ArticlePLoS computational biology2019
A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Kinetic Control of Nuclear-encoded Mitochondrial mRNA Localization and Local Translation.bioRxiv : the preprint server for biology · 2026Article
- FoldDelay web server: an online tool to quantify translation-driven delays in protein native contact formation.Nucleic acids research · 2026Article
- Single-mRNA imaging and modeling reveal coupled translation initiation and elongation rates.eLife · 2026Article
- The cotranslational cycle of the ribosome-bound Hsp70 homolog Ssb.Nature communications · 2026Article
- Optogenetics with Atomic Precision─A Comprehensive Review of Optical Control of Protein Function through Genetic Code Expansion.Chemical reviews · 2025Review
- Native Fold Delay and its implications for co-translational chaperone binding and protein aggregation.Nature communications · 2025Article
- Effect of Translation-Enhancing Nascent SKIK Peptide on the Arrest Peptides Containing Consecutive Proline.ACS synthetic biology · 2024Article
- Understanding the regulation of protein synthesis under stress conditions.Biophysical journal · 2024Article
- Comprehensive translational profiling and STE AI uncover rapid control of protein biosynthesis during cell stress.Nucleic acids research · 2024Article
- Article
- Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1.Nature chemical biology · 2024Article
- Specific codons control cellular resources and fitness.Science advances · 2024Article
- Decoding stoichiometric protein synthesis inBiophysical reports · 2023Article
- How synonymous mutations alter enzyme structure and function over long timescales.Nature chemistry · 2023Article
- Optimization of ribosome utilization inPNAS nexus · 2023Article
- Distal nucleotides affect the rate of stop codon read-through.Quantitative biology (Beijing, China) · 2023Article
- Frozen in time: analyzing molecular dynamics with time-resolved cryo-EM.Structure (London, England : 1993) · 2023Review
- A circadian clock translational control mechanism targets specific mRNAs to cytoplasmic messenger ribonucleoprotein granules.Cell reports · 2022Article
- Translational buffering by ribosome stalling in upstream open reading frames.PLoS genetics · 2022Article
- Article
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7 authors.
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Abstract
Analysis methods based on simulations and optimization have been previously developed to estimate relative translation rates from next-generation sequencing data. Translation involves molecules and chemical reactions, hence bioinformatics methods consistent with the laws of chemistry and physics are more likely to produce accurate results. Here, we derive simple equations based on chemical kinetic principles to measure the translation-initiation rate, transcriptome-wide elongation rate, and individual codon translation rates from ribosome profiling experiments. Our methods reproduce the known rates from ribosome profiles generated from detailed simulations of translation. By applying our methods to data from S. cerevisiae and mouse embryonic stem cells, we find that the extracted rates reproduce expected correlations with various molecular properties, and we also find that mouse embryonic stem cells have a global translation speed of 5.2 AA/s, in agreement with previous reports that used other approaches. Our analysis further reveals that a codon can exhibit up to 26-fold variability in its translation rate depending upon its context within a transcript. This broad distribution means that the average translation rate of a codon is not representative of the rate at which most instances of that codon are translated, and it suggests that translational regulation might be used by cells to a greater degree than previously thought.
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