ArticleBMC bioinformatics2022
Deciphering the role of RNA structure in translation efficiency.
Article in BMC bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 15 citations in OpenAlex.
- An Epstein-Barr virus-encoded snoRNA directs 2'-O-methylation of human rRNAs to control translation and the viral lytic switch.Cell reports · 2026Article
- Massively parallel characterization of RNA G-quadruplex stability and molecular recognition.Nucleic acids research · 2026Article
- seq2ribo: structure-aware integration of machine learning and simulation to predict ribosome location profiles from RNA sequences.Bioinformatics (Oxford, England) · 2026Article
- The Use of Deep Learning in RNA Therapeutic Development.ACS nano · 2026Review
- Domain arrangement-driven immunogenicity of a computationally designed mRNA vaccine targeting PPE68, IrtA, and PE9 of Mycobacterium tuberculosis.Scientific reports · 2026Article
- seq2ribo: Structure-aware integration of machine learning and simulation to predict ribosome location profiles from RNA sequences.bioRxiv : the preprint server for biology · 2026Article
- Review
- Enhancing mRNA translation efficiency with discriminative and generative artificial intelligence by optimizing 5' UTR sequences.iScience · 2025Article
- The intrinsic properties of mRNAs define their translation efficiency at ribosome shortage.Nucleic acids research · 2025Article
- Widespread 3' UTR splicing regulates expression of oncogene transcripts through multiple mechanisms.Nucleic acids research · 2025Article
- Value of Bioinformatics Models for Predicting Translational Control of Angiogenesis.Circulation research · 2025Review
- Comparative Transcriptomic Analysis Provides Insight into Spatiotemporal Expression Patterns of Pivotal Genes During Critical Growth Stages in Min Pig Breed.Biomolecules · 2025Article
- TRANSAID: a hybrid deep learning framework for translation site prediction with integrated biological feature scoring.Frontiers in bioinformatics · 2025Article
- In vivo mRNA expression of a multi-mechanistic mAb combination protects against Staphylococcus aureus infection.Molecular therapy : the journal of the American Society of Gene Therapy · 2024Article
- Remodeling of the ribosomal quality control and integrated stress response by viral ubiquitin deconjugases.Nature communications · 2023Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundRNA secondary structure has broad impact on the fate of RNA metabolism. The reduced stability of secondary structures near the translation initiation site/start codon of the coding region promotes the efficiency of translation in both prokaryotic and eukaryotic species. However, the inaccuracy of in silico folding and the focus on the coding region limit our understanding of the global relationship between the whole mRNA structure and translation efficiency. Leveraging high-throughput RNA structure probing data in the transcriptome, we aim to systematically investigate the role of RNA structure in regulating translation efficiency.
resultsHere, we analyze the influences of hundreds of sequence and structural features on translation efficiency in the mouse embryonic stem cells (mESCs) and zebrafish developmental stages. Our findings reveal that overall in vivo RNA structure has a higher relative importance in predicting translation efficiency than in vitro RNA structure in both mESCs and zebrafish. Also, RNA structures in 3' untranslated region (UTR) have much stronger influence on translation efficiency compared to those in coding regions or 5' UTR. Furthermore, strong alternation between in vitro and in vivo structures in 3' UTR are detected in highly translated mRNAs in mESCs but not zebrafish. Instead, moderate alteration between in vitro and in vivo RNA structures in the 5' UTR and proximal coding regions are detected in highly translated mRNAs in zebrafish.
conclusionsOur results suggest the openness of the 3' UTR promotes the translation efficiency in both mice and zebrafish, with the in vivo structure in 3' UTR more important in mice than in zebrafish. This reveals a novel role of RNA secondary structure on translational regulation.
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