ArticleNucleic acids research2020
Inferring efficiency of translation initiation and elongation from ribosome profiling.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 29 citations in OpenAlex.
- Bridging single-molecule and genome-wide studies of cellular mRNA translation.RNA (New York, N.Y.) · 2026Review
- Acute glucose stimulation drives coordinated translational reprogramming in primary pancreatic islets: from global remodeling to fine-tuned insulin synthesis.Frontiers in endocrinology · 2026Article
- Coupling mechanisms coordinating mRNA translation with stages of the mRNA lifecycle.RNA biology · 2025Review
- Multi-omic assessment of mRNA translation dynamics in liver cancer cell lines.Scientific data · 2025Article
- Exploring the potential of large language model-based chatbots in challenges of ribosome profiling data analysis: a review.Briefings in bioinformatics · 2024Review
- Comprehensive translational profiling and STE AI uncover rapid control of protein biosynthesis during cell stress.Nucleic acids research · 2024Article
- How total mRNA influences cell growth.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Ribosome profiling: a powerful tool in oncological research.Biomarker research · 2024Review
- 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
- Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues.Genomics, proteomics & bioinformatics · 2023Article
- RiboGalaxy: A Galaxy-based Web Platform for Ribosome Profiling Data Processing - 2023 Update.Journal of molecular biology · 2023Article
- Ultradeep characterisation of translational sequence determinants refutes rare-codon hypothesis and unveils quadruplet base pairing of initiator tRNA and transcript.Nucleic acids research · 2023Article
- choros: correction of sequence-based biases for accurate quantification of ribosome profiling data.bioRxiv : the preprint server for biology · 2023Article
- The Translational Landscape Revealed the Sequential Treatment Containing ATRA plus PI3K/AKT Inhibitors as an Efficient Strategy for AML Therapy.Pharmaceutics · 2022Article
- Article
- Chloroplast translational regulation uncovers nonessential photosynthesis genes as key players in plant cold acclimation.The Plant cell · 2022Article
- Article
- Quantitative Modeling of Protein Synthesis Using Ribosome Profiling Data.Frontiers in molecular biosciences · 2021Review
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
One of the main goals of ribosome profiling is to quantify the rate of protein synthesis at the level of translation. Here, we develop a method for inferring translation elongation kinetics from ribosome profiling data using recent advances in mathematical modelling of mRNA translation. Our method distinguishes between the elongation rate intrinsic to the ribosome's stepping cycle and the actual elongation rate that takes into account ribosome interference. This distinction allows us to quantify the extent of ribosomal collisions along the transcript and identify individual codons where ribosomal collisions are likely. When examining ribosome profiling in yeast, we observe that translation initiation and elongation are close to their optima and traffic is minimized at the beginning of the transcript to favour ribosome recruitment. However, we find many individual sites of congestion along the mRNAs where the probability of ribosome interference can reach $50\%$. Our work provides new measures of translation initiation and elongation efficiencies, emphasizing the importance of rating these two stages of translation separately.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.