The X element, a novel LINE transposable element from Drosophila melanogaster

Whilst analysing the nature of repeated DNA sequences in the transition zon e between euchromatin and heterochromatin at the base of the X chromosome o f Drosophila melanogaster, we discovered a novel transposable element of th e LINE class that we have named the X element. Several apparently complete elements have been cloned and analysed, and one has been sequenced. It is 4 740 by long, with a polyadenylation sequence and a run of A residues at one end. It contains two ORFs: the 5 ' ORF is related to the retroviral gag ge ne and encodes a protein with cysteine-rich motifs that are thought to form a "zinc-knuckle" in a nucleic-acid binding protein; the 3 ' ORF encodes a putative reverse transcriptase that includes the conserved domains found in reverse transcriptases from other LINEs and retroviruses. The DNA sequence and the sequences of the predicted gene products are most similar to other LINEs from D. melanogaster, such as the F, jockey, Doc and BS elements. So uthern analysis suggests that there are at least 30 copies in the genome an d that some elements are polymorphic between different strains. Analysis of the DNA sequence of the: euchromatic arms of the Drosophila genome identif ied five full-length elements and a similar number of elements that were in tact at the 3 ' end but had variable 5 ' truncations. Sequences flanking tw o different insertion sites were used to design PCR primers to assess the o ccupancy of sites in wild-type flies of different geographical origins. Fli es that lacked each of the insertions were found, suggesting that the eleme nt is an active transposon.