas no Brasil - Mestrado