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Review

Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities

  • Marcel E. Dinger equal contributor,

    equal contributor Contributed equally to this work with: Marcel E. Dinger, Ken C. Pang, Tim R. Mercer

    Affiliation: ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia

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  • Ken C. Pang equal contributor,

    equal contributor Contributed equally to this work with: Marcel E. Dinger, Ken C. Pang, Tim R. Mercer

    Affiliation: T cell Laboratory, Ludwig Institute for Cancer Research, Melbourne Centre for Clinical Sciences, Austin Health, Heidelberg, Australia

    X
  • Tim R. Mercer equal contributor,

    equal contributor Contributed equally to this work with: Marcel E. Dinger, Ken C. Pang, Tim R. Mercer

    Affiliation: ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia

    X
  • John S. Mattick mail

    j.mattick@imb.uq.edu.au

    Affiliation: ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia

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  • Published: November 28, 2008
  • DOI: 10.1371/journal.pcbi.1000176

Reader Comments (1)

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A lesson from EBV

Posted by forsdyke on 11 Dec 2008 at 23:05 GMT

Yes, “the functionality of any transcript at the RNA level should not be discounted.” The glycine-alanine repeat region in the EBNA1 protein of Epstein-Barr virus (EBV) is an example. The preferential usage of purine-rich codons in stark contrast to other EBV genes implied a selective pressure acting at the mRNA level [1]. Recently, activities attributed to the repeat were found to be changed when alternative synonymous codons (that did not change the encoded amino acid) were employed [2]. This matter is discussed in detail elsewhere [3].

1. Cristillo AD, Mortimer JR, Barrette IH, Lillicrap TP, Forsdyke DR (2001) Double-stranded RNA as a not-self alarm signal: to evade, most viruses purine-load their RNAs, but some (HTLV-1, Epstein-Barr) pyrimidine-load. J Theor Biol 208:475-491.

2. Tellam J, Smith C, Rist M, Webb N, Cooper L, Vuocolo T, Connolly G, Tscharke DC, Devoy MP, Khanna R (2008) Regulation of protein translation through mRNA structure influences MHC class 1 loading and T cell recognition. Proc Natl Acad Sci USA 105:9319-9324.

3. Forsdyke DR (2006) Evolutionary Bioinformatics. Springer, New York.


RE: A lesson from EBV

JohnMattick replied to forsdyke on 12 Dec 2008 at 03:30 GMT

Dear Dr Forsdyke

Many thanks for pointing out this nice example. I was not aware of it previously but shall keep it in mind for the future.

Kind regards

John Mattick