ArticleJournal of virology2020
Using SHAPE-MaP To Model RNA Secondary Structure and Identify 3'UTR Variation in Chikungunya Virus.
Article in Journal of virology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers, 1 of them a synthesis that pooled it.
What it found
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Who cites it
39 citing papers in PubMed, 1 synthesis or guideline pooled it, 42 citations in OpenAlex.
- The life cycle of the alphaviruses: From an antiviral perspective.Antiviral research · 2023Pooled it
- Ewing sarcoma breakpoint region 1 (EWSR1) protein binds to nonstructural protein 2 and non-coding regions of chikungunya virus genome to inhibit virus replication.Journal of virology · 2026Article
- Comparative analysis of flavivirus sfRNA dynamics and secondary structure.Journal of virology · 2026Article
- RNAViruses · 2026Review
- A conserved in-frame stop codon acts as a multipotent defense mechanism in alphaviruses.Science advances · 2026Article
- Open questions on viral frameshifting: Exploiting the structural plasticity of the frameshifting element for therapeutic intervention.Biophysical journal · 2026Review
- Decoding the Structural Complexity of Viral RNAs with SHAPE to Guide Antiviral Therapeutics.Viruses · 2026Review
- Comparative analysis of flavivirus sfRNA dynamics and secondary structure.bioRxiv : the preprint server for biology · 2026Article
- Kinetic Traps in RNA Folding: Targeted Design of Frameshifting Element Mutants by Thermodynamic and Kinetic Analysis of the Chikungunya Virus.The journal of physical chemistry. B · 2026Article
- Review
- The Sindbis virus nsP3 opal codon protects viral RNA and fitness by maintaining replication spherule integrity.bioRxiv : the preprint server for biology · 2025Article
- Functional RNA Elements in Alphavirus Genomes.Current microbiology · 2025Review
- SMDesigner: a program to design sequence mutations to assess RNA structure.RNA (New York, N.Y.) · 2025Article
- High-throughput sequencing: a breakthrough in molecular diagnosis for precision medicine.Functional & integrative genomics · 2025Review
- Pathogenicity and virulence of chikungunya virus.Virulence · 2024Review
- Pathogenicity and virulence of chikungunya virus.Virulence · 2024Review
- Mapping the structural landscape of the yeast Ty3 retrotransposon RNA genome.Nucleic acids research · 2024Article
- Molecular basis of RNA recombination in the 3'UTR of chikungunya virus genome.Nucleic acids research · 2024Article
- Chikungunya Virus RNA Secondary Structures Impact Defective Viral Genome Production.Microorganisms · 2024Article
- Recruitment of multi-segment genomic RNAs by Bluetongue virus requires a preformed RNA network.Nucleic acids research · 2024Article
Corrections and comments
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Authors and funding
15 authors at 1 institution in 1 country.
Funding
Abstract
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus associated with debilitating arthralgia in humans. RNA secondary structure in the viral genome plays an important role in the lifecycle of alphaviruses; however, the specific role of RNA structure in regulating CHIKV replication is poorly understood. Our previous studies found little conservation in RNA secondary structure between alphaviruses, and this structural divergence creates unique functional structures in specific alphavirus genomes. Therefore, to understand the impact of RNA structure on CHIKV biology, we used SHAPE-MaP to inform the modeling of RNA secondary structure throughout the genome of a CHIKV isolate from the 2013 Caribbean outbreak. We then analyzed regions of the genome with high levels of structural specificity to identify potentially functional RNA secondary structures and identified 23 regions within the CHIKV genome with higher than average structural stability, including four previously identified, functionally important CHIKV RNA structures. We also analyzed the RNA flexibility and secondary structures of multiple 3'UTR variants of CHIKV that are known to affect virus replication in mosquito cells. This analysis found several novel RNA structures within these 3'UTR variants. A duplication in the 3'UTR that enhances viral replication in mosquito cells led to an overall increase in the amount of unstructured RNA in the 3'UTR. This analysis demonstrates that the CHIKV genome contains a number of unique, specific RNA secondary structures and provides a strategy for testing these secondary structures for functional importance in CHIKV replication and pathogenesis.
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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.