Unusual structure of the FB family of transposable elements in Drosophila

We have analyzed the construction of the members of the foldback (FB) family of transposable elements in Drosophila by detailed restriction analysis, cross hybridization, electron microscopy, in situ hybridization and nucleotide sequence determination. The members are heterogeneous, with both the inverted terminal repeats and the total element sizes extremely variable. Nevertheless, the ends of the inverted repeats represent closely conserved sequences, similar for all members. Sequence analysis of one of the FB elements revealed an unusual constriction. There are scattered multiple copies of a 10 bp sequence near the inverted repeat termini; 300 bp from the end this sequence is expanded to a 20 bp repeat, and 500 bp from the end it is again expanded to a 31 bp repeat. A large part of the inverted repeats consists of contiguous tandem repeats of this 31 bp sequence. We also find two differences between the two copies of the inverted repeat, one of which involves an intact copy of the 10 bp sequence mentioned above. Sequence analysis of a corresponding DNA segment without this transposable element shows that insertion generates a 9 bp duplication at the target site. In situ hybridizations to polytene chromosomes show about 30 widely scattered positions with homology. Comparison of the hybridization patterns for three strains shows significant interstrain and intrastrain differences in chromosomal locations.