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Dynamics of protein noise can distinguish between alternate sources of gene-expression variability

Within individual cells, two molecular processes have been implicated as sources of noise in gene expression: (i) Poisson fluctuations in mRNA abundance arising from random birth and death of individual mRNA transcripts or (ii) promoter fluctuations arising from stochastic promoter transitions betwe...

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Detalles Bibliográficos
Autores principales: Singh, Abhyudai, Razooky, Brandon S, Dar, Roy D, Weinberger, Leor S
Formato: Online Artículo Texto
Lenguaje:English
Publicado: European Molecular Biology Organization 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3435505/
https://www.ncbi.nlm.nih.gov/pubmed/22929617
http://dx.doi.org/10.1038/msb.2012.38
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author Singh, Abhyudai
Razooky, Brandon S
Dar, Roy D
Weinberger, Leor S
author_facet Singh, Abhyudai
Razooky, Brandon S
Dar, Roy D
Weinberger, Leor S
author_sort Singh, Abhyudai
collection PubMed
description Within individual cells, two molecular processes have been implicated as sources of noise in gene expression: (i) Poisson fluctuations in mRNA abundance arising from random birth and death of individual mRNA transcripts or (ii) promoter fluctuations arising from stochastic promoter transitions between different transcriptional states. Steady-state measurements of variance in protein levels are insufficient to discriminate between these two mechanisms, and mRNA single-molecule fluorescence in situ hybridization (smFISH) is challenging when cellular mRNA concentrations are high. Here, we present a perturbation method that discriminates mRNA birth/death fluctuations from promoter fluctuations by measuring transient changes in protein variance and that can operate in the regime of high molecular numbers. Conceptually, the method exploits the fact that transcriptional blockage results in more rapid increases in protein variability when mRNA birth/death fluctuations dominate over promoter fluctuations. We experimentally demonstrate the utility of this perturbation approach in the HIV-1 model system. Our results support promoter fluctuations as the primary noise source in HIV-1 expression. This study illustrates a relatively simple method that complements mRNA smFISH hybridization and can be used with existing GFP-tagged libraries to include or exclude alternate sources of noise in gene expression.
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spelling pubmed-34355052012-09-07 Dynamics of protein noise can distinguish between alternate sources of gene-expression variability Singh, Abhyudai Razooky, Brandon S Dar, Roy D Weinberger, Leor S Mol Syst Biol Report Within individual cells, two molecular processes have been implicated as sources of noise in gene expression: (i) Poisson fluctuations in mRNA abundance arising from random birth and death of individual mRNA transcripts or (ii) promoter fluctuations arising from stochastic promoter transitions between different transcriptional states. Steady-state measurements of variance in protein levels are insufficient to discriminate between these two mechanisms, and mRNA single-molecule fluorescence in situ hybridization (smFISH) is challenging when cellular mRNA concentrations are high. Here, we present a perturbation method that discriminates mRNA birth/death fluctuations from promoter fluctuations by measuring transient changes in protein variance and that can operate in the regime of high molecular numbers. Conceptually, the method exploits the fact that transcriptional blockage results in more rapid increases in protein variability when mRNA birth/death fluctuations dominate over promoter fluctuations. We experimentally demonstrate the utility of this perturbation approach in the HIV-1 model system. Our results support promoter fluctuations as the primary noise source in HIV-1 expression. This study illustrates a relatively simple method that complements mRNA smFISH hybridization and can be used with existing GFP-tagged libraries to include or exclude alternate sources of noise in gene expression. European Molecular Biology Organization 2012-08-28 /pmc/articles/PMC3435505/ /pubmed/22929617 http://dx.doi.org/10.1038/msb.2012.38 Text en Copyright © 2012, EMBO and Macmillan Publishers Limited https://creativecommons.org/licenses/by-nc-sa/3.0/This is an open-access article distributed under the terms of the Creative Commons Attribution Noncommercial Share Alike 3.0 Unported License, which allows readers to alter, transform, or build upon the article and then distribute the resulting work under the same or similar license to this one. The work must be attributed back to the original author and commercial use is not permitted without specific permission.
spellingShingle Report
Singh, Abhyudai
Razooky, Brandon S
Dar, Roy D
Weinberger, Leor S
Dynamics of protein noise can distinguish between alternate sources of gene-expression variability
title Dynamics of protein noise can distinguish between alternate sources of gene-expression variability
title_full Dynamics of protein noise can distinguish between alternate sources of gene-expression variability
title_fullStr Dynamics of protein noise can distinguish between alternate sources of gene-expression variability
title_full_unstemmed Dynamics of protein noise can distinguish between alternate sources of gene-expression variability
title_short Dynamics of protein noise can distinguish between alternate sources of gene-expression variability
title_sort dynamics of protein noise can distinguish between alternate sources of gene-expression variability
topic Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3435505/
https://www.ncbi.nlm.nih.gov/pubmed/22929617
http://dx.doi.org/10.1038/msb.2012.38
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