ArticleNucleic acids research2010
Genomic analysis of codon, sequence and structural conservation with selective biochemical-structure mapping reveals highly conserved and dynamic structures in rotavirus RNAs with potential cis-acting functions.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
40 citing papers in PubMed, 65 citations in OpenAlex.
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- Engineering human/simian rotavirus VP7 reassortants in the absence of UTR sequence information.Applied microbiology and biotechnology · 2025Article
- Crystal structure and nucleic acid binding mode of CPV NSP9: implications for viroplasm in Reovirales.Nucleic acids research · 2024Article
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- A novel approach to finding conserved features in low-variability gene alignments characterises RNA motifs in SARS-CoV and SARS-CoV-2.Scientific reports · 2023Article
- Rotavirus RNA chaperone mediates global transcriptome-wide increase in RNA backbone flexibility.Nucleic acids research · 2022Article
- Decoding the effects of synonymous variants.Nucleic acids research · 2021Article
- Recent advances in rotavirus reverse genetics and its utilization in basic research and vaccine development.Archives of virology · 2021Review
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- Reovirus RNA recombination is sequence directed and generates internally deleted defective genome segments during passage.Journal of virology · 2021Article
- Intragenic recombination influences rotavirus diversity and evolution.Virus evolution · 2020Article
- Profiling of rotavirus 3'UTR-binding proteins reveals the ATP synthase subunit ATP5B as a host factor that supports late-stage virus replication.The Journal of biological chemistry · 2019Article
- Development of Stable Rotavirus Reporter Expression Systems.Journal of virology · 2019Article
- Genome packaging in multi-segmented dsRNA viruses: distinct mechanisms with similar outcomes.Current opinion in virology · 2018Review
- A new method for detecting signal regions in ordered sequences of real numbers, and application to viral genomic data.PloS one · 2018Article
- Protein-mediated RNA folding governs sequence-specific interactions between rotavirus genome segments.eLife · 2017Article
- Genetic determinants restricting the reassortment of heterologous NSP2 genes into the simian rotavirus SA11 genome.Scientific reports · 2017Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Rotaviruses are a major cause of acute, often fatal, gastroenteritis in infants and young children world-wide. Virions contain an 11 segment double-stranded RNA genome. Little is known about the cis-acting sequences and structural elements of the viral RNAs. Using a database of 1621 full-length sequences of mammalian group A rotavirus RNA segments, we evaluated the codon, sequence and RNA structural conservation of the complete genome. Codon conservation regions were found in eight ORFs, suggesting the presence of functional RNA elements. Using ConStruct and RNAz programmes, we identified conserved secondary structures in the positive-sense RNAs including long-range interactions (LRIs) at the 5' and 3' terminal regions of all segments. In RNA9, two mutually exclusive structures were observed suggesting a switch mechanism between a conserved terminal LRI and an independent 3' stem-loop structure. In RNA6, a conserved stem-loop was found in a region previously reported to have translation enhancement activity. Biochemical structural analysis of RNA11 confirmed the presence of terminal LRIs and two internal helices with high codon and sequence conservation. These extensive in silico and in vitro analyses provide evidence of the conservation, complexity, multi-functionality and dynamics of rotavirus RNA structures which likely influence RNA replication, translation and genome packaging.
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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.