Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2018-12

AUTHORS

Cheryl Chan, Phuong Pham, Peter C. Dedon, Thomas J. Begley

ABSTRACT

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. More... »

PAGES

228

References to SciGraph publications

  • 2016-08. Nucleoside modifications in the regulation of gene expression: focus on tRNA in CELLULAR AND MOLECULAR LIFE SCIENCES
  • 2014-05. The dynamic epitranscriptome: N6-methyladenosine and gene expression control in NATURE REVIEWS MOLECULAR CELL BIOLOGY
  • 2018-12. Elongator and codon bias regulate protein levels in mammalian peripheral neurons in NATURE COMMUNICATIONS
  • 2017-12. Epitranscriptomic influences on development and disease in GENOME BIOLOGY
  • 2013-03. Corrigendum: Global quantification of mammalian gene expression control in NATURE
  • 2010-04. On the Possible Role of tRNA Base Modifications in the Evolution of Codon Usage: Queuosine and Drosophila in JOURNAL OF MOLECULAR EVOLUTION
  • 1999-05. Selenocysteine-containing proteins in mammals in JOURNAL OF BIOMEDICAL SCIENCE
  • 2018-06. Codon-specific translation reprogramming promotes resistance to targeted therapy in NATURE
  • 2016-05. Synchronized mitochondrial and cytosolic translation programs in NATURE
  • 2012-01. Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins in NATURE COMMUNICATIONS
  • 2011-05. Global quantification of mammalian gene expression control in NATURE
  • 2008-02. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? in NATURE REVIEWS GENETICS
  • 2003-10. Global analysis of protein expression in yeast in NATURE
  • 2016-11-11. tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence in NATURE COMMUNICATIONS
  • 2014-04. Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry in NATURE PROTOCOLS
  • 2008-06. DNA methylation landscapes: provocative insights from epigenomics in NATURE REVIEWS GENETICS
  • 2003-07. Selection Conflicts, Gene Expression, and Codon Usage Trends in Yeast in JOURNAL OF MOLECULAR EVOLUTION
  • 2016-04. RNA: Expanding the mRNA epitranscriptome in NATURE REVIEWS MOLECULAR CELL BIOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s13059-018-1611-1

    DOI

    http://dx.doi.org/10.1186/s13059-018-1611-1

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1110911707

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/30587213


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