ArticlePeerJ2018
ScanFold: an approach for genome-wide discovery of local RNA structural elements-applications to Zika virus and HIV.
Article in PeerJ, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed.
- Hierarchical breakdown of RNA structure prediction in CASP16: from reliable local helices to speculative multimer assembly.Bioinformatics (Oxford, England) · 2026Article
- Integrated Bioinformatics and Network Analysis Identifies Key Molecular Targets and Hub Genes in Zika Virus-induced Neuroinflammation.Journal of molecular neuroscience : MN · 2026Article
- RNAStructuromeDB: a transcriptome-wide database of predicted RNA secondary structures with integrated APIs for functional annotation and RNA-targeted drug discovery.NAR genomics and bioinformatics · 2026Article
- Divergent RNA structures support accurate splicing of the SF3B1-sensitivebioRxiv : the preprint server for biology · 2026Article
- Decoding the Structural Complexity of Viral RNAs with SHAPE to Guide Antiviral Therapeutics.Viruses · 2026Review
- Transcriptome-wide analysis of Arabidopsis DICER-LIKE1 RNA substrates.Nucleic acids research · 2026Article
- DMS-informed secondary structure modeling of Epstein-Barr Virus LMP-1 pre-mRNA defines novel elements spanning introns.PloS one · 2026Article
- Discontinuous EBOV RNA synthesis events in patients with Ebola virus disease and their relationship to viral load and outcome of infection.Journal of virology · 2025Article
- Unbiased RNA Degrader Identification Uncovers an LC3B-Recruiting Chimera forJournal of the American Chemical Society · 2025Article
- Identification of conserved RNA secondary structures in human respiratory syncytial virus A (hRSV A).NAR genomics and bioinformatics · 2025Article
- Precursor RNA structural patterns at SF3B1 mutation sensitive cryptic 3' splice sites.RNA biology · 2025Article
- Importance of De Novo Gene Evolution to Emerging Viral Threats: The ORF10 Strain-Restricted Orphan Gene of SARS-CoV-2 Promotes Pathogenesis.Molecular biology and evolution · 2025Article
- A conserved long-range RNA interaction in SARS-CoV-2 recruits ADAR1 to enhance virus proliferation.Nature communications · 2025Article
- Structural analysis of the lncRNA SChLAP1 reveals protein binding interfaces and a conformationally heterogenous retroviral insertion.RNA (New York, N.Y.) · 2025Article
- Identification of a conserved RNA structure in thebioRxiv : the preprint server for biology · 2025Article
- Unraveling unbreakable hairpins: characterizing RNA secondary structures that are persistent after dinucleotide shuffling.RNA (New York, N.Y.) · 2025Article
- The Druggable Transcriptome Project: From Chemical Probes to Precision Medicines.Biochemistry · 2025Review
- Transcriptome-wide prediction of heat-sensitive RNA structures inFrontiers in plant science · 2025Article
- The RNA Revolution in the Central Molecular Biology Dogma Evolution.International journal of molecular sciences · 2024Review
- Intronic RNA secondary structural information captured for the humanNAR genomics and bioinformatics · 2024Article
8 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
In addition to encoding RNA primary structures, genomes also encode RNA secondary and tertiary structures that play roles in gene regulation and, in the case of RNA viruses, genome replication. Methods for the identification of functional RNA structures in genomes typically rely on scanning analysis windows, where multiple partially-overlapping windows are used to predict RNA structures and folding metrics to deduce regions likely to form functional structure. Separate structural models are produced for each window, where the step size can greatly affect the returned model. This makes deducing unique local structures challenging, as the same nucleotides in each window can be alternatively base paired. We are presenting here a new approach where all base pairs from analysis windows are considered and weighted by favorable folding. This results in unique base pairing throughout the genome and the generation of local regions/structures that can be ranked by their propensity to form unusually thermodynamically stable folds. We applied this approach to the Zika virus (ZIKV) and HIV-1 genomes. ZIKV is linked to a variety of neurological ailments including microcephaly and Guillain-Barré syndrome and its (+)-sense RNA genome encodes two, previously described, functionally essential structured RNA regions. HIV, the cause of AIDS, contains multiple functional RNA motifs in its genome, which have been extensively studied. Our approach is able to successfully identify and model the structures of known functional motifs in both viruses, while also finding additional regions likely to form functional structures. All data have been archived at the RNAStructuromeDB (www.structurome.bb.iastate.edu), a repository of RNA folding data for humans and their pathogens.
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