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Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells

In metazoans, both transcription initiation and the escape of RNA polymerase (RNAP) from promoter-proximal pausing are key rate-limiting steps in gene expression. These processes play out at physically proximal sites on the DNA template and appear to influence one another through steric interactions...

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Autores principales: Zhao, Yixin, Liu, Lingjie, Hassett, Rebecca, Siepel, Adam
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10681744/
https://www.ncbi.nlm.nih.gov/pubmed/37889042
http://dx.doi.org/10.1093/nar/gkad843
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author Zhao, Yixin
Liu, Lingjie
Hassett, Rebecca
Siepel, Adam
author_facet Zhao, Yixin
Liu, Lingjie
Hassett, Rebecca
Siepel, Adam
author_sort Zhao, Yixin
collection PubMed
description In metazoans, both transcription initiation and the escape of RNA polymerase (RNAP) from promoter-proximal pausing are key rate-limiting steps in gene expression. These processes play out at physically proximal sites on the DNA template and appear to influence one another through steric interactions. Here, we examine the dynamics of these processes using a combination of statistical modeling, simulation, and analysis of real nascent RNA sequencing data. We develop a simple probabilistic model that jointly describes the kinetics of transcription initiation, pause-escape, and elongation, and the generation of nascent RNA sequencing read counts under steady-state conditions. We then extend this initial model to allow for variability across cells in promoter-proximal pause site locations and steric hindrance of transcription initiation from paused RNAPs. In an extensive series of simulations, we show that this model enables accurate estimation of initiation and pause-escape rates. Furthermore, we show by simulation and analysis of real data that pause-escape is often strongly rate-limiting and that steric hindrance can dramatically reduce initiation rates. Our modeling framework is applicable to a variety of inference problems, and our software for estimation and simulation is freely available.
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spelling pubmed-106817442023-10-27 Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells Zhao, Yixin Liu, Lingjie Hassett, Rebecca Siepel, Adam Nucleic Acids Res Methods In metazoans, both transcription initiation and the escape of RNA polymerase (RNAP) from promoter-proximal pausing are key rate-limiting steps in gene expression. These processes play out at physically proximal sites on the DNA template and appear to influence one another through steric interactions. Here, we examine the dynamics of these processes using a combination of statistical modeling, simulation, and analysis of real nascent RNA sequencing data. We develop a simple probabilistic model that jointly describes the kinetics of transcription initiation, pause-escape, and elongation, and the generation of nascent RNA sequencing read counts under steady-state conditions. We then extend this initial model to allow for variability across cells in promoter-proximal pause site locations and steric hindrance of transcription initiation from paused RNAPs. In an extensive series of simulations, we show that this model enables accurate estimation of initiation and pause-escape rates. Furthermore, we show by simulation and analysis of real data that pause-escape is often strongly rate-limiting and that steric hindrance can dramatically reduce initiation rates. Our modeling framework is applicable to a variety of inference problems, and our software for estimation and simulation is freely available. Oxford University Press 2023-10-27 /pmc/articles/PMC10681744/ /pubmed/37889042 http://dx.doi.org/10.1093/nar/gkad843 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methods
Zhao, Yixin
Liu, Lingjie
Hassett, Rebecca
Siepel, Adam
Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells
title Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells
title_full Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells
title_fullStr Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells
title_full_unstemmed Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells
title_short Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells
title_sort model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells
topic Methods
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10681744/
https://www.ncbi.nlm.nih.gov/pubmed/37889042
http://dx.doi.org/10.1093/nar/gkad843
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