The relative abundance of dinucleotides in transposable elements in five species.

Abstract

Burge, Campbell, and Karlin (1992) observed that the relative frequencies of diand trinucleotides characterize a genome, independent of its base composition and the coding and noncoding capacity of the regions analyzed. Species thus differ with regard to this genomic signature, which is constant in a given genome and shows similarities between related species (Gentles and Karlin 2001). The variation in the relative abundance of dinucleotides is interpreted as reflecting differences between species in the cellular machinery for replication and repair, which may select specific dinucleotides in the sequence (Campbell, Mrazek, and Karlin 1999). A tendency toward the suppression of CG is often observed and is interpreted as resulting from the action of methylation activities (Bird 1986). The dinucleotides pattern of the mitochondrial genome has also been shown to differ from that of the nuclear genome, and the explanation suggests that nuclear and mitochondrial genomes use independent DNA polymerase machinery and different methods of replication (Campbell, Mrazek, and Karlin 1999). We therefore wanted to find out whether transposable elements (TEs), which have been shown to have a greater AT content than their host genes in various species (Shields and Sharp 1989; Lerat, Capy, and Biemont 2002), have the same dinucleotides pattern as their host. TEs are repeated sequences that are able to move from one position to another along chromosomes. They were first discovered in maize by Barbara McClintock (1984) in the 1950s and seem to exist in all living organisms. They are divided into two main classes, according to the transposition intermediate they use (Capy et al. 1997, pp. 1–197). Class I consists of retrotransposons that use an RNA intermediate and are subdivided into two subclasses according to whether they do or do not have long terminal repeats (LTRs) at their extremities, LTR retrotransposons and non-LTR retrotransposons, respectively. Class II consists of transposons that use a DNA intermediate for transposition and code for a transposase. There is a third class that consists of foldback elements and MITEs, the transposition mechanism of which has not yet been elucidated.