Clean molecularly-defined manipulations of single genes at their endogenous loci offer an invaluable tool to study a myriad of questions relevant to eukaryotic biology. Drosophila reverse genetic techniques for generating loss-of-function alleles had proven to be challenging until Golic and colleagues introduced in vivo gene targeting using homologous recombination to Drosophila 1-3. They demonstrated that specific genomic loci could be targeted using a linear fragment of DNA from an integrated transgenic construct. This linear "donor" DNA is generated in vivo through FRT-mediated recombination (to excise the DNA from the chromosome as a circular molecule) followed by linearization with the meganuclease I-SceI. Although this methodology has been successfully used to generate a variety of defined lesions, the technique has not been easily scalable for the manipulation of numerous genes in parallel because each individual knockout construct requires distinct and custom design. For example, difficulties in seamlessly manipulating large fragments of DNA (>5 kb) in vitro using classical restriction enzyme/ligation cloning or PCR, as well as the size limitations of traditional in vivo transformation vectors often interfere with the rapid creation of homologous recombination targeting vectors. To overcome these limitations, we combined the recombineering/transgenesis P[acman] system, which allows the sub-cloning and transgenesis of up to 100 kb of DNA, with the ends-out gene targeting methodology to establish an efficient and relatively rapid platform that facilitates Drosophila gene targeting.
Recombination-mediated genetic engineering (recombineering) is a powerful homologous recombination-based cloning technology 4,5. In contrast to conventional restriction enzyme/ligase cloning, recombineering is not limited by the sequence or size of the manipulated DNA. Recombineering uses a special E. coli strain that harbors recombination machinery provided by a defective λ prophage 4. This technique has recently been adopted for use in Drosophila 6,7. Recombineering in Drosophila relies on a modified conditionally amplifiable bacterial artificial chromosome (BAC) vector called P[acman] 6,7. This vector carries two origins of replication: OriV, which produces high-copy number upon chemical induction for the purification of large quantities of DNA required for sequencing and embryo injection and OriS, which maintains low-copy number under basal conditions. Additionally, the P[acman] vector is equipped with a bacterial attachment (attB) site. The attB site serves as a substrate for ΦC31 integrase-mediated transgenesis that allows incorporation of large DNA fragments into a predetermined landing site within the Drosophila genome 8,9.
We have generated a P[acman] vector (referred to as P[acman]-KO 1.0) that can be used as a targeting vector for ends-out homologous recombination 10,11. To incorporate ends-out gene targeting technology into the system, we added two FRT and two I-SceI sites. We have also included a Gateway cassette within this modified vector to streamline the process of incorporating the homology arms into P[acman]-KO 1.0. This provides a rapid and simple way to introduce virtually any genomic region of interest into the targeting vector. In this protocol we will describe how to engineer a targeting vector using P[acman]-KO 1.0, and how to mobilize this vector in vivo to target the endogenous locus. For the purpose of this protocol we will use the RFP/Kan cassette to replace a gene of interest, but a variety of cassettes that contain an antibiotic selection marker can be used with this protocol. We have designed and successfully used a set of cassettes for gene replacement and tagging 10,11.