ArticleNucleic acids research2008
Bioinformatic and functional analysis of RNA secondary structure elements among different genera of human and animal caliciviruses.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
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Who cites it
75 citing papers in PubMed.
- Article
- Highs and Lows in Calicivirus Reverse Genetics.Viruses · 2024Review
- Production of infectious reporter murine norovirus by VP2Journal of virology · 2024Article
- Comprehensive full genome analysis of norovirus strains from eastern India, 2017-2021.Gut pathogens · 2024Article
- Recent insights into reverse genetics of norovirus.Virus research · 2023Review
- Review
- Positive strand RNA viruses differ in the constraints they place on the folding of their negative strand.RNA (New York, N.Y.) · 2022Article
- Article
- Swine Norovirus: Past, Present, and Future.Viruses · 2022Review
- Article
- Protein Nucleotidylylation in +ssRNA Viruses.Viruses · 2021Review
- Review
- Genome-wide analyses of human noroviruses provide insights on evolutionary dynamics and evidence of coexisting viral populations evolving under recombination constraints.PLoS pathogens · 2021Article
- Article
- The dinucleotide composition of the Zika virus genome is shaped by conflicting evolutionary pressures in mammalian hosts and mosquito vectors.PLoS biology · 2021Article
- Impact of virus subtype and hostRNA (New York, N.Y.) · 2020Article
- Recombination at the emergence of the pathogenic rabbit haemorrhagic disease virus Lagovirus europaeus/GI.2.Scientific reports · 2020Article
- Viral replicons as valuable tools for drug discovery.Drug discovery today · 2020Review
- Article
- A functional investigation of the suppression of CpG and UpA dinucleotide frequencies in plant RNA virus genomes.Scientific reports · 2019Article
15 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The mechanism and role of RNA structure elements in the replication and translation of Caliciviridae remains poorly understood. Several algorithmically independent methods were used to predict secondary structures within the Norovirus, Sapovirus, Vesivirus and Lagovirus genera. All showed profound suppression of synonymous site variability (SSSV) at genomic 5' ends and the start of the sub-genomic (sg) transcript, consistent with evolutionary constraints from underlying RNA structure. A newly developed thermodynamic scanning method predicted RNA folding mapping precisely to regions of SSSV and at the genomic 3' end. These regions contained several evolutionarily conserved RNA secondary structures, of variable size and positions. However, all caliciviruses contained 3' terminal hairpins, and stem-loops in the anti-genomic strand invariably six bases upstream of the sg transcript, indicating putative roles as sg promoters. Using the murine norovirus (MNV) reverse-genetics system, disruption of 5' end stem-loops produced approximately 15- to 20-fold infectivity reductions, while disruption of the RNA structure in the sg promoter region and at the 3' end entirely destroyed replication ability. Restoration of infectivity by repair mutations in the sg promoter region confirmed a functional role for the RNA secondary structure, not the sequence. This study provides comprehensive bioinformatic resources for future functional studies of MNV and other caliciviruses.
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