Modelling the secondary structures of slippage-prone hypervariable RNA regions: the example of the tiger beetle 18S rRNA variable region V4 - PubMed (original) (raw)

Modelling the secondary structures of slippage-prone hypervariable RNA regions: the example of the tiger beetle 18S rRNA variable region V4

J M Hancock et al. Nucleic Acids Res. 1998.

Abstract

Variable regions within ribosomal RNAs frequently vary in length as a result of incorporating products of slippage. This makes constructing secondary structure models problematic because base homology is difficult or impossible to establish between species. Here, we model such a region by comparing the results of the MFOLD suboptimal folding algorithm for different species to identify conserved structures. Based on the reconstruction of base change on a phylogenetic tree of the species and comparison against null models of character change, we devise a statistical analysis to assess support of these structures from compensatory and semi-compensatory (i.e. G.C to G.U or A.U to G.U) mutations. As a model system we have used variable region V4 from cicindelid (tiger beetle) small subunit ribosomal RNAs (SSU rRNAs). This consists of a mixture of conserved and highly variable subregions and has been subject to extensive comparative analysis in the past. The model that results is similar to a previously described model of this variable region derived from a different set of species and contains a novel structure in the central, highly variable part. The method we describe may be useful in modelling other RNA regions that are subject to slippage.

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References

    1. FEBS Lett. 1988 May 9;232(1):115-20 - PubMed
    1. Nucleic Acids Res. 1997 Jan 1;25(1):111-6 - PubMed
    1. Mol Biol Evol. 1988 Jul;5(4):377-91 - PubMed
    1. Mol Biol Evol. 1988 Jul;5(4):393-414 - PubMed
    1. Science. 1989 Apr 7;244(4900):48-52 - PubMed

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