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Depositordc.contributorSimpson, Colin
Funderdc.contributor.otherWellcome Trusten_UK
Spatial Coveragedc.coverage.spatialUKen
Spatial Coveragedc.coverage.spatialUNITED KINGDOMen
Time Perioddc.coverage.temporalstart=2014-02-01; end=2014-04-30; scheme=W3C-DTFen
Data Creatordc.creatorSimmonds, Peter
Date Accessioneddc.date.accessioned2014-11-19T10:13:27Z
Date Availabledc.date.available2014-11-19T10:13:27Z
Citationdc.identifier.citationSimmonds, Peter. (2014). RNA composition metrics, 2014 [dataset]. University of Edinburgh. Roslin Institute. https://doi.org/10.7488/ds/188.en
Persistent Identifierdc.identifier.urihttps://hdl.handle.net/10283/671
Persistent Identifierdc.identifier.urihttps://doi.org/10.7488/ds/188
Dataset Description (abstract)dc.description.abstractMutating RNA virus genomes to alter codon pair (CP) frequencies and reduce translation efficiency has been advocated as a method to generate safe, attenuated virus vaccines. However, selection for disfavoured CPs leads to unintended increases in CpG and UpA dinucleotide frequencies that also attenuate replication. We designed and phenotypically characterised mutants of the picornavirus, echovirus 7, in which these parameters were independently varied to determine which most influenced virus replication. CpG and UpA dinucleotide frequencies primarily influenced virus replication ability while no fitness differences were observed between mutants with different CP usage where dinucleotide frequencies were kept constant. Contrastingly, translation efficiency was unaffected by either CP usage or dinucleotide frequencies. This mechanistic insight is critical for future rational design of live virus vaccines and their safety evaluation; attenuation is mediated through enhanced innate immune responses to viruses with elevated CpG/UpA dinucleotide frequencies rather the viruses themselves being intrinsically defective.en_UK
Dataset Description (TOC)dc.description.tableofcontents1) Supplementary File 1: Nucleotide sequences of mutants used in the study Supplementary File 1.doc 2) Composition and codon usage metrics for human mRNA Human mRNA composition.xls 3) Composition and codon usage metrics for A. thaliana mRNA A.thaliana Composition table.xls 4) Composition and codon usage metrics for C. elegans mRNA C.elegans_Composition table.xls 5) Composition and codon usage metrics for E. coli mRNA E.coli_Composition table.xls 6) Codon pair usage tables for human, A. thaliana, C. elegans and E. coli. CPS tables.xlsen_UK
Languagedc.language.isoengen_UK
Publisherdc.publisherUniversity of Edinburgh. Roslin Instituteen_UK
Relation (Is Version Of)dc.relation.isversionofNoen_UK
Relation (Is Referenced By)dc.relation.isreferencedbyPending.en_UK
Subjectdc.subjectdinucleotide, RNA, virus, codon pairen_UK
Subject Classificationdc.subject.classificationBiological Sciencesen_UK
Titledc.titleRNA composition metricsen_UK
Typedc.typedataseten_UK

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