Efficient gap repair in Drosophila melanogaster requires a maximum of 31 nucleotides of homologous sequence at the searching ends

P Transposable Elements in Drosophila and other Eukaryotic Organisms

P transposable elements were discovered in Drosophila as the causative agents of a syndrome of genetic traits called hybrid dysgenesis. Hybrid dysgenesis exhibits a unique pattern of maternal inheritance linked to the germline-specific small RNA piwi-interacting (piRNA) pathway. The use of P transposable elements as vectors for gene transfer and as genetic tools revolutionized the field of Drosophila molecular genetics. P element transposons have served as a useful model to investigate mechanisms of cut-and-paste transposition in eukaryotes. Biochemical studies have revealed new and unexpected insights into how eukaryotic DNA-based transposons are mobilized. For example, the P element transposase makes unusual 17nt-3' extended double-strand DNA breaks at the transposon termini and uses guanosine triphosphate (GTP) as a cofactor to promote synapsis of the two transposon ends early in the transposition pathway. The N-terminal DNA binding domain of the P element transposase, called a THAP domain, contains a C2CH zinc-coordinating motif and is the founding member of a large family of animal-specific site-specific DNA binding proteins. Over the past decade genome sequencing efforts have revealed the presence of P element-like transposable elements or P element transposase-like genes (called THAP9) in many eukaryotic genomes, including vertebrates, such as primates including humans, zebrafish and Xenopus, as well as the human parasite Trichomonas vaginalis, the sea squirt Ciona, sea urchin and hydra. Surprisingly, the human and zebrafish P element transposase-related THAP9 genes promote transposition of the Drosophila P element transposon DNA in human and Drosophila cells, indicating that the THAP9 genes encode active P element "transposase" proteins.

Gamma-irradiation stimulates homology-directed DNA double-strand break repair in Drosophila embryo

To test the DNA double-strand break (DSB) repair activities present in Drosophila early embryos, we have analyzed the circularization of a microinjected linear plasmid. In order to study repair by homologous recombination, the linear plasmid was injected with an homologous fragment encompassing the break. After extraction from embryos, repair products were analyzed directly by PCR and after their cloning into bacteria. We demonstrate, in addition to the repair by homologous recombination, the presence of an efficient end-joining activity in embryos. Plasmid circularization by end-joining was accompanied by short deletions frequently associated with non-random insertions. Most importantly, pre-irradiation of embryos specifically enhanced the accurate repair by homologous recombination. Such a stimulation is described for the first time in the context of a whole higher organism.

Gene targeting by homologous recombination in Drosophila

Drosophila offers many advantages as an experimental organism. However, in comparison with yeast and mouse, two other widely used eukaryotic model systems, Drosophila suffers from an inability to perform homologous recombination between introduced DNA and the corresponding chromosomal loci. The ability to specifically modify the genomes of yeast and mouse provides a quick and easy way to generate or rescue mutations in genes for which a DNA clone or sequence is available. A method is described that enables analogous manipulations of the Drosophila genome. This technique may also be applicable to other organisms for which gene-targeting procedures do not yet exist.

I-SceI endonuclease, a new tool for studying DNA double-strand break repair mechanisms in Drosophila

As a step toward the development of a homologous recombination system in Drosophila, we have developed a methodology to target double-strand breaks (DSBs) to a specific position in the Drosophila genome. This method uses the mitochondrial endonuclease I-SceI that recognizes and cuts an 18-bp restriction site. We find that >6% of the progeny derived from males that carry a marker gene bordered by two I-SceI sites and that express I-SceI in their germ line lose the marker gene. Southern blot analysis and sequencing of the regions surrounding the I-SceI sites revealed that in the majority of the cases, the introduction of DSBs at the I-SceI sites resulted in the complete deletion of the marker gene; the other events were associated with partial deletion of the marker gene. We discuss a number of applications for this novel technique, in particular its use to study DSB repair mechanisms.

Interspersed DNA element restricted to a specific group of telomeres in the dipteran Chironomus pallidivittatus

Telomeres in the dipteran Chironomus pallidivittatus terminate with 340bp tandem DNA repeats belonging to different subfamilies with characteristic intertelomeric distribution. We have now found, interspersed between such repeats, a composite element of approx. 1400bp present in two similar size variants, with several components of nontelomeric origin. There were about 50 copies of the element, predominantly or exclusively present in a previously defined group of telomeres, characterized by a unique set of telomeric tandem repeat subfamilies. Elements were integrated at irregular distances from each other, and intervening telomeric tandem repeat DNA was variable in composition. Nevertheless, the flanks immediately surrounding the elements were identical for different elements; in other words, there was a site-specific insertion. We suggest that this selective invasion of a small part of the genome by an interspersed, probably rapidly evolving element is best explained by repeated gene conversions.

Conversion of lacZ enhancer trap lines to GAL4 lines using targeted transposition in Drosophila melanogaster

Since the development of the enhancer trap technique, many large libraries of nuclear localized lacZ P-element stocks have been generated. These lines can lend themselves to the molecular and biological characterization of new genes. However they are not as useful for the study of development of cellular morphologies. With the advent of the GAL4 expression system, enhancer traps have a far greater potential for utility in biological studies. Yet generation of GAL4 lines by standard random mobilization has been reported to have a low efficiency. To avoid this problem we have employed targeted transposition to generate glial-specific GAL4 lines for the study of glial cellular development. Targeted transposition is the precise exchange of one P element for another. We report the successful and complete replacement of two glial enhancer trap P[lacZ, ry+] elements with the P[GAL4, w+] element. The frequencies of transposition to the target loci were 1.3% and 0.4%. We have thus found it more efficient to generate GAL4 lines from preexisting P-element lines than to obtain tissue-specific expression of GAL4 by random P-element mobilization. It is likely that similar screens can be performed to convert many other P-element lines to the GAL4 system.

In vivo gap repair in Drosophila: a one-way street with many destinations

While it has long been possible to study the process of recombination in yeast and other single-celled organisms, it has been difficult to distinguish between pathways of meiotic and mitotic recombination in multicellular eukaryotes. The experimental system described here bridges the historically separated fields of Genetic Recombination and DNA Repair in Drosophila. It is now feasible to study the repair of unique double-strand breaks induced in the Drosophila genome by the excision of a P-transposable element or by cleavage at an introduced endonuclease recognition sequence. This repair can be studied in both somatic cells and mitotically dividing germ cells. The repair of these breaks occurs mainly by copying sequence from a template located anywhere in the karyoplasm, and occurs in both male and female flies. This system, which was the first of its kind in metazoan organisms, is now being used for gene targeting in Drosophila. This review summarizes results that provide new insights into the process of gap repair in Drosophila and outline some recent experiments that demonstrate the power of the gene targeting technique.

Transposable element-host interactions: regulation of insertion and excision

Transposable elements propagate by inserting into new locations in the genomes of the hosts they inhabit. Their transposition might thus negatively affect the fitness of the host, suggesting the requirement for a tight control in the regulation of transposable element mobilization. The nature of this control depends on the structure of the transposable element. DNA elements encode a transposase that is necessary, and in most cases sufficient, for mobilization. In general, regulation of these elements depends on intrinsic factors with little direct input from the host. Retrotransposons require an RNA intermediate for transposition, and their frequency of mobilization is controlled at multiple steps by the host genome by regulating both their expression levels and their insertional specificity. As a result, a symbiotic relationship has developed between transposable elements and their host. Examples are now emerging showing that transposons can contribute significantly to the well being of the organisms they populate.

Homology requirements for targeting heterologous sequences during P-induced gap repair in Drosophila melanogaster

The effect of homology on gene targeting was studied in the context of P-element-induced double-strand breaks at the white locus of Drosophila melanogaster. Double-strand breaks were made by excision of P-w(hd), a P-element insertion in the white gene. A nested set of repair templates was generated that contained the 8 kilobase (kb) yellow gene embedded within varying amounts of white gene sequence. Repair with unlimited homology was also analyzed. Files were scored phenotypically for conversion of the yellow gene to the white locus. Targeting of the yellow gene was abolished when all of the 3' homology was removed. Increases in template homology up to 51 base pairs (bp) did not significantly promote targeting. Maximum conversion was observed with a construct containing 493 bp of homology, without a significant increase in frequency when homology extended to the tips of the chromosome. These results demonstrate that the homology requirements for targeting a large heterologous insertion are quite different than those for a point mutation. Furthermore, heterologous insertions strongly affect the homology requirements for the conversion of distal point mutations. Several aberrant conversion tracts, which arose from templates that contained reduced homology, also were examined and characterized.

Drosophila P-element transposase is a novel site-specific endonuclease

We developed in vitro assays to study the first step of the P-element transposition reaction: donor DNA cleavage. We found that P-element transposase required both 5' and 3' P-element termini for efficient DNA cleavage to occur, suggesting that a synaptic complex forms prior to cleavage. Transposase made a staggered cleavage at the P-element termini that is novel for all known site-specific endonucleases: the 3' cleavage site is at the end of the P-element, whereas the 5' cleavage site is 17 bp within the P-element 31-bp inverted repeats. The P-element termini were protected from exonucleolytic degradation following the cleavage reaction, suggesting that a stable protein complex remains bound to the element termini after cleavage. These data are consistent with a cut-and-paste mechanism for P-element transposition and may explain why P elements predominantly excise imprecisely in vivo.