Site-specific DNA recombinases are widely used in multicellular organisms to manipulate the structure of genomes and, in turn, to control gene expression (for reviews see refs below). These enzymes, derived from bacteria and fungi, catalyze directionally sensitive DNA exchange reactions between short (30–40 nucleotides) target site sequences that are specific to each recombinase . These reactions enable four basic functional modules—excision/insertion, inversion, translocation and cassette exchange—that have been used individually or combined in a wide range of configurations to control gene expression (Fig. 1).
Cre recombinase, like all site-specific recombinases (SSRs), excises or recombines DNA depending on the relative orientation of short, directional DNA sequences . The 34 base pair (bp) lox sites, recognized by Cre, consist of two 13 bp palindromic regions and an intervening non-palindromic 8 bp spacer that determines the orientation of the site. When two lox sites are oriented in the same direction, Cre excises the DNA flanked by the lox sites, leaving a single lox site behind. Conversely, when the lox sites are oriented in the opposite direction, Cre flips the flanked DNA into the antisense orientation. Both reactions involve the exchange of DNA between the two lox sites and are normally reversible .
Differences in palindromic or spacer regions of lox sites, either naturally occurring  or randomly mutated , can confer specificity to Cre recognition. Exploiting lox variants that undergo variant-specific recombination has enabled strategies for making Cre recombination effectively irreversible [7, 8, 9, 10]. The FLEx system, first used as a Cre-reporter (Schnütgen et al. 2003) and then applied to rAAV transgenes [10, 11], uses recombination between two pairs of like loxP and lox2272 sites to confer a permanent recombination event. Expression in the presence of Cre (“Cre-On”) is achieved by FLEx recombination of a transgene that changes the orientation of the coding sequence with respect to the promoter from the anti-sense to sense. Conversely, inactivation of expression in the presence of Cre (“Cre-Off”) can be achieved by simply starting the transgene in the sense orientation.
Cre-On rAAVs have been used widely to study the function of Cre-expressing neuron populations ([12, 13] and Cardin et al. 2009), whereas Cre-Off rAAVs, despite their experimental value, have received only minor attention [10, 14].
- Lox FAS .
Flp is the most widely used recombinase in Drosophila, encoded by the Saccharomyces cerevisiae 2-μm plasmid . Flp was first shown to work in a heterologous, multicellular organism by Golic and Lindquist in 1989  who demonstrated the excision reaction on chromosomally inserted target sites (FRTs). Since that time FLP/FRT recombination has been widely used in Drosophila in applications based on excision  and translocation (Golic 1991) [18, 19].
See for example: Nern et al., 2011. Multiple new site-specific recombinases for use in manipulating animal genomes, Proc Natl Acad Sci U S A. 2011 Aug 23;108(34):14198-203. . Nern et al tested 4 new recombinases derived from yeast: KD, B2, B3, and R.
- Atasoy et al. A FLEX switch targets Channelrhodopsin-2 to multiple cell types for imaging and long-range circuit mapping. J Neurosci. 2008 Jul 9;28(28):7025-30. .
- Livet et al. Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature. 2007 Nov 1;450(7166):56-62. .
- Cre-Lox recombination on Wikipedia.
- Site-specific recombinase technology on Wikipedia.
- Brainbow on Wikipedia.
- García-Otín AL, Guillou F. Mammalian genome targeting using site-specific recombinases. Front Biosci. 2006 Jan 1;11:1108-36.
- Dymecki SM, Kim JC. Molecular neuroanatomy's "Three Gs": a primer. Neuron. 2007 Apr 5;54(1):17-34.
- Luan H, White BH. Combinatorial methods for refined neuronal gene targeting. Curr Opin Neurobiol. 2007 Oct;17(5):572-80.
- Birling MC, Gofflot F, Warot X. Site-specific recombinases for manipulation of the mouse genome. Methods Mol Biol. 2009;561:245-63.
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