The use of site-specific recombinase systems has revolutionized our ability to genetically manipulate embryonic stem (ES) cells and mice. Recent advances using the Cre-loxP and Flp-FRT systems have now made it possible to generate ‘clean’ germline mutations following a single gene targeting event, as well as to (in)activate genes in a conditional manner in the living mouse. Not only can target gene mutations be induced in a spatially and temporally restricted fashion, but lineage tracers can be activated in specific progenitor populations to chart cell fate directly in the wild-type or mutant mouse. This chapter introduces site-specific recombination and details a variety of applications, many of which are extensions of the gene targeting vectors and manipulations presented by Hasty et al. in Chapter 1. Many of the mutagenesis techniques which exploit the Cre-loxP system have been compiled earlier in an excellent book by Torres and Kühn (1). In this chapter, I present the Flp-FRT system in addition to the Cre-loxP system, for individual or combined uses. Together, these surveys and protocols should provide a basis for a wide variety of studies on gene function in vivo. As novel recombinase based applications continue to be developed, the possibilities for genome engineering appear without limit. The simplest site-specific recombination systems are comprised of two elements: the recombinase enzyme and a small stretch of DNA specifically recognized by the particular recombinase. These two elements work together to either delete, insert, invert, or translocate associated DNA. Two such recombinase systems have been established in mice (2-5) providing the basic tools for in vivo genetic engineering: the Cre-loxP system from the bacteriophage P1 and the Flp-FRT system from the budding yeast Saccharomyces cerevisiae. Both Cre and Flp are members of the λ integrase superfamily of site-specific recombinases (6) that cleave DNA at a distinct target sequence and then ligate it to the cleaved DNA of a second identical site to generate a contiguous strand. This recombination reaction is carried out with absolute fidelity, such that not a single nucleotide is gained or lost overall, and with no other requirements than the recombinase, the specific target DNA sequence, and some mono- or divalent cations (7).
Xer-mediated site-specific recombination at cer generates Holliday junctions in vivo.
