ArticlePloS one2014
Quantifying the effect of ribosomal density on mRNA stability.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 42 citations in OpenAlex.
- Physical modeling of ribosomes along messenger RNA: Estimating kinetic parameters from ribosome profiling experiments using a ballistic model.PLoS computational biology · 2023Article
- Nanobiotechnology-Enabled mRNA Stabilization.Pharmaceutics · 2023Review
- Microtubule integrity regulates budding yeast RAM pathway gene expression.Frontiers in cell and developmental biology · 2022Article
- RNA degradation is required for the germ-cell to maternal transition in Drosophila.Current biology : CB · 2021Article
- Modeling, optimization, and comparable efficacy of T cell and hematopoietic stem cell gene editing for treating hyper-IgM syndrome.EMBO molecular medicine · 2021Article
- Variability in mRNA translation: a random matrix theory approach.Scientific reports · 2021Article
- The effects of codon bias and optimality on mRNA and protein regulation.Cellular and molecular life sciences : CMLS · 2021Review
- Determinants of efficient modulation of ribosomal traffic jams.Computational and structural biotechnology journal · 2021Article
- Protein dosage of theJournal of bacteriology · 2020Article
- The CCR4-NOT complex maintains liver homeostasis through mRNA deadenylation.Life science alliance · 2020Article
- Article
- Codon bias confers stability to human mRNAs.EMBO reports · 2019Article
- Novel insights into gene expression regulation during meiosis revealed by translation elongation dynamics.NPJ systems biology and applications · 2019Article
- Translational Control through Differential Ribosome Pausing during Amino Acid Limitation in Mammalian Cells.Molecular cell · 2018Article
- An integrated view of the role of miR-130b/301b miRNA cluster in prostate cancer.Experimental hematology & oncology · 2018Article
- Ribosome flow model with extended objects.Journal of the Royal Society, Interface · 2017Article
- A clinician's guide to microbiome analysis.Nature reviews. Gastroenterology & hepatology · 2017Review
- Optimal Translation Along a Circular mRNA.Scientific reports · 2017Article
- Multiple Transcript Properties Related to Translation Affect mRNA Degradation Rates inG3 (Bethesda, Md.) · 2016Article
- Article
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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
Gene expression is a fundamental cellular process by which proteins are eventually synthesized based on the information coded in the genes. This process includes four major steps: transcription of the DNA segment corresponding to a gene to mRNA molecules, the degradation of the mRNA molecules, the translation of mRNA molecules to proteins by the ribosome and the degradation of the proteins. We present an innovative quantitative study of the interaction between the gene translation stage and the mRNA degradation stage using large scale genomic data of S. cerevisiae, which include measurements of mRNA levels, mRNA half-lives, ribosomal densities and protein abundances, for thousands of genes. The reported results support the conjecture that transcripts with higher ribosomal density, which is related to the translation stage, tend to have elevated half-lives, and we suggest a novel quantitative estimation of the strength of this relation. Specifically, we show that on average, an increase of 78% in ribosomal density yields an increase of 25% in mRNA half-life, and that this relation between ribosomal density and mRNA half-life is not function specific. In addition, our analyses demonstrate that ribosomal density along the entire ORF, and not in specific locations, has a significant effect on the transcript half-life. Finally, we show that the reported relation cannot be explained by different expression levels among genes. A plausible explanation for the reported results is that ribosomes tend to protect the mRNA molecules from the exosome complexes degrading them; however, additional non-mutually exclusive possible explanations for the reported relation and experiments for their verifications are discussed in the paper.
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