ArticleNucleic acids research2016
Identification of the mRNA targets of tRNA-specific regulation using genome-wide simulation of translation.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 26 citations in OpenAlex.
- Calibrated ribosome profiling assesses the dynamics of ribosomal flux on transcripts.Nature communications · 2024Article
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- Using mechanistic models and machine learning to design single-color multiplexed nascent chain tracking experiments.Frontiers in cell and developmental biology · 2023Article
- Inferring efficiency of translation initiation and elongation from ribosome profiling.Nucleic acids research · 2020Article
- Whole cell biophysical modeling of codon-tRNA competition reveals novel insights related to translation dynamics.PLoS computational biology · 2020Article
- Impact of Pus1 Pseudouridine Synthase on Specific Decoding Events inBiomolecules · 2020Article
- Computational design and interpretation of single-RNA translation experiments.PLoS computational biology · 2019Article
- Live-Cell Single RNA Imaging Reveals Bursts of Translational Frameshifting.Molecular cell · 2019Article
- Transcriptome analysis reveals a stress response of Shewanella oneidensis deprived of background levels of ionizing radiation.PloS one · 2018Article
- Gene length as a regulator for ribosome recruitment and protein synthesis: theoretical insights.Scientific reports · 2017Article
- Novel mRNA-specific effects of ribosome drop-off on translation rate and polysome profile.PLoS computational biology · 2017Article
- Role of Pseudouridine Formation by Deg1 for Functionality of Two Glutamine Isoacceptor tRNAs.Biomolecules · 2017Article
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
tRNA gene copy number is a primary determinant of tRNA abundance and therefore the rate at which each tRNA delivers amino acids to the ribosome during translation. Low-abundance tRNAs decode rare codons slowly, but it is unclear which genes might be subject to tRNA-mediated regulation of expression. Here, those mRNA targets were identified via global simulation of translation. In-silico mRNA translation rates were compared for each mRNA in both wild-type and a [Formula: see text] sup70-65 mutant, which exhibits a pseudohyphal growth phenotype and a 75% slower CAG codon translation rate. Of 4900 CAG-containing mRNAs, 300 showed significantly reduced in silico translation rates in a simulated tRNA mutant. Quantitative immunoassay confirmed that the reduced translation rates of sensitive mRNAs were [Formula: see text] concentration-dependent. Translation simulations showed that reduced [Formula: see text] concentrations triggered ribosome queues, which dissipated at reduced translation initiation rates. To validate this prediction experimentally, constitutive gcn2 kinase mutants were used to reduce in vivo translation initiation rates. This repaired the relative translational rate defect of target mRNAs in the sup70-65 background, and ameliorated sup70-65 pseudohyphal growth phenotypes. We thus validate global simulation of translation as a new tool to identify mRNA targets of tRNA-specific gene regulation.
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