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Cooperative transcription of ribosomal genes in Escherichia coli using a stochastic model sequence-dependet

Grant number: 13/06683-2
Support type:Scholarships in Brazil - Master
Effective date (Start): August 01, 2013
Effective date (End): February 28, 2015
Field of knowledge:Biological Sciences - Biochemistry - Molecular Biology
Principal researcher:Ney Lemke
Grantee:Rafael Takahiro Nakajima
Home Institution: Instituto de Biociências (IBB). Universidade Estadual Paulista (UNESP). Campus de Botucatu. Botucatu , SP, Brazil


The process of transcription by RNA polymerase (RNAP) is responsible for gene expression and metabolism control, and consequently, for individual development. The transcription is divided into three principal parts: initiation, elongation and termination. Several methods were utilized to study these processes, like atomic-force microscopy, single-molecule fluorescence and optical traps. These experiments show the complexity of the transcription process and, thus, models were proposed to explain this phenomenon and simulate the transcription. However, recent experiments exhibit an interesting transcription behavior in ribosomal sequences of Escherichia coli (E. coli) in the presence of high concentration of RNAP, which differ from the model predictions. The presence of anti-termination complexes and multiple enzymes increase the activity ratio and velocity of transcription. Although in silico models are available they consider a constant rate or disconsider RNAP interactions. In this project we propose the simulation of a stochastic kinetic sequence dependent model for RNAP movement in the template of ribosomal DNA of E. coli, that considers molecular interaction. The model will be validated through comparison with experimental results.

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Scientific publications
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
NAKAJIMA, RAFAEL TAKAHIRO; COSTA, PEDRO RAFAEL; LEMKE, NEY. Cooperative and sequence-dependent model for RNAP dynamics: Application to ribosomal gene transcription. Journal of Theoretical Biology, v. 488, MAR 7 2020. Web of Science Citations: 0.
Academic Publications
(References retrieved automatically from State of São Paulo Research Institutions)
NAKAJIMA, Rafael Takahiro. Transcrição cooperativa de genes ribossomais em Escherichia coli usando um modelo estocástico e dependente de sequência. 2015. Master's Dissertation - Universidade Estadual Paulista (Unesp). Instituto de Biociências. Botucatu Botucatu.

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