P elements are thought to replicate themselves starting with the association of the left and right ends, followed by a cutcopy-paste process. An abnormal form of this process has been shown to occur when the associated left and right ends come from sister elements rather than from the same element, leading to formation of a 'hybrid element.' These ends can insert nearby in the genome to produce recombination, with associated structural changes. We have previously increased the frequency of such 'hybrid element insertion' by combining end-deleted elements in trans in a genotype with a left-end on one chromosome and a right-end on the homologous chromosome. Although many recombinants produced by this genotype have structural changes expected with insertion, nearly 50% of the predicted insertional recombinants contain no structural change. We present evidence using RFLP markers closely linked to the end-deleted elements that in these cases the P element ends dissociate before insertion, and are subsequently ligated together following a process analogous to synthesis-dependent strand annealing. The results suggest that broken ends containing P elements are resolved by the same repair process as ends not containing P elements, and that such repair from hybrid element events may occur in the majority of cases.

P-element-induced recombination in Drosophila melanogaster occurs premeiotically. Recombinants are therefore expected to accumulate in the stem cells of the germline of Pelement-carrying males. We show that both the recombination frequency and the incidence of “clustering” increase with the age of males carrying various P-element derivatives. The combination of end-deleted elements can lead to average recombination frequencies >50% with individual instances of 100% recombination. These elements also lowered the fertility of the carriers. We investigated these features by constructing an analytical and a computer simulation model of the course of events in the germline, incorporating the recently proposed hybrid element insertion (HEI) model of Pelement activity. The model is able to predict extreme recombination levels, segregation ratio biases and lowered fertility through cell death in a single analysis.

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.