Stochastic model of transcription initiation of closely spaced promoters in escherichia coli

Detalhes bibliográficos
Autor(a) principal: Martins, Leonardo Pedro Donas-Boto de Vilhena
Data de Publicação: 2011
Tipo de documento: Dissertação
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10362/7009
Resumo: Dissertação para obtenção do Grau de Mestre em Engenharia Biomédica
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spelling Stochastic model of transcription initiation of closely spaced promoters in escherichia coliStochastic simulationTranscription initiationProkaryotic gene expressionRregulation mechanismsPromoter arrangementsDissertação para obtenção do Grau de Mestre em Engenharia BiomédicaThe regulatory mechanisms of transcription allow organisms to quickly adapt to changes in their environment and often act during transcription initiation. Here, a stochastic model of transcription initiation at the nucleotide level is proposed to study the dynamics of RNA production in closely spaced promoters and their regulatory mechanisms. We study how different arrangements (convergent e divergent), distance between transcription start sites (TSS), and various kinetic parameters affect the dynamics of RNA production. Further, we analyze how the kinetics of various steps in transcription initiation can be regulated by varying locations of repressor binding sites. From the results, we observe that the rate limiting steps have strong influence in the kinetics of RNA production. We find that interferences between RNA polymerases in divergent overlapped and convergent geometries causes the distribution of time intervals between the production of consecutive RNA molecules from each TSS to increase in mean and standard deviation, which leads to stronger fluctuations in the temporal levels of RNA molecules. We observe that small changes in the distance between TSSs can lead to abrupt transitions in the dynamics of RNA production, particularly when this change changes the geometry from overlapped to non-overlapped promoters. From the study of the correlation in the choices of directionality and on the time series of RNA productions we show that by tuning the distances and directions of the two TSS one can obtain both negative and positive correlations. We further show that distinct repression mechanisms of transcription initiation in steps such as the open and closed complex formation and promoter escape have different effects on the dynamics of RNA production. The study of these models will help the study of how genetic circuits have evolved and assist in designing artificial genetic circuits with desired dynamics.Faculdade de Ciências e TecnologiaFonseca, JoséRibeiro, AndréRUNMartins, Leonardo Pedro Donas-Boto de Vilhena2012-02-13T09:55:03Z20112011-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesisapplication/pdfhttp://hdl.handle.net/10362/7009enginfo:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-03-11T03:38:32Zoai:run.unl.pt:10362/7009Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:17:09.443047Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv Stochastic model of transcription initiation of closely spaced promoters in escherichia coli
title Stochastic model of transcription initiation of closely spaced promoters in escherichia coli
spellingShingle Stochastic model of transcription initiation of closely spaced promoters in escherichia coli
Martins, Leonardo Pedro Donas-Boto de Vilhena
Stochastic simulation
Transcription initiation
Prokaryotic gene expression
Rregulation mechanisms
Promoter arrangements
title_short Stochastic model of transcription initiation of closely spaced promoters in escherichia coli
title_full Stochastic model of transcription initiation of closely spaced promoters in escherichia coli
title_fullStr Stochastic model of transcription initiation of closely spaced promoters in escherichia coli
title_full_unstemmed Stochastic model of transcription initiation of closely spaced promoters in escherichia coli
title_sort Stochastic model of transcription initiation of closely spaced promoters in escherichia coli
author Martins, Leonardo Pedro Donas-Boto de Vilhena
author_facet Martins, Leonardo Pedro Donas-Boto de Vilhena
author_role author
dc.contributor.none.fl_str_mv Fonseca, José
Ribeiro, André
RUN
dc.contributor.author.fl_str_mv Martins, Leonardo Pedro Donas-Boto de Vilhena
dc.subject.por.fl_str_mv Stochastic simulation
Transcription initiation
Prokaryotic gene expression
Rregulation mechanisms
Promoter arrangements
topic Stochastic simulation
Transcription initiation
Prokaryotic gene expression
Rregulation mechanisms
Promoter arrangements
description Dissertação para obtenção do Grau de Mestre em Engenharia Biomédica
publishDate 2011
dc.date.none.fl_str_mv 2011
2011-01-01T00:00:00Z
2012-02-13T09:55:03Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/masterThesis
format masterThesis
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10362/7009
url http://hdl.handle.net/10362/7009
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Faculdade de Ciências e Tecnologia
publisher.none.fl_str_mv Faculdade de Ciências e Tecnologia
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
repository.mail.fl_str_mv
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