ArticlePLoS computational biology2012
Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells.
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
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77 citing papers in PubMed, 124 citations in OpenAlex.
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- Genome-wide impact of codon usage bias on translation optimization in Drosophila melanogaster.Nature communications · 2024Article
- Next generation sequencing technologies to address aberrant mRNA translation in cancer.NAR cancer · 2024Review
- Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1.Nature chemical biology · 2024Article
- Differential subcellular localization of ASPM RNA and protein.microPublication biology · 2024Article
- Distal nucleotides affect the rate of stop codon read-through.Quantitative biology (Beijing, China) · 2023Article
- Evaluating data integrity in ribosome footprinting datasets through modelled polysome profiles.Nucleic acids research · 2022Article
- Efficient Amber SuppressionACS synthetic biology · 2022Article
- The landscape of translational stall sites in bacteria revealed by monosome and disome profiling.RNA (New York, N.Y.) · 2022Article
- Thermal adaptation of mRNA secondary structure: stability versus lability.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- EGGTART: A tool to visualize the dynamics of biophysical transport under the inhomogeneous l-TASEP.Biophysical journal · 2021Article
- Unpacking Pandora From Its Box: Deciphering the Molecular Basis of the SARS-CoV-2 Coronavirus.International journal of molecular sciences · 2020Review
- What determines eukaryotic translation elongation: recent molecular and quantitative analyses of protein synthesis.Open biology · 2020Review
- Comparative analysis of protein synthesis rate in COVID-19 with other human coronaviruses.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2020Article
- Determinants of translation efficiency in the evolutionarily-divergent protist Trichomonas vaginalis.BMC molecular and cell biology · 2020Article
- Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing.Genome research · 2020Article
- Composition of human-specific slow codons and slow di-codons in SARS-CoV and 2019-nCoV are lower than other coronaviruses suggesting a faster protein synthesis rate of SARS-CoV and 2019-nCoV.Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi · 2020Article
- Genome-wide Survey of Ribosome Collision.Cell reports · 2020Article
17 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ribosomal profiling is a promising approach with increasing popularity for studying translation. This approach enables monitoring the ribosomal density along genes at a resolution of single nucleotides.In this study, we focused on ribosomal density profiles of mouse embryonic stem cells. Our analysis suggests, for the first time, that even in mammals such as M. musculus the elongation speed is significantly and directly affected by determinants of the coding sequence such as: 1) the adaptation of codons to the tRNA pool; 2) the local mRNA folding of the coding sequence; 3) the local charge of amino acids encoded in the codon sequence. In addition, our analyses suggest that in general, the translation velocity of ribosomes is slower at the beginning of the coding sequence and tends to increase downstream.Finally, a comparison of these data to the expected biophysical behavior of translation suggests that it suffers from some unknown biases. Specifically, the ribosomal flux measured on the experimental data increases along the coding sequence; however, according to any biophysical model of ribosomal movement lacking internal initiation sites, the flux is expected to remain constant or decrease. Thus, developing experimental and/or statistical methods for understanding, detecting and dealing with such biases is of high importance.
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