Properties of re-arranged P elements in Drosophila melanogaster

Abstract

P elements, both complete and incomplete, contain a left and right end, normally depicted as pointing away from each other. Here, we examine the properties of P elements that may be described as 're-arranged elements' or 'inside-out elements', containing inverted ends. Two such structures exist, having either ends pointing towards each other, 'headto-head or H-H', or ends pointing in the same direction 'head-to-tail or H-T'. We show that both structures are unstable in the presence of P element transposase. For the H-H element there is a high frequency of deletion of the intervening material and almost exact rejoining of element ends with the 4 bp CATG palindromic end sequence shared by the two element ends. This result is predicted by the Beall and Rio model of P element excision. For the H-T element there is a high frequency of exact excision of the entire inverted right-end, a result again predicted by the Beall and Rio model. Both structures lead to recombination in the way expected from a normal element. The rates of recombination are, however, much lower than might be expected from the organization of ends, a result that can be explained in terms of the low likelihood of insertion into a chromosomal region lacking another P element end. We also investigate the properties of combinations of re-arranged and normal elements, and show that there is a directionality property when left and right ends are combined in trans that can be explained in terms of strand repair.

The Tempo and Mode of Evolution of Transposable Elements as Revealed by Molecular Phylogenies Reconstructed From Mosquito Genomes

“…Recombination can occur in adjacent copies of very similar sequences, and recombinant hybrid P elements have indeed been described in Drosophila (Svoboda et al 1995). A recent work analyzing recombination in Drosophila's P elements indicated not only the recombination rates to be small, leading mostly to deletions or inversions, but also fusion of truncated elements (Liang and Sved 2009). A logical extension to the work would be to partition the alignment and estimate the evolutionary rates for different TE structures separately.…”