ArticleNucleic acids research2017
In-cell SHAPE uncovers dynamic interactions between the untranslated regions of the foot-and-mouth disease virus RNA.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 25 citations in OpenAlex.
- Decoding the Structural Complexity of Viral RNAs with SHAPE to Guide Antiviral Therapeutics.Viruses · 2026Review
- Ins and outs of IRES elements: function and significance.Biochemical Society transactions · 2025Review
- Review
- RNA levers and switches controlling viral gene expression.Trends in biochemical sciences · 2023Review
- Recent advances in RNA structurome.Science China. Life sciences · 2022Review
- Picornavirus translation strategies.FEBS open bio · 2022Review
- Article
- RNA-Binding Proteins at the Host-Pathogen Interface Targeting Viral Regulatory Elements.Viruses · 2021Article
- Activation of viral transcription by stepwise largescale folding of an RNA virus genome.Nucleic acids research · 2020Article
- Lead-seq: transcriptome-wide structure probing in vivo using lead(II) ions.Nucleic acids research · 2020Article
- Physical and Functional Analysis of Viral RNA Genomes by SHAPE.Annual review of virology · 2019Review
- Rab1b and ARF5 are novel RNA-binding proteins involved in FMDV IRES-driven RNA localization.Life science alliance · 2019Article
- Deconstructing internal ribosome entry site elements: an update of structural motifs and functional divergences.Open biology · 2018Review
- The Structure-To-Function Relationships of Gammaherpesvirus-Encoded Long Non-Coding RNAs and Their Contributions to Viral Pathogenesis.Non-coding RNA · 2018Review
- Emergency Services of Viral RNAs: Repair and Remodeling.Microbiology and molecular biology reviews : MMBR · 2018Review
- Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis.The journal of physical chemistry. B · 2018Article
- Ribosome-dependent conformational flexibility changes and RNA dynamics of IRES domains revealed by differential SHAPE.Scientific reports · 2018Article
- The Functional Role of the 3' Untranslated Region and Poly(A) Tail of Duck Hepatitis A Virus Type 1 in Viral Replication and Regulation of IRES-Mediated Translation.Frontiers in microbiology · 2018Article
- A Dual Interaction Between the 5'- and 3'-Ends of the Melon Necrotic Spot Virus (MNSV) RNA Genome Is Required for Efficient Cap-Independent Translation.Frontiers in plant science · 2018Article
- Insights into Structural and Mechanistic Features of Viral IRES Elements.Frontiers in microbiology · 2017Review
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The genome of RNA viruses folds into 3D structures that include long-range RNA–RNA interactions relevant to control critical steps of the viral cycle. In particular, initiation of translation driven by the IRES element of foot-and-mouth disease virus is stimulated by the 3΄UTR. Here we sought to investigate the RNA local flexibility of the IRES element and the 3΄UTR in living cells. The SHAPE reactivity observed in vivo showed statistically significant differences compared to the free RNA, revealing protected or exposed positions within the IRES and the 3΄UTR. Importantly, the IRES local flexibility was modified in the presence of the 3΄UTR, showing significant protections at residues upstream from the functional start codon. Conversely, presence of the IRES element in cis altered the 3΄UTR local flexibility leading to an overall enhanced reactivity. Unlike the reactivity changes observed in the IRES element, the SHAPE differences of the 3΄UTR were large but not statistically significant, suggesting multiple dynamic RNA interactions. These results were supported by covariation analysis, which predicted IRES-3΄UTR conserved helices in agreement with the protections observed by SHAPE probing. Mutational analysis suggested that disruption of one of these interactions could be compensated by alternative base pairings, providing direct evidences for dynamic long-range interactions between these distant elements of the viral genome.
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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.