RNA composition metrics

  • Peter Simmonds (Infection and Immunity, Roslin Institute, University of Edinburgh, Edinburgh United Kingdom.) (Creator)
  • Colin Simpson (Creator)



1) 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.xls


Mutating 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.

Data Citation

Simmonds, Peter. (2014). RNA composition metrics, 2014 [dataset]. University of Edinburgh. Roslin Institute. http://dx.doi.org/10.7488/ds/188.
Date made available19 Nov 2014
PublisherEdinburgh DataShare
Temporal coverage1 Feb 2014 - 30 Apr 2014

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