ArticlePLoS computational biology2013
Ribosome traffic on mRNAs maps to gene ontology: genome-wide quantification of translation initiation rates and polysome size regulation.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed.
- Microfluidics-mediated spatial control of mRNA lipid nanoparticles primes translation and enhances vaccine potency.Nature biomedical engineering · 2026Article
- Integrated analysis of post-transcriptional regulations reveals insights into acute myeloid leukemia.Communications biology · 2025Article
- Near-cognate tRNAs dominate codon decoding times in simulated ribosomes.Nucleic acids research · 2025Article
- Gene cloning of S100β and NGF and localization of their expression in the small intestine of broilers of various ages.Scientific reports · 2025Article
- Understanding the regulation of protein synthesis under stress conditions.Biophysical journal · 2024Article
- A data-driven estimation of the ribosome drop-off rate inNAR genomics and bioinformatics · 2024Article
- How total mRNA influences cell growth.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Decoding stoichiometric protein synthesis inBiophysical reports · 2023Article
- Comprehensive quantitative modeling of translation efficiency in a genome-reduced bacterium.Molecular systems biology · 2023Article
- Physical modeling of ribosomes along messenger RNA: Estimating kinetic parameters from ribosome profiling experiments using a ballistic model.PLoS computational biology · 2023Article
- Optimization of ribosome utilization inPNAS nexus · 2023Article
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- Protein degradation sets the fraction of active ribosomes at vanishing growth.PLoS computational biology · 2022Article
- Combinations of slow-translating codon clusters can increase mRNA half-life inProceedings of the National Academy of Sciences of the United States of America · 2021Article
- A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion.Genome biology · 2021Article
- Modelling the effect of ribosome mobility on the rate of protein synthesis.The European physical journal. E, Soft matter · 2021Article
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- A Modelling Framework Linking Resource-Based Stochastic Translation to the Optimal Design of Synthetic Constructs.Biology · 2021Article
- Quantitative Modeling of Protein Synthesis Using Ribosome Profiling Data.Frontiers in molecular biosciences · 2021Review
6 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
To understand the complex relationship governing transcript abundance and the level of the encoded protein, we integrate genome-wide experimental data of ribosomal density on mRNAs with a novel stochastic model describing ribosome traffic dynamics during translation elongation. This analysis reveals that codon arrangement, rather than simply codon bias, has a key role in determining translational efficiency. It also reveals that translation output is governed both by initiation efficiency and elongation dynamics. By integrating genome-wide experimental data sets with simulation of ribosome traffic on all Saccharomyces cerevisiae ORFs, mRNA-specific translation initiation rates are for the first time estimated across the entire transcriptome. Our analysis identifies different classes of mRNAs characterised by their initiation rates, their ribosome traffic dynamics, and by their response to ribosome availability. Strikingly, this classification based on translational dynamics maps onto key gene ontological classifications, revealing evolutionary optimisation of translation responses to be strongly influenced by gene function.
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