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Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation
To monitor eukaryotic mRNA metabolism, we developed comparative dynamic transcriptome analysis (cDTA). cDTA provides absolute rates of mRNA synthesis and decay in Saccharomyces cerevisiae (Sc) cells with the use of Schizosaccharomyces pombe (Sp) as an internal standard. cDTA uses nonperturbing metab...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory Press
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3396375/ https://www.ncbi.nlm.nih.gov/pubmed/22466169 http://dx.doi.org/10.1101/gr.130161.111 |
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author | Sun, Mai Schwalb, Björn Schulz, Daniel Pirkl, Nicole Etzold, Stefanie Larivière, Laurent Maier, Kerstin C. Seizl, Martin Tresch, Achim Cramer, Patrick |
author_facet | Sun, Mai Schwalb, Björn Schulz, Daniel Pirkl, Nicole Etzold, Stefanie Larivière, Laurent Maier, Kerstin C. Seizl, Martin Tresch, Achim Cramer, Patrick |
author_sort | Sun, Mai |
collection | PubMed |
description | To monitor eukaryotic mRNA metabolism, we developed comparative dynamic transcriptome analysis (cDTA). cDTA provides absolute rates of mRNA synthesis and decay in Saccharomyces cerevisiae (Sc) cells with the use of Schizosaccharomyces pombe (Sp) as an internal standard. cDTA uses nonperturbing metabolic labeling that supersedes conventional methods for mRNA turnover analysis. cDTA reveals that Sc and Sp transcripts that encode orthologous proteins have similar synthesis rates, whereas decay rates are fivefold lower in Sp, resulting in similar mRNA concentrations despite the larger Sp cell volume. cDTA of Sc mutants reveals that a eukaryote can buffer mRNA levels. Impairing transcription with a point mutation in RNA polymerase (Pol) II causes decreased mRNA synthesis rates as expected, but also decreased decay rates. Impairing mRNA degradation by deleting deadenylase subunits of the Ccr4–Not complex causes decreased decay rates as expected, but also decreased synthesis rates. Extended kinetic modeling reveals mutual feedback between mRNA synthesis and degradation that may be achieved by a factor that inhibits synthesis and enhances degradation. |
format | Online Article Text |
id | pubmed-3396375 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-33963752013-01-01 Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation Sun, Mai Schwalb, Björn Schulz, Daniel Pirkl, Nicole Etzold, Stefanie Larivière, Laurent Maier, Kerstin C. Seizl, Martin Tresch, Achim Cramer, Patrick Genome Res Method To monitor eukaryotic mRNA metabolism, we developed comparative dynamic transcriptome analysis (cDTA). cDTA provides absolute rates of mRNA synthesis and decay in Saccharomyces cerevisiae (Sc) cells with the use of Schizosaccharomyces pombe (Sp) as an internal standard. cDTA uses nonperturbing metabolic labeling that supersedes conventional methods for mRNA turnover analysis. cDTA reveals that Sc and Sp transcripts that encode orthologous proteins have similar synthesis rates, whereas decay rates are fivefold lower in Sp, resulting in similar mRNA concentrations despite the larger Sp cell volume. cDTA of Sc mutants reveals that a eukaryote can buffer mRNA levels. Impairing transcription with a point mutation in RNA polymerase (Pol) II causes decreased mRNA synthesis rates as expected, but also decreased decay rates. Impairing mRNA degradation by deleting deadenylase subunits of the Ccr4–Not complex causes decreased decay rates as expected, but also decreased synthesis rates. Extended kinetic modeling reveals mutual feedback between mRNA synthesis and degradation that may be achieved by a factor that inhibits synthesis and enhances degradation. Cold Spring Harbor Laboratory Press 2012-07 /pmc/articles/PMC3396375/ /pubmed/22466169 http://dx.doi.org/10.1101/gr.130161.111 Text en © 2012, Published by Cold Spring Harbor Laboratory Press This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/. |
spellingShingle | Method Sun, Mai Schwalb, Björn Schulz, Daniel Pirkl, Nicole Etzold, Stefanie Larivière, Laurent Maier, Kerstin C. Seizl, Martin Tresch, Achim Cramer, Patrick Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation |
title | Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation |
title_full | Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation |
title_fullStr | Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation |
title_full_unstemmed | Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation |
title_short | Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation |
title_sort | comparative dynamic transcriptome analysis (cdta) reveals mutual feedback between mrna synthesis and degradation |
topic | Method |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3396375/ https://www.ncbi.nlm.nih.gov/pubmed/22466169 http://dx.doi.org/10.1101/gr.130161.111 |
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