Nucleic Acids Research, Vol 26, Issue 7 1689-1699, Copyright © 1998 by Oxford University Press
JM Hancock and AP Vogler
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.
ARTICLES
Modelling the secondary structures of slippage-prone hypervariable RNA regions: the example of the tiger beetle 18S rRNA variable region V4
Gene and Genome Evolution Group, Medical Research Council Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital, London W12 0NN, UK. jhancock@rpms.ac.uk
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