ArticleRNA biology2013
Using RNA inverse folding to identify IRES-like structural subdomains.
Article in RNA biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 21 citations in OpenAlex.
- RNA design: update on computational frameworks and programs for inverse RNA folding.Briefings in bioinformatics · 2026Review
- Identification of a novel equine rhinitis B virus detected in horse from Japan.The Journal of veterinary medical science · 2026Article
- Host-like RNA Elements Regulate Virus Translation.Viruses · 2024Review
- RNA-protein coevolution study of Gemin5 uncovers the role of the PXSS motif of RBS1 domain for RNA binding.RNA biology · 2020Article
- RNA-mediated translation regulation in viral genomes: computational advances in the recognition of sequences and structures.Briefings in bioinformatics · 2020Review
- A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites.Nature communications · 2019Article
- Deconstructing internal ribosome entry site elements: an update of structural motifs and functional divergences.Open biology · 2018Review
- Design of RNAs: comparing programs for inverse RNA folding.Briefings in bioinformatics · 2018Review
- Insights into Structural and Mechanistic Features of Viral IRES Elements.Frontiers in microbiology · 2017Review
- incaRNAfbinv: a web server for the fragment-based design of RNA sequences.Nucleic acids research · 2016Article
- RNAiFold2T: Constraint Programming design of thermo-IRES switches.Bioinformatics (Oxford, England) · 2016Article
- Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements.Scientific reports · 2016Article
- RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.Nucleic acids research · 2015Article
- An Efficient Minimum Free Energy Structure-Based Search Method for Riboswitch Identification Based on Inverse RNA Folding.PloS one · 2015Article
- Magnesium-dependent folding of a picornavirus IRES element modulates RNA conformation and eIF4G interaction.The FEBS journal · 2014Article
- Functional and structural analysis of maize hsp101 IRES.PloS one · 2014Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Internal ribosome entry site (IRES) elements govern protein synthesis of mRNAs that bypass cap-dependent translation inhibition under stress conditions. Picornavirus IRES are cis-acting elements, organized in modular domains that recruit the ribosome to internal mRNA sites. The aim of this study was to retrieve short RNA sequences with the capacity to adopt RNA folding patterns conserved with IRES structural subdomains, likely corresponding to RNA modules. We have applied a new program, RNAiFold, an inverse folding algorithm that determines all sequences whose minimum free energy structure is identical to that of the structural domains of interest. Sequences differing by more than 1 nt were clustered. Then, BLASTing one randomly chosen sequence from each cluster of the RNAiFold output, we retrieved viral and cellular sequences among output hits. As a proof of principle, we present the data corresponding to a coding region of Drosophila melanogaster TAF6, a transcription factor-associated protein that contains a structural motif within its coding region potentially folding into an IRES-like subdomain. This RNA region shows a biased codon usage, as predicted from structural constraints at the RNA level, it harbors conserved IRES structural motifs in loops, and interestingly, it has the capacity to confer internal initiation of translation in tissue culture cells.
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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.