The Importance of Transpositions and Recombination to Genome Instability According hobo-Element Distribution Pattern in Completely Sequenced Genome of Drosophila melanogaster

Abstract

Transposable elements (TEs) constitute a considerable part of many eukaryotic genomes; therefore, the interest in the patterns of TE distribution in genomes is natural. We have analyzed the distribution of hobo transposon in the Drosophila melanogaster strain y cn bw sp, whose genome is almost completely sequenced. Based on the experimental and in silico data, we have grouped all hobo into the “old” and “new” sites and demonstrated that the old hobo sites are short variable regions predominantly located near the chromocenter, whereas the new sites are spread over the genome with the preference of chromosome central regions. As a rule, the defective hobo copies have lost the terminal repeats and the central part of DNA sequence, containing potential TATA boxes. Except for the complete hobo, only one defective hobo variant is able to transpose in this genome. The active (capable of transposing) hobo variants are excised, whereas the passive variants accumulate in the pericentromeric regions. The inactive deficient hobo sequences are accumulated in the chromosome regions with a decreased recombination frequency, whereas the active copies, moved mainly by transposases, do not follow this rule. Analysis of the direct repeat formed at the sites of hobo insertion and belonging to hobo sequences has demonstrated that some number of hobo copies can increase due to an unequal crossing-over. Recombinations are more frequently observed between the neighboring than between remote hobo elements, as defective hobo from the neighboring chromosome regions display a higher homology to each other than to the hobo elements located on different chromosomes. Such recombination can produce locus-specific instability as was shown before. Computer analysis of the number of hypothetical direct repeats remaining after the excision of hobo confirms the earlier published hypothesis that the last hobo invasion into D. melanogaster genome could occur nearly 100 years ago. Nevertheless, in spite of high hobo transposition and recombination frequency there is no one detected hobo dependent genetic event in the D. melanogaster y cn bw sp genome.