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Dynamic profiling of mRNA turnover reveals gene-specific and system-wide regulation of mRNA decay

RNA levels are determined by the rates of both transcription and decay, and a mechanistic understanding of the complex networks regulating gene expression requires methods that allow dynamic measurements of transcription and decay in living cells with minimal perturbation. Here, we describe a metabo...

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Autores principales: Munchel, Sarah E., Shultzaberger, Ryan K., Takizawa, Naoki, Weis, Karsten
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The American Society for Cell Biology 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3145553/
https://www.ncbi.nlm.nih.gov/pubmed/21680716
http://dx.doi.org/10.1091/mbc.E11-01-0028
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author Munchel, Sarah E.
Shultzaberger, Ryan K.
Takizawa, Naoki
Weis, Karsten
author_facet Munchel, Sarah E.
Shultzaberger, Ryan K.
Takizawa, Naoki
Weis, Karsten
author_sort Munchel, Sarah E.
collection PubMed
description RNA levels are determined by the rates of both transcription and decay, and a mechanistic understanding of the complex networks regulating gene expression requires methods that allow dynamic measurements of transcription and decay in living cells with minimal perturbation. Here, we describe a metabolic pulse-chase labeling protocol using 4-thiouracil combined with large-scale RNA sequencing to determine decay rates of all mRNAs in Saccharomyces cerevisiae. Profiling in various growth and stress conditions reveals that mRNA turnover is highly regulated both for specific groups of transcripts and at the system-wide level. For example, acute glucose starvation induces global mRNA stabilization but increases the degradation of all 132 detected ribosomal protein mRNAs. This effect is transient and can be mimicked by inhibiting the target-of-rapamycin kinase. Half-lives of mRNAs critical for galactose (GAL) metabolism are also highly sensitive to changes in carbon source. The fast reduction of GAL transcripts in glucose requires their dramatically enhanced turnover, highlighting the importance of mRNA decay in the control of gene expression. The approach described here provides a general platform for the global analysis of mRNA turnover and transcription and can be applied to dissect gene expression programs in a wide range of organisms and conditions.
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spelling pubmed-31455532011-10-16 Dynamic profiling of mRNA turnover reveals gene-specific and system-wide regulation of mRNA decay Munchel, Sarah E. Shultzaberger, Ryan K. Takizawa, Naoki Weis, Karsten Mol Biol Cell Articles RNA levels are determined by the rates of both transcription and decay, and a mechanistic understanding of the complex networks regulating gene expression requires methods that allow dynamic measurements of transcription and decay in living cells with minimal perturbation. Here, we describe a metabolic pulse-chase labeling protocol using 4-thiouracil combined with large-scale RNA sequencing to determine decay rates of all mRNAs in Saccharomyces cerevisiae. Profiling in various growth and stress conditions reveals that mRNA turnover is highly regulated both for specific groups of transcripts and at the system-wide level. For example, acute glucose starvation induces global mRNA stabilization but increases the degradation of all 132 detected ribosomal protein mRNAs. This effect is transient and can be mimicked by inhibiting the target-of-rapamycin kinase. Half-lives of mRNAs critical for galactose (GAL) metabolism are also highly sensitive to changes in carbon source. The fast reduction of GAL transcripts in glucose requires their dramatically enhanced turnover, highlighting the importance of mRNA decay in the control of gene expression. The approach described here provides a general platform for the global analysis of mRNA turnover and transcription and can be applied to dissect gene expression programs in a wide range of organisms and conditions. The American Society for Cell Biology 2011-08-01 /pmc/articles/PMC3145553/ /pubmed/21680716 http://dx.doi.org/10.1091/mbc.E11-01-0028 Text en © 2011 Munchel et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0). “ASCB®”,” “The American Society for Cell Biology®,” and “Molecular Biology of the Cell®” are registered trademarks of The American Society of Cell Biology.
spellingShingle Articles
Munchel, Sarah E.
Shultzaberger, Ryan K.
Takizawa, Naoki
Weis, Karsten
Dynamic profiling of mRNA turnover reveals gene-specific and system-wide regulation of mRNA decay
title Dynamic profiling of mRNA turnover reveals gene-specific and system-wide regulation of mRNA decay
title_full Dynamic profiling of mRNA turnover reveals gene-specific and system-wide regulation of mRNA decay
title_fullStr Dynamic profiling of mRNA turnover reveals gene-specific and system-wide regulation of mRNA decay
title_full_unstemmed Dynamic profiling of mRNA turnover reveals gene-specific and system-wide regulation of mRNA decay
title_short Dynamic profiling of mRNA turnover reveals gene-specific and system-wide regulation of mRNA decay
title_sort dynamic profiling of mrna turnover reveals gene-specific and system-wide regulation of mrna decay
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3145553/
https://www.ncbi.nlm.nih.gov/pubmed/21680716
http://dx.doi.org/10.1091/mbc.E11-01-0028
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