Jm. Hancock et Ap. Vogler, MODELING THE SECONDARY STRUCTURES OF SLIPPAGE-PRONE HYPERVARIABLE RNAREGIONS - THE EXAMPLE OF THE TIGER BEETLE 18S RIBOSOMAL-RNA VARIABLE REGION V4, Nucleic acids research, 26(7), 1998, pp. 1689-1699
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 diffic
ult or impossible to establish between species. Here, we model such a
region by comparing the results of the MFOLD suboptimal folding algori
thm for different species to identify conserved structures. Based on t
he reconstruction of base change on a phylogenetic tree of the species
and comparison against null models of character change, we devise a s
tatistical analysis to assess support of these structures from compens
atory 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 (ti
ger beetle) small subunit ribosomal RNAs (SSU rRNAs). This consists of
a mixture of conserved and highly variable subregions and has been su
bject to extensive comparative analysis in the past. The model that re
sults is similar to a previously described model of this variable regi
on derived from a different set of species and contains a novel struct
ure in the central, highly variable part. The method we describe may b
e useful in modelling other RNA regions that are subject to slippage.