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The core regulation module of stress-responsive regulatory networks in yeast

How does a cell respond to numerous external stresses with a limited number of internal molecular components? It has been observed that there are some common responses of yeast to various stresses, but most observations were based on gene-expression profiles and only some part of the common response...

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Detalles Bibliográficos
Autores principales: Kim, Dongsan, Kim, Man-Sun, Cho, Kwang-Hyun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3467048/
https://www.ncbi.nlm.nih.gov/pubmed/22784859
http://dx.doi.org/10.1093/nar/gks649
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author Kim, Dongsan
Kim, Man-Sun
Cho, Kwang-Hyun
author_facet Kim, Dongsan
Kim, Man-Sun
Cho, Kwang-Hyun
author_sort Kim, Dongsan
collection PubMed
description How does a cell respond to numerous external stresses with a limited number of internal molecular components? It has been observed that there are some common responses of yeast to various stresses, but most observations were based on gene-expression profiles and only some part of the common responses were intensively investigated. So far there has been no system-level analysis to identify commonly responsive or regulated genes against various stresses. In this study, we identified a core regulation module (CRM), a commonly involved regulation structure in the regulatory networks of yeast, which cells reuse in response to an array of environmental stresses. We found that regulators in the CRM constitute a hierarchical backbone of the yeast regulatory network and that the CRM is evolutionarily well conserved, stable against genetic variations and crucial for cell growth. All these findings were consistently held up to considerable noise levels that we introduced to address experimental noise and the resulting false positives of regulatory interactions. We conclude that the CRM of yeast might be an evolutionarily conserved information processing unit that endows a cell with enhanced robustness and efficiency in dealing with numerous environmental stresses with a limited number of internal elements.
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spelling pubmed-34670482012-10-10 The core regulation module of stress-responsive regulatory networks in yeast Kim, Dongsan Kim, Man-Sun Cho, Kwang-Hyun Nucleic Acids Res Computational Biology How does a cell respond to numerous external stresses with a limited number of internal molecular components? It has been observed that there are some common responses of yeast to various stresses, but most observations were based on gene-expression profiles and only some part of the common responses were intensively investigated. So far there has been no system-level analysis to identify commonly responsive or regulated genes against various stresses. In this study, we identified a core regulation module (CRM), a commonly involved regulation structure in the regulatory networks of yeast, which cells reuse in response to an array of environmental stresses. We found that regulators in the CRM constitute a hierarchical backbone of the yeast regulatory network and that the CRM is evolutionarily well conserved, stable against genetic variations and crucial for cell growth. All these findings were consistently held up to considerable noise levels that we introduced to address experimental noise and the resulting false positives of regulatory interactions. We conclude that the CRM of yeast might be an evolutionarily conserved information processing unit that endows a cell with enhanced robustness and efficiency in dealing with numerous environmental stresses with a limited number of internal elements. Oxford University Press 2012-10 2012-07-10 /pmc/articles/PMC3467048/ /pubmed/22784859 http://dx.doi.org/10.1093/nar/gks649 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Computational Biology
Kim, Dongsan
Kim, Man-Sun
Cho, Kwang-Hyun
The core regulation module of stress-responsive regulatory networks in yeast
title The core regulation module of stress-responsive regulatory networks in yeast
title_full The core regulation module of stress-responsive regulatory networks in yeast
title_fullStr The core regulation module of stress-responsive regulatory networks in yeast
title_full_unstemmed The core regulation module of stress-responsive regulatory networks in yeast
title_short The core regulation module of stress-responsive regulatory networks in yeast
title_sort core regulation module of stress-responsive regulatory networks in yeast
topic Computational Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3467048/
https://www.ncbi.nlm.nih.gov/pubmed/22784859
http://dx.doi.org/10.1093/nar/gks649
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