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Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses
Cells adapt to stress by altering gene expression at multiple levels. Here, we propose a new mechanism regulating stress-dependent gene expression at the level of translation, with coordinated interplay between the tRNA epitranscriptome and biased codon usage in families of stress-response genes. In...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6307160/ https://www.ncbi.nlm.nih.gov/pubmed/30587213 http://dx.doi.org/10.1186/s13059-018-1611-1 |
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author | Chan, Cheryl Pham, Phuong Dedon, Peter C. Begley, Thomas J. |
author_facet | Chan, Cheryl Pham, Phuong Dedon, Peter C. Begley, Thomas J. |
author_sort | Chan, Cheryl |
collection | PubMed |
description | Cells adapt to stress by altering gene expression at multiple levels. Here, we propose a new mechanism regulating stress-dependent gene expression at the level of translation, with coordinated interplay between the tRNA epitranscriptome and biased codon usage in families of stress-response genes. In this model, auxiliary genetic information contained in synonymous codon usage enables regulation of codon-biased and functionally related transcripts by dynamic changes in the tRNA epitranscriptome. This model partly explains the association between synchronous stress-dependent epitranscriptomic marks and significant multi-codon usage skewing in families of translationally regulated transcripts. The model also predicts translational adaptation during viral infections. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-018-1611-1) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6307160 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-63071602019-01-02 Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses Chan, Cheryl Pham, Phuong Dedon, Peter C. Begley, Thomas J. Genome Biol Opinion Cells adapt to stress by altering gene expression at multiple levels. Here, we propose a new mechanism regulating stress-dependent gene expression at the level of translation, with coordinated interplay between the tRNA epitranscriptome and biased codon usage in families of stress-response genes. In this model, auxiliary genetic information contained in synonymous codon usage enables regulation of codon-biased and functionally related transcripts by dynamic changes in the tRNA epitranscriptome. This model partly explains the association between synchronous stress-dependent epitranscriptomic marks and significant multi-codon usage skewing in families of translationally regulated transcripts. The model also predicts translational adaptation during viral infections. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-018-1611-1) contains supplementary material, which is available to authorized users. BioMed Central 2018-12-27 /pmc/articles/PMC6307160/ /pubmed/30587213 http://dx.doi.org/10.1186/s13059-018-1611-1 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Opinion Chan, Cheryl Pham, Phuong Dedon, Peter C. Begley, Thomas J. Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses |
title | Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses |
title_full | Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses |
title_fullStr | Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses |
title_full_unstemmed | Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses |
title_short | Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses |
title_sort | lifestyle modifications: coordinating the trna epitranscriptome with codon bias to adapt translation during stress responses |
topic | Opinion |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6307160/ https://www.ncbi.nlm.nih.gov/pubmed/30587213 http://dx.doi.org/10.1186/s13059-018-1611-1 |
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