ArticleNucleic acids research2014
Deciphering the rules by which dynamics of mRNA secondary structure affect translation efficiency in Saccharomyces cerevisiae.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
53 citing papers in PubMed.
- The KLF14 Variant is Associated with Type 2 Diabetes and HbABiochemical genetics · 2021Trial
- Position-dependent codon occurrence is associated with patterns of translational efficiency and ribosomal occupancy in the human transcriptome.PLoS computational biology · 2026Article
- Multiscale modeling guided potency assessment of mRNA-lipid nanoparticles.Molecular therapy. Nucleic acids · 2026Article
- Soluble Expression of Recombinant Human Mitsugumin 53 in Escherichia coli NiCo21(DE3).The protein journal · 2026Article
- P-bodies act as dynamic control hubs for RNA processing and storage.The Journal of biological chemistry · 2026Article
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- In vivo RNA structure influences the translation and stability of plant long non-coding RNAs.Plant communications · 2026Article
- The differential subcellular localization of soybean transcripts, an additional regulatory mechanism of gene activity.Genome biology · 2025Article
- The intrinsic properties of mRNAs define their translation efficiency at ribosome shortage.Nucleic acids research · 2025Article
- RNA Structure: Past, Future, and Gene Therapy Applications.International journal of molecular sciences · 2024Review
- Computational Analysis of MDR1 Variants Predicts Effect on Cancer Cells via their Effect on mRNA Folding.PLoS computational biology · 2024Article
- Utilizing 5' UTR Engineering Enables Fine-Tuning of Multiple Genes within Operons to Balance Metabolic Flux inBiology · 2024Article
- RNA structure profiling at single-cell resolution reveals new determinants of cell identity.Nature methods · 2024Article
- Readthrough-induced misincorporated amino acid ratios guide mutant-specific therapeutic approaches for two CFTR nonsense mutations.Frontiers in pharmacology · 2024Article
- Efficient Prediction Model of mRNA End-to-End Distance and Conformation: Three-Dimensional RNA Illustration Program (TRIP).Methods in molecular biology (Clifton, N.J.) · 2024Article
- Synonymous codon usage regulates translation initiation.Cell reports · 2023Article
- Article
- Article
- Global 5'-UTR RNA structure regulates translation of a SERPINA1 mRNA.Nucleic acids research · 2022Article
- A transformation clustering algorithm and its application in polyribosomes structural profiling.Nucleic acids research · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Messenger RNA (mRNA) secondary structure decreases the elongation rate, as ribosomes must unwind every structure they encounter during translation. Therefore, the strength of mRNA secondary structure is assumed to be reduced in highly translated mRNAs. However, previous studies in vitro reported a positive correlation between mRNA folding strength and protein abundance. The counterintuitive finding suggests that mRNA secondary structure affects translation efficiency in an undetermined manner. Here, we analyzed the folding behavior of mRNA during translation and its effect on translation efficiency. We simulated translation process based on a novel computational model, taking into account the interactions among ribosomes, codon usage and mRNA secondary structures. We showed that mRNA secondary structure shortens ribosomal distance through the dynamics of folding strength. Notably, when adjacent ribosomes are close, mRNA secondary structures between them disappear, and codon usage determines the elongation rate. More importantly, our results showed that the combined effect of mRNA secondary structure and codon usage in highly translated mRNAs causes a short ribosomal distance in structural regions, which in turn eliminates the structures during translation, leading to a high elongation rate. Together, these findings reveal how the dynamics of mRNA secondary structure coupling with codon usage affect translation efficiency.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.