Author/Editor | Hancock, John M.; Vogler, Alfried P. | |
Title | Modelling the secondary structures of slippage-prone hypervariable RNA regions | |
Type | članek | |
Vol. and No. | Letnik 26, št. 7 | |
Publication year | 1998 | |
Volume | str. 1689-1699 | |
ISSN | 0305-1048 - Nucleic acids research | |
Language | eng | |
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. | |
Keywords | hipervariabilne regije RNA modeliranje sekundarnih struktur ohranjene strukture hypervariable RNA regions modelling the secondary structures conserved structures |