ArticleBMC bioinformatics2007
AUG_hairpin: prediction of a downstream secondary structure influencing the recognition of a translation start site.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed, 56 citations in OpenAlex.
- Regulation of translation by upstream translation initiation codons of surfactant protein A1 splice variants.American journal of physiology. Lung cellular and molecular physiology · 2015Trial
- Position-dependent codon occurrence is associated with patterns of translational efficiency and ribosomal occupancy in the human transcriptome.PLoS computational biology · 2026Article
- The role of FMR1 mRNA structure on the efficiency of non-canonical translation of toxic polyglycine protein.Nucleic acids research · 2026Article
- Macroevolutionary divergence of gene expression driven by selection on protein abundance.Science (New York, N.Y.) · 2025Article
- CriticalNAR genomics and bioinformatics · 2024Article
- Tailor made: the art of therapeutic mRNA design.Nature reviews. Drug discovery · 2024Review
- Thousands of human non-AUG extended proteoforms lack evidence of evolutionary selection among mammals.Nature communications · 2022Article
- Human UFSP1 translated from an upstream near-cognate initiation codon functions as an active UFM1-specific protease.The Journal of biological chemistry · 2022Article
- Translational control in aging and neurodegeneration.Wiley interdisciplinary reviews. RNA · 2021Review
- Control of translation by eukaryotic mRNA transcript leaders-Insights from high-throughput assays and computational modeling.Wiley interdisciplinary reviews. RNA · 2021Review
- Article
- Repeat-Associated Non-ATG Translation in Neurological Diseases.Cold Spring Harbor perspectives in biology · 2018Review
- Non-AUG translation: a new start for protein synthesis in eukaryotes.Genes & development · 2017Review
- RNA biology of disease-associated microsatellite repeat expansions.Acta neuropathologica communications · 2017Review
- Article
- Article
- Characterisation of Structural Proteins from Chronic Bee Paralysis Virus (CBPV) Using Mass Spectrometry.Viruses · 2015Article
- Linking RNA Dysfunction and Neurodegeneration in Amyotrophic Lateral Sclerosis.Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics · 2015Review
- Multiple roles of the coding sequence 5' end in gene expression regulation.Nucleic acids research · 2015Review
- Rationally designed, heterologous S. cerevisiae transcripts expose novel expression determinants.RNA biology · 2015Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe translation start site plays an important role in the control of translation efficiency of eukaryotic mRNAs. The recognition of the start AUG codon by eukaryotic ribosomes is considered to depend on its nucleotide context. However, the fraction of eukaryotic mRNAs with the start codon in a suboptimal context is relatively large. It may be expected that mRNA should possess some features providing efficient translation, including the proper recognition of a translation start site. It has been experimentally shown that a downstream hairpin located in certain positions with respect to start codon can compensate in part for the suboptimal AUG context and also increases translation from non-AUG initiation codons. Prediction of such a compensatory hairpin may be useful in the evaluation of eukaryotic mRNA translation properties.
resultsWe evaluated interdependency between the start codon context and mRNA secondary structure at the CDS beginning: it was found that a suboptimal start codon context significantly correlated with higher base pairing probabilities at positions 13 - 17 of CDS of human and mouse mRNAs. It is likely that the downstream hairpins are used to enhance translation of some mammalian mRNAs in vivo. Thus, we have developed a tool, AUG_hairpin, to predict local stem-loop structures located within the defined region at the beginning of mRNA coding part. The implemented algorithm is based on the available published experimental data on the CDS-located stem-loop structures influencing the recognition of upstream start codons.
conclusionAn occurrence of a potential secondary structure downstream of start AUG codon in a suboptimal context (or downstream of a potential non-AUG start codon) may provide researchers with a testable assumption on the presence of additional regulatory signal influencing mRNA translation initiation rate and the start codon choice. AUG_hairpin, which has a convenient Web-interface with adjustable parameters, will make such an evaluation easy and efficient.
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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.