Properties of Insertion Regions of Drosophila LTR Retrotransposons

Abstract

We applied in silico methods to analyze contextual and structural characteristics of Drosophila DNA in the regions of insertions of LTR retrotransposons belonging to 12 families, namely, 17.6, 297, blood, copia, Dm412 (mdg2), gypsy, HMSBeagle, mdgl, mdg3, roo (B104), tirant, and yoyo, and to detect the properties that might determine why these regions are preferable for integration of a particular LTR retrotransposon. Samples of genomic sequences with a length of 60 bp containing 4–5-bp target sites per se, which are duplicated during integration of LTR retrotransposons, and the sequences flanking target site, were studied. The insertions regions fall into three groups with respect to variation pattern of mononucleotide context of the target sites and their flanking regions. Each of the three groups displays a characteristic distribution of the DNA local conformational and physicochemical properties in the regions of insertions, which might determine that this particular region is chosen as preferable for insertion. Preferential insertion of retrotransposons in the regions of host DNA displaying certain specific conformational and physicochemical properties may reflect the distinctions between the structures of DNA-recognizing domains of integrases of particular LTR retrotransposons.