# Patent

## Title
Method for the stable inversion of DNA sequence by site-specific recombination and DNA vectors and transgenic cells thereof

## Abstract

The invention relates to a method for the stable inversion of a DNA fragment upon recombinase-mediated rearrangements using two sets of two incompatible site-specific recombinase targeting sites (SSRTS) in the same order but in reverse orientation flanking the DNA fragment to be inverted. The invention also relates to a method for the stable inversion of the DNA fragment upon rearrangement mediated by a recombinase such as Cre recombinase. The invention also relates to a method for obtaining a transgenic cell of which at least one allele of a DNA sequence of interest is invalidated by a process of conditional deletion and the genome of which has a reporter gene inserted at the place of the DNA fragment deleted by the process of conditional deletion. A method to generate targeting sites to perform site-specific recombination mediated cassette exchange is also provided.

## Background
The present invention relates to biology and the technical field of genetic manipulation in a cell-free system, in isolated cells or in living organisms. More precisely, the invention relates to an isolated DNA molecule comprising at least a sequence A flanked by at least site specific recombinase targeting sequences (SSRTS) L1, and at least a sequence B flanked by at least site specific recombinase targeting sequences (SSRTS) L2, said SSRTS L1 and SSRTS L2 being unable to recombine with one another, and wherein sequences L1 are in an opposite orientation, sequences L2 are in an opposite orientation, and the order of SSRTS sequences in said DNA molecule is 5′-L1-L2-L1-L2-3′. The invention also relates to a method for the stable inversion of said DNA fragment A and/or B upon rearrangement mediated by recombinase such as Cre recombinase. The invention also relates to a method for obtaining a transgenic cell of which at least one allele of a DNA sequence of interest is invalidated by a process of conditional deletion and the genome of which comprises a reporter gene inserted at the place of the DNA fragment deleted by said process of conditional deletion. The invention also concerns a method to generate targeting sites allowing site-specific recombination mediated cassette exchange. The corresponding vector, host cells, and transgenic animals are claimed.
The advent of homologous recombination in mouse embryonic stem (ES) cells has provided a powerful system to analyze mammalian gene functions (Capecchi, 1989). In most studies, the primary goal has been to generate germ line null mutations (knockouts) of given genes, i.e. inactivation in all stages of life throughout the body. Such mutations have shown the extreme complexity of genetic determination in mammals. We are now facing several complicating phenomena, such as functional redundancy between genes belonging to large families, and developmental lethal phenotypes that prevent the study of either the complete spectrum of actions, or later functions of a given gene, respectively (Thomas, 1993; Copp, 1995).
The use of site-specific recombinases, mainly the Cre recombinase of the bacteriophage P1 and the yeast FLP recombinase, that catalyze the recombination of DNA between two specific targeting-sites [loxP and FRT sites, respectively (Sauer, 1988; O'Gorman, 1991)], now permits to study mice harboring somatic gene alterations which are either temporally- or spatially-restricted (Sauer et Henderson, 1989; Orban et al., 1992; Gu et al., 1993; Tsien et al., 1996; Nagy et al., 2000). The recent development of inducible forms of recombinases further gives the opportunity to induce gene alterations both at precise time points, and in specific cell types (Logie et Stewart, 1995; Metzger et al., 1995; Kellendonk et al., 1996; Brocard et al., 1997; Danielan et al., 1998; Schwenk et al., 1998; Li et al., 2000). These recombination-based strategies are likely to have a profound impact on developmental biology and the elucidation of gene physiological functions, and will also allow the generation of models for human diseases particularly when the underlying genetic changes, such as initiation of cancer, are somatic in nature. However, these strategies all require the availability of recombinase-expressing transgenic mouse lines, whose recombinase activity must be carefully characterized at the cellular level. This is usually performed using additional transgenic lines, whose capacity to express a reporter gene in given cells is dependent on a recombinase-mediated event (Akagi et al., 1997; Lobe et al., 1999; Mao et al., 1999; Soriano et al., 1999; Kawamoto et al., 2000; Novak et al., 2000). However, a frequently encountered problem in transgenic animal studies is position effect variegation, that frequently leads to mosaicism of transgene expression (Koestier et al., 1996). Concomitant mosaic expression of both the recombinase and reporter transgenes in 60% of the target cell population would dramatically limit the final reporter expression to only 36% (reviewed in Sauer, 1998). Moreover, even when both the recombinase and reporter transgene are expressed in the same cell, the latter may lie in a chromatin configuration inaccessible to recombination, further confounding analyses (Kellendonk et al., 1999). Altogether, these observations lead to the conclusion that one cannot easily extrapolate from the expression pattern of a reporter transgene to an identical targeting pattern for a conditional allele of a given gene.
The problem to be solved is to develop a system that would permit a clear identification of each individual cell in which recombination has taken place, at a given gene locus.
The inventors have solved the problem underlying the invention by developing a novel strategy that allows to readily detect individual cells in which Cre-mediated rearrangements have occurred. It relies upon (i) the property of Cre recombinase to both invert and excise any intervening DNA flanked by two loxP sites placed in opposite and identical orientations, respectively (Abremski et al., 1983), and (ii) the use of lox511 mutant sites, that can recombine with themselves, but not with wild type loxP sites (Hoess et al., 1986). Making use of this strategy for gene targeting in ES cells not only facilitates the identification of individual cells that undergo conditional gene inactivation in the mouse, but also allows spatio-temporally controlled sophisticated site-specific DNA modifications.
The present invention provides an isolated DNA molecule comprising at least a sequence A flanked by at least site specific recombinase targeting sequences (SSRTS) L1, and at least a sequence B flanked by at least site specific recombinase targeting sequences (SSRTS) L2, said SSRTS L1 and SSRTS L2 being unable to recombine with one another, and wherein the sequences L1 are in an opposite direction, the sequences L2 are in an opposite direction, and wherein the order of SSRTS sequences in said DNA molecule is 5′-L1-L2-L1-L2-3′. In one embodiment the order of sequences in said DNA molecule is: 5′-L1-sequence A-L2-sequence B-L1-L2-3′. In another embodiment, the order of sequences in said DNA molecule is: 5′-L1-L2-sequence A-sequence B-L1-L2-3′. In another embodiment, the order of sequences in said DNA molecule is 5′-L1-L2-sequence A-L1-sequence B-L2-3′.
As used herein, the term “DNA molecule” refers to a polynucleotide sequence such as a single or double stranded DNA sequence; such a polynucleotide sequence has been isolated or synthesized and may be constituted with natural or non natural nucleotides. In a preferred embodiment the DNA molecule of the invention is a double stranded DNA molecule.
Site specific recombinases are enzymes that are present in some viruses and bacteria and have been characterized to have both endonuclease and ligase properties. These recombinases (along with associated proteins in some cases) recognize specific sequences of bases in DNA and exchange the DNA segments flanking those segments (Landy et al., 1993). Site specific recombinases catalyze at least the following four events (1) deletion of a DNA fragment flanked by compatible site-specific recombinase targeting sites (SSRTS) in the same orientation (e.g. head-to-tail or tail-to-head); (b) inversion of a DNA fragment flanked by compatible SSRTS in opposite orientation (e.g. head-to-head or tail-to-tail); (c) integration of a cyclic DNA fragment containing an SSRTS into a compatible SSRTS; and (d) chromosomal translocation between compatible SSRTS located on different chromosomes. To perform those reactions, the site-specific recombinase has typically at least the following four activities: (1) recognition of one or two specific DNA sequences; (2) cleavage of said DNA sequence or sequences; (3) DNA topoisomerase activity involved in strand exchange; and (4) DNA ligase activity to reseal the cleaved strands of DNA (Sauer, 1994). Numerous recombination systems from various organisms have been described (Hœss, 1986; Abremski et al., 1986, Campbell, 1992; Qian et al., 1992; Araki et al., 1992; Maeser et al., 1991; Argos et al., 1986). Perhaps the best studied of these are the Integrase/att system from bacteriophage λ (Landy, 1993), the Cre/loxP system from bacteriophage P1 (Hœss and Abremski (1990), and the FLP/FRT system from the Saccharomyces cerevisiae 2 mu circle plasmid (Broach et al., 1982). Bebee et al. (U.S. Pat. No. 5,434,066) discloses the use of site-specific recombinases such as Cre for DNA containing two loxP sites is used for in vivo recombination between the sites. Hasan and Szybalski (1987) discloses the use of λInt recombinase in vivo for intramolecular recombination between wild type attP and attB sites which flank a promoter. Because the orientations of these sites are inverted relative to each other, this causes an irreversible flipping of the promoter region relative to the gene of interest. Posfai et al. (1994) discloses a method for inserting into genomic DNA partial expression vectors having a selectable marker, flanked by two wild-type FRT recognition sequences. FLP site-specific recombinase as present in the cells is used to integrate the vectors into the genome at predetermined sites. Schlake & Bode (1994) discloses an in vivo method to exchange expression cassettes at defined chromosomal locations, each flanked by a wild type and a spacer-mutated FRT recombination site. A double-reciprocal crossover was mediated in cultured mammalian cells by using this FLP/FRT system for site-specific recombination.
The recombinase specific of said SSRTS is selected from the group of site-specific recombinases composed of the Cre recombinase of bacteriophage P1, the FLP recombinase of Saccharomyces cerevisiae, the R recombinase of Zygosaccharomyces rouxii pSR1, the A recombinase of Kluyveromyces drosophilarium pKD1, the A recombinase of Kluyveromyces waltii pKW1, the integrase λInt, the recombinase of the GIN recombination system of the Mu phage, of the bacterial β recombinase or a variant thereof. In a preferred embodiment, the recombinase is the Cre recombinase of bacteriophage P1 (Abremski et al., 1984), or its natural or synthetic variants. Cre is available commercially (Novagen, Catalog No. 69247-1). Recombination mediated by Cre is freely reversible. Cre works in simple buffers with either magnesium or spermidine as a cofactor, as is well known in the art. The DNA substrates can be either linear or supercoiled. A number of mutant loxP sites have been described (Hoess et al., 1986; Lee et al., 1998), indeed, the corresponding SSRTS L1 and/or L2 specific for said Cre recombinase are chosen from the group composed of the sequences Lox P1 (ATCC 53 254 et 20 773), Lox 66, Lox 71, Lox 511, Lox 512, Lox 514, Lox B, Lox L, Lox R and mutated sequences of Lox P1 site harboring at least one point mutation in the 8 nucleotide spacer sequence. In one embodiment, the point mutation is substitution of A for G at position 7 of the eight base spacer sequence of the wild type Lox P1 sequence, referred to herein as the Lox511 sequence. Preferred SSRTS are Lox P1 (SEQ ID N° 52) and Lox 511 (SEQ ID N° 53).
Such Lox 511 recombines with another Lox 511 site, but cannot recombine with another Lox P site such as a Lox P1 site. Accordingly, in a preferred embodiment, the SSRTS L1 comprises the Lox P1 nucleotide sequence and SSRTS L2 comprises the Lox 511 nucleotide sequence or SSRTS L1 comprises the Lox 511 sequence and SSRTS L2 comprises Lox P1 sequence. In another embodiment, the recombinase is the FLP recombinase of Saccharomyces cerevisiae, or its natural or synthetic variants and the SSRTS L1 and/or L2 specific for said FLP recombinase are chosen from the group composed of the sequences FRT-S and FRT-F30.88.
Site-specific recombinase variants means the wild type recombinases, or fragments thereof, that correspond to truncations, substitutions, deletions and/or additions of amino acid moieties. In a preferred embodiment, these recombinases and the fragments thereof correspond to variations due to genetic polymorphism. Recombinase fragment means any part of the recombinase with at least a recombinase activity. Site-specific recombinase variants also means synthetic variants in which the preceding modifications are not naturally present but have been artificially introduced, by genetic engineering for example. Indeed recombinases obtained by chimeric fusions represent synthetic variants of the invention. Such recombinases have been described in Shaikh and Sadowski (2000). In one embodiment, the site-specific recombinases of the invention can be genetically engineered to be expressed as a fusion protein with a nuclear receptor for a steroid hormone such as the estrogen nuclear receptor or the glucocorticoid nuclear receptor for example. Such chimeric recombinases can be temporarily activated by the natural or a synthetic ligand of such a nuclear receptor (For review, see Feil et al., 1996; Brocard et al., 1997; Indra et al., 1999; Schwenk et al., 1998).
In one embodiment, the recombinase specific to said SSRTS L1 and the recombinase specific to said SSRTS L2 are the same. By “same recombinase” it is meant that the recombinase specific to SSRTS L1 catalyzes recombination at SSRTS L1 and L2 and the recombinase specific to SSRTS L2 catalyzes recombination at SSRTS L2 and L1. For example, site-specific recombination is catalyzed by the “same” Cre recombinase at LoxP1 and Lox511 sequences. In another embodiment, the recombinase specific to said SSRTS L1 and the recombinase specific to said SSRTS L2 are different. By “different recombinase” it is meant that the recombinase specific to SSRTS L1 cannot catalyze recombination at a SSRTS L2 sequence and the recombinase specific to SSRTS L2 cannot catalyze recombination at a SSRTS L1. An example of site-specific recombinations catalyzed by “different” recombinases is the recombination by the Cre recombinase at the SSRTS L1 sequence corresponding to a LoxP1 site and the recombination by the FLP recombinase at the SSRTS L2 sequence corresponding to a FRT site. In another embodiment, different recombinases can respectively catalyze recombination at both SSRTS L1 and SSRTS L2 sequences; for example, a wild type and a mutated Cre recombinases can both catalyze recombination at the SSRTS L1 sequence corresponding to a LoxP1 and at the SSRTS L2 sequence corresponding to a Lox511, but these two recombinases will have a better specificity for one or the other recombination sequence.
The site-specific recombinase targeting sequences (SSRTS) are particular DNA sequences which a protein, DNA, or RNA molecule (e.g. restriction endonuclease, a modification methylase, or a recombinase) recognizes and binds. For example, the recognition sequence for Cre recombinase is loxP (locus of Cross over) which is a 34 base pair sequence comprised of two 13 base pair inverted repeats (serving as the recombinase binding sites) flanking an 8 base pair core sequence (See FIG. 1 of Sauer, 1994). As used herein, the term “direction of SSRTS” refers to the orientation of its spacer region, which determines the orientation of the complete SSRTS.
Other examples of recognition sequences are the attB, attP, attL, and attR sequences which are recognized by the recombinase enzyme λ integrase (Landy, 1993) or FRT sequences which are recognized by the FLP recombinase.
The term “SSRTS sequences unable to recombine with one another” or incompatible SSRTS sequences refers to two or more SSRTS sequences (referred to herein as L1, L2, but also L3, L4, L5, L6, . . . L10 etc . . . ) which differ from one another and, therefore, can not undergo recombination with one another. For example, lox sequences can be rendered incompatible if their nucleotide sequences differ by only one nucleotide, particularly in their spacer regions. In contrast, the term “compatible lox sequences” refers to two or more lox sequences, which can recombine when, catalyzed to do so by a recombinase.
The above recombinases and corresponding recombinase-targeting sites are suitable for use in recombination cloning according to the present invention. However, wild-type recombination targeting sites can contain sequences that reduce the efficiency or specificity of recombination reactions as applied in methods of the present invention. For example, multiple stop codons in attB, attR, attP, attL and loxP recombination sites occur in multiple reading frames on both strands, so recombination efficiencies are reduced, e.g., where the coding sequence must cross the recombination sites, (only one reading frame is available on each strand of loxP and attB sites), or impossible (in attP, attR or attL). Accordingly, the present invention also uses engineered recombination sites. For example, Lox sites can be engineered to have one or multiple mutations to enhance specificity or efficiency of the recombination reaction and the properties of the DNA of the invention, or to decrease the reverse reaction. The testing of these mutants determines which mutants yield sufficient recombinational activity to be suitable for recombination reaction according to the present invention. Mutations can therefore be introduced into recombination sites or into recombinases for enhancing site specific recombination. Such mutations introduced into recombination sites include, but are not limited to, recombination sites without translation stop codons that allow fusion proteins to be encoded, recombination sites recognized by the same proteins but differing in base sequence such that they react largely or exclusively with their homologous partners to allow multiple reactions to be contemplated. Which particular reactions take place can be specified by which particular partners are present in the reaction mixture. There are well known procedures for introducing specific mutations into nucleic acid sequences. A number of these are described in Ausubel et al. (1989). Mutations can be designed into oligonucleotides, which can be used to modify existing cloned sequences, or in amplification reactions. Random mutagenesis can also be employed if appropriate selection methods are available to isolate the desired mutant DNA or RNA. The presence of the desired mutations can be confirmed by sequencing the nucleic acid by well-known methods.
In another embodiment, said DNA molecule of the invention is further flanked by at least site specific recombinase targeting sequences (SSRTS). Such SSRTS sequences are the same or are different from the preceding ones. In a preferred embodiment such SSRTS sequences are different and are placed in the same orientation to further allow the excision of said DNA molecule, or are placed in the opposite orientation to further allow the inversion of said DNA molecule or are incompatible sequences to allow site-specific recombination mediated cassette exchange (RMCE). It is also in the scope of the present invention to create DNA molecules of the invention or to use the method of the invention with additional sets of SSRTS sequences (L3, L4, L5, L6, . . . , L10 etc . . . ) in order to multiply the possibilities of such a system.
In a preferred embodiment, the sequences A and B are in the opposite orientation. By sequences A and B in the opposite orientation, it means that the coding sequences of sequences A and B are not present on the same DNA strand. Thus, on the same strand, sequence A is orientated 5′ to 3′ and sequence B is orientated 3′ to 5′. In another embodiment, the sequences A and B are in the same orientation; this means that the coding sequences of sequences A and B are present on the same DNA strand. Sequences A and B comprise at least non transcribed sequences, transcribed but not translated sequences, transcribed and translated sequences (i.e. gene). In a preferred embodiment, sequences A and/or B can encode for at least one gene. The term “gene” refers to a nucleic acid sequence that encodes a protein or a peptide. This gene can derive from genomic DNA or recombinant DNA such as cDNA. Said gene encodes a protein, a polypeptide, a peptide, protein fragments, for example an exon; more precisely said protein is selected in the group consisting of reporter proteins, selectable markers and proteins of interest.
The reporter protein of the invention is selected in the group consisting of autofluorescent proteins and enzymes detectable by a histochemical process. The autofluorescent protein is selected in the group consisting of the green fluorescence protein (GFP), the enhanced green fluorescence protein (EGFP), the red fluorescence protein (RFP), the blue fluorescence protein (BFP), the yellow fluorescence protein (YFP) and the fluorescent variant of these proteins. The enzyme detectable by a histochemical process is selected in the group consisting of β-galactosidase, β-glucoronidase, alcaline phosphatase, luciferase, alcohol deshydrogenase, chloramphenicol-acetyl transferase, peroxydase. In a preferred embodiment, the β-galactosidase gene is used. The substrate to be used with these specific enzymes are generally chosen for the production, upon hydrolysis by the corresponding enzyme, of a detectable colour change. Substrate can be soluble or insoluble, added into the culture medium or in the organism, or present in the host cell, depending upon the chosen method. For example, 5-bromo-4-chloro-3-indoyl phosphate/nitroblue tetrazolium is suitable for use with alkaline phosphatase conjugates; for peroxidase conjugates, 1,2-phenylenediamine-5-aminosalicylic acid, 3,3,5,5,-tetramethylbenzidine, tolidine or dianisidine are commonly used.
In a second preferred embodiment, the reporter gene is the luciferase gene.
Selectable marker means a DNA segment that allows one to select for or against a molecule or a cell that contains it, often under particular conditions. These markers can encode an activity, such as, but not limited to, production of RNA, peptide, or protein, or can provide a binding site for RNA, peptides, proteins, inorganic and organic compounds or compositions and the like. Examples of selectable markers include but are not limited to DNA segments that encode products which provide resistance against otherwise toxic compounds (e.g., antibiotics). For example, the ampicillin or the neomycin resistance genes constitute selectable marker of the invention. These selectable markers can be either positive or negative (see Capecchi et al., U.S. Pat. No. 5,631,153). For example, the pair (positive selectable marker gene/selective agent) is selected among: (Neomycine resistance gene/G418), (Hygromycine resistance gene/Hygromycine), (His D gene/Histidinol), (Gpt gene/Xanthine), (HGPRT gene/Hypoxanthine).
For example, the pair (negative selectable marker/selective agent) is selected among: (HSV-TK gene/Acyclovir-Gancyclovir), (HPRT/6-Thioguanine), (GPT/6-Thioguanine), (Cytosine deaminase/5 fluoro-cytosine). The selectable marker can also be the diphteric toxin A (DTA).
Selectable markers also include DNA segments that encode products which are otherwise lacking into the recipient cell (e.g., tRNA genes, auxotrophic markers), or DNA segments that encode products which suppress the activity of a gene product.
The protein of interest of the present invention can be any protein. For example, the protein of interest can be a therapeutic protein, such as α-, β-, δ-globin, blood coagulation factors (e.g., Factors VIII and IX), cell surface receptors, enzymes and other desirable proteins, for example, to correct inherited or acquired deficiencies of these proteins in an individual.
In one embodiment, the sequences A and/or B are coding for at least one exon, or a fragment thereof. In a preferred embodiment, said exon differs from the wild type exon of a protein of interest by one or more point mutations. Those point mutations can be deletions, insertions or substitutions. In the case that a fusion translation product is synthetized, one can introduce an IRES (Internal ribosome entry site) in the gene sequence. For example, said protein can be encoded by a cDNA sequence, and an IRES sequence can be inserted in a position 5′, or 3′, or 5′ and 3′ to said cDNA sequence.
Sequences A and/or B can contain all the genetic information needed for gene(s) expression such as promoter sequences, regulatory upstream elements, transcriptional and/or translational initiation, termination and/or regulation elements.
The present invention also provides a vector comprising the isolated DNA molecule of the invention. A “vector” is a replicon in which another polynucleotide segment is attached, so as to allow the replication and/or expression of the attached segment. Examples of vectors include plasmids, phages, cosmids, phagemids, yeast artificial chromosomes (YAC), bacterial artificial chromosomes (BAC), human artificial chromosomes (HAC), viral vectors, such as adenoviral vectors, retroviral vectors, and other DNA sequences which are able to replicate or to be replicated in vitro or in a host cell, or to convey a desired DNA segment to a desired location within a host cell. A vector can have one or more restriction endonuclease recognition sites at which the DNA sequences can be cut in a determinable fashion without loss of an essential biological function of the vector, and into which a DNA fragment can be spliced in order to bring about its replication and cloning. Vectors can further provide primer sites (e.g. for PCR), transcriptional and/or translational initiation and/or regulation sites, recombinational signals, replicons, selectable markers, etc. Beside the use of homologous recombination or restriction enzymes to insert a desired DNA fragment into the vector, UDG cloning of PCR fragments (U.S. Pat. No. 5,334,575), T:A cloning, and the like can also be applied. The cloning vector can further contain a selectable marker suitable for use in the identification of cells transformed with the cloning vector.
The present invention also relates to the use of the isolated DNA molecule or the vector of the invention as a transgene. Such transgene can be introduced into a host cell either in vivo or in vitro using known techniques, such as CaPO4 precipitation, electroporation, cationic lipofection, use of artificial viral envelopes, direct injection (e.g., intravenous, intraperitoneal or intramuscular micro-injection into a zygote or a pronucleus of a zygote) Thus, the invention relates to an isolated transgenic host cell transformed by an isolated DNA molecule or a vector according to the invention. A “host”, as the term is used herein, includes prokaryotic or eukaryotic organisms that can be genetically engineered. For examples of such hosts, see Sambrook et al., (1989).
In a preferred embodiment, the isolated DNA molecule or vector of the invention is integrated by homologous recombination in at least one targeted locus of the genome of the isolated transgenic host cell of the invention. To perform such homologous recombination, it is preferable that sequences of homology are present at both extremities of said DNA molecule.
In another embodiment, said isolated DNA molecule or said vector is integrated in sites of the genome of said isolated transgenic host cell chosen among polyA sites and gene promoters. The specific embodiment allows one to perform gene trapping which is a general method for mutagenesis based on random integration of a DNA fragment encoding for a reporter gene or a selectable marker gene (Hill and Wurst, 1993). Two gene trap methods are commonly used, the polyA trap based method and the promoter based method.
In another embodiment said isolated DNA molecule or said vector is randomly integrated in at least one locus of the genome of said isolated transgenic host cell.
In another embodiment said isolated DNA molecule or said vector is maintained in an episomal form in said isolated transgenic host cell.
The present invention also relates to the transgenic organism, comprising at least one cell according to the invention. An “organism” as the term is used herein, includes but is not limited to, bacteria, yeast, animal, plants. Among the animals, one can designate mammals, such as rodents, primates, including humans, farm animals. In a preferred embodiment, the animal is a mouse, a rat, a Guinea pig, a hamster, a rabbit, a pig, a cow, a horse, a goat, a sheep.
In another embodiment, the invention relates to a method for the stable inversion of a DNA sequence comprising the steps of (i) contacting a DNA molecule according to the invention, or a DNA vector according to the invention with at least one recombinase specific of said SSRTS L1 and one recombinase specific specific to said SSRTS L2; and (ii) inversion of said sequences A and B or sequence A or sequence B by recombination catalyzed by said recombinase at either SSRTS L1 or L2 sequences; and (iii) excision by recombination catalyzed by said recombinase of a DNA fragment comprised between the SSRTS L1 or L2 sequences that are now present in the same orientation following the inversion of step (ii), and that are able to recombine with one another. In a preferred embodiment, said DNA fragment excised in step (iii) comprises the sequence A.
In another embodiment, the invention relates to a method for obtaining a transgenic cell of which at least one allele of a DNA sequence of interest is invalidated by a process of conditional deletion and the genome of which comprises a reporter gene and/or a marker gene and/or a gene encoding a protein of interest inserted at the place of the DNA fragment deleted by said process of conditional deletion, said method comprises the steps of (i) preparation of a DNA molecule according to the invention wherein sequence A or sequence B is coding at least for part of the DNA fragment of interest to be invalidated and sequence B or sequence A is coding at least for a reporter gene and/or a marker gene and/or a gene encoding a protein of interest; (ii) obtention of a transgenic cell genetically modified by the targeted insertion by homologous recombination at the place of said DNA sequence of interest, of a DNA molecule prepared at step (i); (iii) contacting said DNA molecule with at least one recombinase specific to SSRTS L1 and one recombinase specific to SSRTS L2; (iv) inversion of sequences A and B or sequence A or sequence B by recombination catalyzed by said recombinase at either SSRTS L1 or SSRTS L2 sequences; and (v) excision of a DNA sequence by recombination catalyzed by said recombinase at SSRTS L2 or SSRTS L1 respectively, these SSRTS L2 or SSRTS L1 sequences being now present in the same orientation following the inversion of step (iii), and being able to recombine with one another. In a preferred embodiment, the order of sequences in said DNA molecule is 5′-L1-sequence A-L2-sequence B-L1-L2-3′ and a sequence of homology with the DNA sequence of interest are present at both extremities of said DNA molecule in order to perform homologous recombination and the DNA fragment excised in step (v) comprises sequence A. In another embodiment, the order of sequences in said DNA molecule is 5′-L1-L2-sequence A-sequence B-L1-L2-3′ and a sequence of homology with the DNA sequence of interest is present at both extremities of said DNA molecule. In another embodiment, the order of sequences in said DNA molecule is 5′-L1-L2-sequence A-L1-sequence B-L2-3′ and a sequence of homologis with the DNA sequence of interest are present at both extremities of said DNA molecule. In a preferred embodiment, said reporter gene, marker gene, and gene encoding the protein of interest of the invention encoded by the DNA sequence is only expressed following the inversion step (iv). The reporter gene, the marker gene, the gene encoding the protein of interest of the invention can be promotorless so that it will only be expressed when integrated into the targeted DNA molecule (i.e. the acceptor molecule) containing a promoter to drive its expression.
In another embodiment, the invention relates to a method to generate targeting sites allowing site-specific recombination mediated cassette exchange (RMCE), said method comprising the steps of (i) preparation of a first DNA molecule comprising a first DNA sequence of interest flanked by incompatible SSRTS L1 and L2 in an opposite orientation, obtainable by the method of the invention; (ii) preparation of a second DNA molecule comprising a second DNA sequence of interest flanked by the same incompatible SSRTS L1 and L2 as in step (i) in an opposite orientation, by an in vitro DNA cloning method; (iii) contacting said first and said second DNA molecule with at least one recombinase specific to said SSRTS L1 and one recombinase specific to said SSRTS L2; and (iv) exchange by recombination catalyzed by said recombinase of said first and said second DNA sequence of interest comprised between the SSRTS L1 and L2. Said in vitro DNA cloning method of step (ii) is any method known by the man skilled in the art that can be used to clone said second molecule. Such methods use basic tools that are described in Sambrook et al. (1989) for example. In another embodiment, said second DNA molecule of step (ii) is obtainable by the method of the invention. The method of the present invention, to perform site-specific RMCE, utilizes a recombinase mediated exchange reaction which takes place between identical or compatible (i.e., able to recombine with one another) SSRTS sequences. The efficient exchange of DNA between identical or compatible SSRTS sequences enables transfer of DNA from an acceptor (said first DNA molecule) to a donor (the second DNA molecule), each of which contains identical or compatible SSRTS sites. However, once transferred from donor to acceptor vector (i.e., intermolecular transfer), the transferred DNA is “locked” into place due to the incompatibility of the two SSRTS L1 and L2 sequences within the acceptor vector which prevent intramolecular exchange and excision of the transferred DNA. Therefore, the transferred DNA is integrated in a highly stable manner. The DNA which is transferred from the donor to the acceptor vector by way of the site-specific recombination method of the invention can be any DNA desired for stable integration into a host cell genome.
In a first embodiment, the steps of the methods of the invention are performed in a cell free system.
In a second embodiment, the steps of the methods of the invention are performed in the isolated host cell or in the cell of the organism of the invention. In these latter cases, these methods can further comprise a step of introducing into the cell a gene encoding the corresponding site-specific recombinase. The introduction of the site-specific recombinase can be made via the introduction of an expression vector comprising a gene coding for said recombinase. In a preferred embodiment, such gene encoding said site-specific recombinase is stably inserted into the genome of said cell. In another embodiment said vector is maintained in said cell in an episomal form. The Recombinase expression can be driven by a promoter or a tissue-specific promoter: the expression can be either constitutive or inducible. In another embodiment, the recombinase gene or the recombinase gene product is injected into the cell by micro-injection, or by liposome fusion for example.
In a preferred embodiment, of the methods of the invention, the SSRTS L1 sequence comprises the Lox P1 sequence and SSRTS L2 sequence comprises the Lox 511 sequence, or SSRTS L1 sequence comprises the Lox 511 sequence and SSRTS L2 sequence comprises Lox P1 sequence, and the corresponding site-specific recombinase is Cre or its natural or synthetic variants.
More generally, the invention relates to the use of a DNA molecule, and/or a vector, and/or a cell of the invention to perform site-specific stable inversion of a DNA sequence. In a preferred embodiment, the invention relates to the use of a DNA molecule, and/or a vector, and/or a cell of the invention to perform site-specific recombination mediated cassette exchange (RCME).
It is also a goal of the invention to furnish kits for performing stable inversion of DNA sequence and/or site-specific recombination cassette exchange (RCME), said kit comprising at least a DNA molecule, and/or a vector, and/or a cell of the invention.
It is also a goal of the invention to furnish a living organism, except human, that comprises at least one transgenic cell obtainable by the method of the invention. Said organism is selected in the group consisting of bacteria, yeast, Caenorhabditis elegans, Drosophila melanogaster, zebrafish, mice, rat, rabbit, hamster, Guinea pig, cow, pig, goat, sheep, horse, primate. In a preferred embodiment, the living organism of the invention is a mouse. In another preferred embodiment, the living organism of the invention is a yeast.
Accordingly, the methods, DNA molecules and vectors of the invention can be used for a variety of therapeutic and diagnostic applications which require stable and efficient integration of transgene sequences into genomic DNA of cells (gene therapy). The methods, DNA molecules and vectors can be used to transform a wide variety of eukaryotic cells (e.g., mammalian) cells and provide the advantage of high efficiency DNA transfer.
The figures and examples presented below are provided as further guide to the practitioner of ordinary skill in the art and are not to be construed as limiting the invention in anyway.



BRIEF DESCRIPTION OF THE DRAWINGS
FIGS. 1A–1D. General scheme of the proposed methods. (A) Schematic drawing of a DNA, allowing conditional exchange of fragment 1 (or fragment A) by fragment 2 (or fragment B), consisting of SSRTS L1, DNA fragment 1, SSRTS L2 in sense orientation, DNA fragment 2, in antisense orientation, SSRTS L1 and SSRTS L2 reversely orientated to the first SSRTS L1 and to the first SSRTS L2, respectively. (B) Intermediate step after recombinase-mediated inversion at SSRTS L1, leading to directly repeated SSRTS L2 (asterisk) flanking DNA fragment 1. This reaction represents an equilibrium with the substrate (A). (C) Intermediate step after recombinase-mediated inversion at SSRTS L2, leading to directly repeated SSRTS L1 (asterisk) flanking DNA fragment 1. This reaction represents an equilibrium with the substrate (A). (D) Final DNA after recombinase-mediated excision of DNA fragment 1 between the directly repeated SSRTS (asterisks). This reaction is not reversible and will shift the equilibrium from the first reaction towards the product (D).
FIGS. 2A–D. Schematic representation of the construct pFlExR and of the expected plasmids after Cre-mediated rearrangement. (A) pFlExR (SEQ ID N.degree. 54) contains, in the following order, the SV40 promoter (broken arrow), a loxP site (open arrowhead), a lox511 site (closed arrowhead), the coding sequence for the enhanced-green fluorescent protein (EGFP) linked to a poly-adenylation signal, the .beta.-galactosidase promoter-less minigene (LacZ) in the antisense orientation, a loxP and a lox511 sites in inverted orientations. The SV40 promoter first drives the expression of EGFP. (B) Intermediate step after Cre-mediated inversion at the loxP sites. (C) Intermediate step after Cre-mediated inversion at the lox511 sites. (D) Final product after Cre-mediated excision between the two lox511 or the two loxP sites (asterisks). In this plasmid, SV40 promoter now drives beta-galactosidase expression. This reaction is not reversible, as the final plasmid contains single loxP and lox511 sites, which cannot recombine together.
FIGS. 3A–D. In vitro Cre recombinase-mediated inversion/excision assay. (A) Schematic drawing of the ploxLacZlox construct used to check for Cre preparation efficiency before (upper panel) and after (lower panel) Cre-mediated recombination. EcoRV restriction sites and location of probes 1 and 2 are indicated. (B) Schematic drawing of pFlExR (SEQ ID N.degree. 54) before (upper panel) and after (lower panel, pFlExRrec) Cre-mediated recombination. EcoRV and XbaI restriction sites, together with location of probes 1 and 2 are indicated. (C) Evidence for Cre-mediated recombination by Southern blot analysis of plasmids digested with EcoRV and XbaI using probe 1. Lane 1 and 2, loxP-flanked LacZ plasmid (ploxLacZlox); lane 3 and 4, pFlExR; lane 5 and 6, pFlExRrec (inverted/excised pFlExR, see Materials and Methods). A crude Cre preparation was added in reactions illustrated in lanes 2, 4 and 6, whereas a heat-inactivated Cre preparation was added in reactions shown in lanes 1, 3 and 5. (D) Evidence for Cre-mediated recombination probing the same Southern blot as in (C) using probe 2 (for details see Materials and Methods). Note that the excised lacZlox fragment (3.7 kb), which does not contain plasmid sequences, was lost during amplification in bacteria. Open arrowhead, loxP site; closed arrowhead, lox511 site.
FIGS. 4A–H. In vivo Cre recombinase-mediated inversion/excision assay. COS-1 cells were transiently transfected with either pFlExR in absence (A and C) or in presence (B and D) of five fold excess pSG5-Cre, and transfected with pFlExRrec in absence (E and G) or in presence (F and H) of excess pSG5-Cre. Detection of EGFP was examined by fluorescence microscopy (A, B, E and F) and LacZ expression was assessed by light microscopy after X-Gal staining (C, D, G and H). Note that the background blue staining in FIG. 3C most probably reflects a low level of transcription of the beta-galactosidase minigene initiated from the non-coding strand of the pFlExR.
FIGS. 5A–D. Generation of a conditonal RAR.gamma. allele by homologous recombination. (A) Schematic drawing of the RAR.gamma. locus. Exons 7 to 14 are shown as solid boxes. As indicated, E7 is specific for RAR.gamma..sup.2, while E8 to E14 are common to all isoforms. The promoter (P2) is indicated by a broken arrow. 5′ and 3′ untranslated regions are shown as white boxes. Exon 8, whose splice acceptor is shown as waved lines, was chosen for the conditional disruption of RAR.gamma. (B) Structure of the targeting vector (p.gamma.6.0Flex.beta.-Gal) (SEQ ID N.degree. 55). (C) Structure of the recombinant allele following homologous recombination. (D) Structure of the recombinant allele after FLP-mediated removal of the selection cassette.
FIGS. 6A–D. Expected structures of the RAR.gamma. locus after Cre mediated recombination. (A) Structure of the modified RAR.gamma. locus, after FLP-mediated removal of the selection cassette. Dotted lines represent the expected splicing of the primary transcript. (B) Transient structure of RAR.gamma. locus of A after Cre-mediated inversion of the DNA fragment flanked by loxP sites. The asterisk points to the direct repeat of lox511 sites. (C) Transient structure of RAR.gamma. locus after Cre-mediated inversion of the DNA fragment flanked by lox511 sites. The asterisk points to the direct repeat of loxP sites. (D) Structure of RAR.gamma. locus after Cre-mediated excision at the repeated lox sites (asterisks in B and C). Dotted lines represent the expected splicing of the primary transcript.
FIGS. 7A–E. Possible applications of the present invention. (A) Conditional knockout linked to simultaneous activation of a reporter. The scheme represents a conditional allele expressing the wild type protein (left side); upon Cre-mediated rearrangement (right side), exon 2 is removed and replaced by the reporter gene and its polyadenylation signal. Thus, replacement of the normal gene product by the reporter protein renders possible the direct identification of individual cells that underwent recombination (i.e. gene knockout). (B) Cassette exchange. The scheme represents a locus after Cre-mediated inversion/excision (left side). A further Cre-mediated rearrangement in the presence of a circular DNA containing a loxP-Cre-lox511 cassette (right side) leads to the exchange between the reporter and Cre genes. (C) Conditional rescue. The scheme represents a knock-in reporter allele (left side). After Cre-mediated rearrangement (right side), the reporter cassette is removed together with its polyadenylation signal, while the wild type exon is restored in the sense orientation. (D) Conditional point mutation. The scheme represents a conditional allele expressing the wild type protein (left side). Upon Cre-mediated rearrangement (right side), exon 2 is removed and replaced by mutated exon 2 (E2m), giving rise to the synthesis of a mutated protein. (E) Conditional gene replacement. The scheme represents a conditional allele expressing the wild type protein (left side). After Cre-mediated rearrangement (right side), exon 2 is removed and replaced by a cassette containing an internal ribosomal entry site (IRES) followed by a chosen cDNA and a polyadenylation signal. Synthesis of the wild type protein is abrogated, whereas the introduced cDNA is now expressed. Dotted lines represent the expected splicing of the primary transcript, and E1 to E3 stands for exons. Open and closed arrowheads represent loxP and lox511, respectively.
FIGS. 8A–D. Description of the construct pJMG and the expected variants after Cre-mediated rearrangement. (A) Schematic drawing of pJMG which contains, in the following order, an FRT site (closed flag), a loxP site (open arrowhead), a lox511 site (closed arrowhead), a DNA cassette consisting of the rabbit .beta.-globin intron splice acceptor site (SA), an IRES sequence linked to the promoter-less nls-.beta.-galactosidase mini gene (LacZ) and a loxP site in antisense orientation, a PGK promoter (broken arrow) driving expression of the neomycin phosphotransferase coding sequence (Neo) linked to the OBS sequence and a synthetic splice donor (SD), a lox511 site and a mutated FRT site (FRTm; open flag) in antisense orientation. (B) Intermediate step after Cre-mediated inversion at the loxP sites. (C) Intermediate step after Cre-mediated inversion at the lox511 sites. (D) Final product after Cre-mediated excision between the two lox511 or the two loxP sites (asterisks), removing the PGK Neo Cassette. This reaction is not reversible, as the final plasmid contains single loxP and lox511 sites, which cannot recombine together.
FIGS. 9A–C. In vitro Cre recombinase-mediated inversion/excision assay on plasmid pJMG (SEQ ID N.degree. 56). (A) Schematic drawing of pJMG (upper panel), the intermediate construct pJMG-f (middle panel) and the final construct pJMG-fx (lower panel). HindIII restriction sites, together with the location of the probe are indicated. (B) Evidence for Cre-mediated recombination assessed by ethidium bromide stained agarose gel analysis of HindIII digested plasmids. Lane 1 and 2, loxP-flanked LacZ plasmid (ploxLacZlox); lane 3 and 4, pJMG; lane 5 and 6, pJMF-f (inverted pJMG, see Materials and Methods); lane 7 and 8, pJMG-fx (inverted and excised pJMG, see Materials and Methods). A Cre preparation was added in the reactions illustrated in lanes 2, 4, 6 and 8, whereas a heat-inactivated Cre preparation was added in the reactions shown in lanes 1, 3, 5 and 7. The sizes of the expected HindIII fragments are indicated on the right. (C) Evidence for Cre-mediated recombination assessed by Southern blot using a probe recognizing the rabbit beta-globin splice acceptor site (for details see Materials and Methods) Note that this probe does not hybridise to the ploxLacZlox. Open arrowhead, loxP site; closed arrowhead, lox511 site; closed flag, FRT site; open flag, FRTm site, SD, synthetic splice donor.
FIGS. 10A–D. Scheme of the gene trap strategy. Upon insertion of the pJMG vector into an intron of a transcribed locus, transcription of the trapped gene should not be affected (Trapped allele, WT). The PGK promoter drives the expression of the NEO cassette linked to the 3′ part of the trapped gene that provides the poly-A signal necessary to produce a stable mRNA. The cell is thus resistant to G418 selection (NeoR), whereas the LacZ gene is silent (LacZ0). Upon Cre-mediated recombination, the Neo gene is removed and LacZ is inverted. The cell becomes sensitive to G418 selection (NeoS), whereas the LacZ gene is expressed under the control of the trapped promoter (LacZ+). Dotted lines represent the expected splicing of the primary transcript; E1 and E2 stands for exons 1 and 2; SA indicates rabbit .beta.-globin splice acceptor site; IRES stands for internal ribosomal entry site. Open and closed arrowheads represent loxP and lox511 sites, respectively. Closed and open flags represent FRT and mutated FRT sites, respectively, SD, synthetic splice donor.
FIGS. 11A–I. In vivo assay to test for functionality of the splice acceptor-IRES LacZ cassette and/or the polyA trap based method in F9 cells. F9 cells were stably transfected with the NotI fragment of pJMG-f, selected against G418 for 12 days and subjected to X-gal staining. As expected, neomycin resistant clones were obtained, out of which some of them expressed lacZ. Panels A-1 depict individual clones showing varying degrees of activity.
FIGS. 12A–I. Possible applications using recombinase mediated cassette exchange. (A) The scheme represents a trapped genetic locus after Cre-mediated inversion/excision (left side). The LacZ reporter is expressed under the control of the trapped gene promoter. A further Cre- or FLP-mediated rearrangement, in the presence of a circular DNA containing a Cre cassette flanked with appropriate recombinases specific target sites, leads to the exchange between the reporter and Cre (right side). Then Cre is expressed under the control of the trapped gene promoter. (B) The scheme represents a trapped genetic locus after Cre-mediated inversion/excision (left side). A further FLP-mediated recombination in the presence of a circular DNA containing a cDNA cassette flanked with a FRT sequence on its 5′ side and of a FRTm sequence on its 3′ side leads to the exchange between the reporter and cDNA (right side). As the cDNA is itself flanked by two pairs of loxP and lox511 sites, expression of the cDNA depends on the presence of Cre (conditional allele upon Cre-mediated recombination). (C) The scheme represents a trapped genetic locus after Cre-mediated inversion/excision (left side). A further Cre-mediated recombination in the presence of a circular DNA containing a cDNA cassette flanked with a loxP sequence on its 5′ side and of a lox511 sequence on its 3′ side leads to the exchange between the reporter and cDNA (right side). As the cDNA is itself flanked by a FRT sequence on its 5′ side and of a FRTm sequence on its 3′ side, expression of the cDNA depends on the presence of FLP (conditional allele upon FLP-mediated recombination). Dotted lines represent the expected splicing of the primary transcript; E1 and E2 stand for exons 1 and 2; SA indicates rabbit .beta.-globin splice acceptor site; IRES stands for internal ribosomal entry site. Open and closed arrowheads represent loxP and lox511 sites, respectively. Closed and open flags represent FRT and FRTm sites, respectively.



EXAMPLES
1. Materials and Methods
1.1. DNA Constructs.
To construct plasmid pFlExP (SEQ ID NO. 54) (FIG. 1A), a loxP site, in the sense orientation, followed by a 21-bp spacer (oligos R1/R2; Table 1) was introduced into the EcoRI site of pSG5 (Green et al., 1988). A lox511 site (Hoess et al., 1986), also in the sense orientation, followed by a 21-bp spacer (oligos R3/R4) was introduced 3′ to the loxP site. A second loxP site, in the antisense orientation, followed by a 21-bp spacer (oligos R5/R6) was introduced 3′ to the first loxP and lox511 sites. A second lox511 site, also in the antisense orientation, followed by a 21-bp spacer (oligos R7/R8), was introduced 3′ to the latter loxP site. The coding sequence of the enhanced green fluorescent protein (Zhang et al., 1996) (EGFP; PCR-amplified using oligos R9/R10) and an NLS-β-galactosidase pA cassette (LacZ) (Bonnerot et al., 1987) were introduced between the two sets of loxP sites, in the sense and the antisense orientation, respectively. Finally, the remaining LacZ sequences of pSG5 were removed by digestion with BsaAI and SfiI, and repair by homologous recombination in E. coli using a SV40 promoter fragment (PCR amplified using oligos R11/R12). All cloning steps were checked by sequencing. The final constructs were again sequenced in all modified parts before starting in vitro Cre-mediated recombination or cell culture experiments. Modifications were all carried out following standard protocols (Ausubel et al., 1989). To obtain plasmid pFlExRrec, pFlExR was incubated with the Cre preparation (see below), and the recombined DNA was cloned in E. coli. pFlExRrec structure was checked by restriction mapping and sequencing of the regions containing loxP and lox511 sites. Plasmids ploxlacZlox and pSG5-Cre have been described elsewhere (Feil et al., 1997).







TABLE 1







Sequences of primers used for construction of


the pFlExR plasmid (SEQ ID NO 54).








Name
Sequence












R1
5′-ATTGATAACTTCGTATAGCATACATTATACGAAGTTATCCAAGCTTCACCATCGACCCG-3′
(SEQ ID NO 1)


 


R2
5′-AATTCGGGTCGATGGTGAAGCTTGGATAACTTCGTATAATGTATGCTATACGAAGTTATC-3′
(SEQ ID NO 2)


 


R3
5′-AATTGCCAAGCATCACCATCGACCCATAACTTCGTATAGTATACATTATACGAAGTTATCG-3′
(SEQ ID NO 3)


 


R4
5′-AATTCGATAACTTCGTATAATGTATACTATACGAAGTTATGGGTCGATGGTGATGCTTGGC-3′
(SEQ ID NO 4)


 


R5
5′-CTAGTGGATCCGATAACTTCGTATAATGTATGCTATACGAAGTTATCCAAGCATCACCATCGACCCT-3′
(SEQ ID NO 5)


 


R6
5′-CTAGAGGGTCGATGGTGATGCTTGGATAACTTCGTATAGCATACATTATACGAAGTTATCGGATCCA-3′
(SEQ ID NO 6)


 


R7
5′-CTAGTCCAGATCTCACCATCGACCCATAACTTCGTATAATGTATACTATACGAAGTTATT-3′
(SEQ ID NO 7)


 


R8
5′-CTAGAATAACTTCGTATAGTATACATTATACGAAGTTATGGGTCGATGGTGAGATCTGGA-3′
(SEQ ID NO 8)


 


R9
5′-GGGGAATTCTTCTTGTACAGCTCGTCCA-3′
(SEQ ID NO 9)


 


R10
5′-GGGGAATTCCCATGGTGAGCAAGGGCGAGGAG-3′
(SEQ ID NO 10)


 


R11
5′-CTATCAGGGCGATGGCCCACTACGTGTTCTGAGGCGGAAAGAACCA-3′
(SEQ ID NO 11)


 


R12
5′-GGAATAGCTCAGAGGCCGAGGCGGCCTCGGCCTCTGCATAAATAAAA-3′
(SEQ ID NO 12)









LoxP and lox511 sites are bold, point mutations in lox511 (oligos R3, R4, R7 and R8) are upper case, and restriction sites are underlined.
1.2. In Vitro Cre Reactions.
To perform Cre-mediated rearrangements in vitro, bacterial extracts containing an active Cre were prepared from E. coli 294-Cre strain 43. Cells were grown overnight at 37° C. in 500 ml LB medium, harvested by centrifugation, resuspended in 10 ml Cre Buffer (50 mM Tris/HCl pH 7.5, 33 mM NaCl, 10 mM MgCl2, 5% glycerol, 0.02% NaN3), and lysed by sonification. The soluble supernatant containing the Cre recombinase (Cre preparation) was recovered by centrifugation (14000×g, 15 min, 4° C.). The relevant plasmids (3 μg) were incubated with 100 μl of the Cre preparation for 1 hour at 37° C. For the control reactions, Cre was heat-inactivated by incubating the Cre preparation for 10 mm at 70° C. Plasmids were then isolated using the standard alkaline lysis method for DNA preparation (Ausubel et al., 1989). The recovered DNA was then used to transform competent XL1-Blue cells, which were grown overnight in 2 ml of LB at 37° C. Plasmids were isolated, digested by EcoRV and XbaI, separated on agarose gels and analyzed by Southern blotting using the radio-labelled oligos 5′-GTGCATCTGCCAGTTTGAGG-3′ (SEQ ID NO. 13) or 5′-AATACGACTCACTATAG-3′ (SEQ ID NO. 14) recognizing lacZ sequence or T7 promoter, respectively.
1.3. Cell Culture, EGFP Detection and LacZ Staining.
COS-1 cells were cultured and transfected according to Bocquel et al. (1989). For each plasmid, five independent transfection experiments were done. After transfection, the cells were incubated at 37° C. for 72 h, and then fixed for 5 min with 2% formaldehyde in phosphate-buffered saline (PBS). For EGFP detection, cells were examined with a Leica MS FL-III stereo dissecting microscope equipped with epifluorescence optics, and digital images were generated using a Photometrics Coolsnap CCD camera. For β-galactosidase activity detection, cells were incubated overnight at 37° C. in staining solution (5 mM potassium ferricyanide, 5 mM potassium ferrocyanide, 2 mM MgCl2, 1 mg/ml X-Gal) After washing with PBS, cells were post-fixed in 4% paraformaldehyde in PBS and digital images were generated using the Leica MS FL-III microscope.
1.4. Construction of Plasmid pγ6.0FlExβ-Gal (SEQ ID NO. 55).
To construct plasmid pγ6.0FlExβ-Gal, the RARγ exon 8 splice acceptor (oligos G3/G4; Table 2) was inserted by homologous recombination in E. coil into an XbaI digested pBluescript SK+ (Pharmacia) containing a loxP site (oligos G1/G2) in the sense orientation at its NotI site and from which the LacZ sequences were removed. After insertion of a 62 bp fragment (oligos G5/G6) into the XbaI site, the (NLS) β-gal pA cassette (Bonnerot et al., 1987) was introduced by homologous recombination in E. coli. A SnaBI and a lox511 site (oligos G7/G8) in the sense orientation was then introduced 5′ of the loxP site into the SacII site. A second SnaBI site (oligo G9) was inserted into the BamHI site. An FRT site (oligos G10/G11) was inserted into the NotI site. The FRT/PGK/Neo/pA/FRT cassette was inserted into the XbaI site oligos G10/G11 giving rise to plasmid ploxP/lox511/lacZ/Neo. A loxP site was inserted in the sense orientation into the HpaI site of pSKγ6.0 (Lohnes et al., 1993) (oligos G12/G13). A lox511 site was introduced in the sense orientation into the 3′ reconstructed HpaI site (oligos G14/G15). The EcoRI insert of this plasmid was ligated into a pGEX4T3 to obtain a LacZ sequence-deficient vector (pGEXγ6.0-loxP-lox511). The SnaBI fragment from plasmid plox P-lox511-lac2-Neo was isolated and inserted into the SfiI site of pGEXγ6.0/loxP/lox511 to obtain pγ6.0Flexβ-Gal (SEQ ID NO. 55).







TABLE 2







Sequences of primers used for construction


of the pγ6.0FlExβ-Gal plasmid (SEQ ID NO 55).








Name
Sequences












G1
5′-GGCCGCATAACTTCGTATAATGTATGCTATACGAAGTTAT-3′
(SEQ ID NO 15)


 


G2
5′-GGCCATAACTTCGTATGCATACATTATACGAAGTTATGC-3′
(SEQ ID NO 16)


 


G3
5′-TATAATGTATGCTATACGAAGTTATTCCTTGGCCTGGAATTTGCAGAATT-3′
(SEQ ID NO 17)


 


G4
5′-GCCCGGGGGATCCACTAGTTCTAGATGTCTCCACCGCTGAATGAAAAGCA-3′
(SEQ ID NO 18)


 


G5
5′-CTAGTATGGATAAAGTTTTCCGGAATTCCGCTCTAGACTCATCAATGTTATCTTATCATGTCTA-3′
(SEQ ID NO 19)


 


G6
5′-CTAGTAGACATGATAAGATAACATTGATGAGTCTAGAGCGGAATTCCGGAAAACTTTATCCATA-3′
(SEQ ID NO 20)


 


G7
5′-GCTACGTAATAACTTCGTATAATGTATACTATACGAAGTTATGGGTCGATGGTGAGATCTCCGC-3′
(SEQ ID NO 21)


 


G8
5′-GGAGATCTCACCATCGACCCATAACTTCGTATAGTATACATTATACGAAGTTATTACGTAGCGC-3′
(SEQ ID NO 22)


 


G9
5′-GATCTTACGTAA-3′
(SEQ ID NO 23)


 


G10
3′-GGCCGGGAAGTTCCTATTCTCTAGAAAGTATAGGAACTTCCC-3′
(SEQ ID NO 24)


 


G11
5′-GGCCGGGAAGTTCCTATACTTTCTAGAGAATAGGAACTTCCC-3′
(SEQ ID NO 25)


 


G12
5′-AAGATAACTTCGTATAATGTATGCTATACGAAGTTATCCAAGCATCACCATCGACCCGTT-3′
(SEQ ID NO 26)


 


G13
5′-AACGGGTCGATGGTGATGCTTGGATAACTTCGTATAGCATACATTATACGAAGTTATCTT-3′
(SEQ ID NO 27)


 


G14
5′-AAGCCAAGCATCACCATCGACCCATAACTTCGTATAATGTATACTATACGAAGTTATGTT-3′
(SEQ ID NO 28)


 


G15
5′-AACATAACTTCGTATAGTATACATTATACGAAGTTATGGGTCGATGGTGATGCTTGGCTT-3′
(SEQ ID NO 29)









LoxP or lox511 sites are shown in bold. The point mutations are lower case. Restriction sites are underlined.
1.5. Generation of the Gene Trap Construct
To construct the plasmid pJMG (SEQ ID NO. 56), a PCR amplified PGK Neo cassette containing the OBS sequence and the synthetic splice donor site (SD; oligos J1/J2; Table 3) was introduced into the EcoRI site of pBluescript SK+ resulting in pJMG1. A cassette containing the FRT, loxP and lox511 sites was prepared by subsequent insertion of oligos J3 to J8 into a shuttle vector. This cassette was recovered by NruI and HindIII digest, repaired and introduced in front of the PGK-Neo gene of pJMG1. The lacZ sequence of the pBluescript SK+ was removed from pJMG1. A lox511 site (oligos J9/J10) and a FRTm site (oligos J11/J12) were subsequently introduced 3′ to the synthetic splice donor site. The β-globin splice acceptor site (SA) followed by the IRES sequence were amplified by overlap extension PCR using oligos J13–J16. This fragment was introduced between the loxP site and the nls-LacZ polyA minigene of plasmid ploxP-nls-LacZ-pA. The obtained loxP-SD-IRES-nls-LacZ-pA DNA fragment was recovered and introduced, in antisense orientation at the BamHI site located in between the lox511 site and the PGK promoter to give to pJMG. The gene trap construct was excised from pJMG by NotI digestion and purification on a sucrose gradient.







TABLE 3







Sequences of primers used for


construction of the plasmid pJMG.








Name
Sequences












J1
5′-ACTAGTGGATCCCCCGGGCTGCAGGAATTCTACCGGGTAGGGGAGGCGCTT-3′
(SEQ ID NO 30)


 


J2
5′-GTATCGATAAGCTTGATATCGCCGCTCGAGACTTACCTGACTGGCCGTCGTTTTACAGTCAGAAGAACTCGTCAAGAAG
(SEQ ID NO 31)



-3′


 


J3
5′-CTCGCGAGGAATTCAACCAGAAGTTCCTATTCTCTAGAAAGTATAGGAACTTCCAGCT-3′
(SEQ ID NO 32)


 


J4
5′-GGAAGTTCCTATACTTTCTAGAGAATAGGAACTTCTGGTTGAATTCCTCGCGAGAGCT-3′
(SEQ ID NO 33)


 


J5
5′-AATGCCTACCGGACCATCATAACTTCGTATAATGTATACTATACGAAGTTATAAGCTTGCA-3′
(SEQ ID NO 34)


 


J6
5′-AGCTTATAACTTCGTATAGTATACATTATACGAAGTTATGATGGTCCGGTAGGCATTTGCA-3′
(SEQ ID NO 35)


 


J7
5′-GAGCTCATAACTTCGTATAATGTATGCTATACGAAGTTATCCAAGCATCACCATATGCA-3′
(SEQ ID NO 36)


 


J8
5′-TATGGTGATGCTTGGATAACTTCGTATAGCATACATTATACGAAGTTATGAGCTCTGCA-3′
(SEQ ID NO 37)


 


J9
5′-TCGACATAACTTCGTATAATGTATACTATACGAAGTTATAC-3′
(SEQ ID NO 38)


 


J10
5′-TCGAGTATAACTTCGTATAGTATACATTATACGAAGTTATG-3′
(SEQ ID NO 39)


 


J11
5′-TCGAAGAAGTTCCTAATCTATTTGAAGTATAGGAACTTCGCGGCCGCA-3′
(SEQ ID NO 40)


 


J12
5′-TCGATGCGGCCGCGAAGTTCCTATACTTCAAATAGATTAGGAACTTCT-3′
(SEQ ID NO 41)


 


J13
5′-CCGGTCCTTGGCCTGGAATTTGCACTCTGTTGACAACCATTGTCTCCT-3′
(SEQ ID NO 42)


 


J14
5′-GTAATACGACTCACTATAGGGAATTCCGCCCCTCTCCCTC-3′
(SEQ ID NO 43)


 


J15
5′-GAGGGAGAGGGGCGGAATTCCCTATAGTGAGTCGTATTAC-3′
(SEQ ID NO 44)


 


J16
5′-CTCCACCGCTGAATGAAAAGCAGCATGGTTGTGGCAAGCTTATCAT-3′
(SEQ ID NO 45)









1.6. In Vitro Cre Reaction for Poly A Trap Experiments
To test for functionality of loxP and lox511 sites of pJMG, an in vitro Cre reaction was carried out (Schnütgen et al., 2001). Briefly, a crude extract of E. coli 294-Cre cells (Cre preparation; Buchholz et al., 1996) was incubated with 3 μg of the plasmids and the resulting DNA was transformed into E. coli DH5α and directly amplified in liquid medium. Amplified plasmid DNA was recovered and analysed by Southern blotting using the probe 5′-TAACAATTTCACACAGGA-3′ (SEQ ID NO. 46), recognising the rabbit β-globin intron splice acceptor sequence (Green et al., 1988), to reveal the Cre-mediated rearranged constructs. To obtain the pJMG-f plasmid (FIG. 8B) pJMG was incubated for 5 min with the Cre preparation and transformed into E. coli DH5α. Individual clones were picked and analysed by restriction mapping and sequencing.
1.7. F9 Cell Culture
F9 cells were stably transfected with the NotI-excised fragment of pJMG-f, according to Taneja et al., (1995). 5–10×106 cells were trypsinised, washed, resuspended in 0.8 ml PBS and transferred into an electroporation cuvette. 10 μg of the purified DNA was added and cells were electroporated at 250 volts and 950° F. and seeded into 5 gelatinised 10 cm petri dishes. On the next day, 0.5 mg/ml G418 was added to the medium which was changed every 2 days for 14 days. 24 colonies were randomly chosen and amplified for further RNA isolation. The petri dishes from which the clones were chosen were subjected to X-Gal staining (Schnütgen et al., 2001).
1.8 RACE PCR
3′ RACE was carried out as described by Frobman (1994). Briefly, a first RT-PCR was carried out using the oligonucleotides Qt (5′-CCAGTGAGCAGAGTGACGAGGACTCGAGCTCAAGCT17-3′) (SEQ ID N° 47) as anchor primer, as well as Q0 (5′-CCAGTGAGCAGAGTGACG-3′) (SEQ ID N° 48) and Neo1 (3′-ACCGCTTCCTCGTGCTTTAC-3′) (SEQ ID N° 49) for amplification. An aliquot of 1 μl of this reaction was used for a nested amplification using Q1 (5′-GAGGACTCGAGCTCAAGC-3′) (SEQ ID N° 50) and Neo2 (5′-GCCTTCTTGACGAGTTCTTC-3′) (SEQ ID N° 51) primers. The resulting PCR fragments were purified using the NucleoSpin kit (Macherey-Nagel) and sequenced using the Neo2 or OBS (5′-CTGTAAAACGACGGCCAGTC-3′) (SEQ ID N° 57) primers.
Example 1
In Vitro Site-specific Recombination
The principle of the inventors' novel recombination strategy is illustrated in FIG. 1. pFlExR (SEQ ID NO. 54), a pSG5-based reporter plasmid was designed (FIG. 2) to test its feasability. It contains one pair of wild type loxP sites (open arrowheads), and one pair of lox511 sites (closed arrowheads), the loxP sites within each pair being oriented head to head. This organization (i.e. alternate loxP, lox511 and again loxP, lox511) is important. Both loxP and lox511 sites are recognized by Cre recombinase; however, they are “incompatible”, as lox511 sites can efficiently recombine with themselves, but not with loxP sites (Hoess et al., 1986). Between the two sets of loxP-lox511 sites, the plasmid contains the coding region for the enhanced green-fluorescent protein (EGFP) in the sense orientation, and a promoter-less LacZ reporter gene in the antisense orientation. In this reporter plasmid, the SV40 promoter first directs expression of EGFP (FIG. 2A). Cre-mediated recombination may initially induce inversion of the intervening DNA at either the loxP sites (FIG. 23, open arrowheads), or the lox511 sites (FIG. 2B, closed arrowheads). Due to the reversibility of these reactions, an equilibrium between the states (A) and (B or C) is formed. However, inversion induces a direct repeat of either two lox511 sites (FIG. 2B; closed arrowheads) or two loxP sites (FIG. 2C; open arrowheads). A further Cre-mediated excision will then remove the DNA located (between the two loxP or between the two lox511 sites (FIG. 2B and C; asterisks). In the resulting plasmid (pFlExRrec), single loxP and lox511 sites are left, making further inversion of the intervening DNA impossible (FIG. 2D). The SV40 promoter now drives expression of LacZ, instead of EGFP.
To test the feasibility of these Cre-mediated events, the inventors produced an E. coli extract containing a functional Cre recombinase (Cre preparation), and performed in vitro Cre-mediated rearrangements. The plasmids (FIGS. 3A and B) were incubated either with the Cre preparation (FIGS. 3C and D, lanes 2, 4 and 6), or with a heat-inactivated Cre preparation (FIGS. 3C and D, lanes 1, 3 and 5). They were digested with EcoRV and XbaI and analyzed by Southern blotting using probes 1 and 2 (see FIGS. 3A and B). To check the activity of the Cre preparation, a loxP-flanked LacZ sequence was used (plasmid ploxLacZlox, FIG. 3A). Cre recombinase mediated excision of the LacZ sequence, as assessed by the presence of the additional 3.0 kb EcoRV DNA fragment recognized by probe 1 (FIG. 3C, lane 2). Some unexcised plasmid was left (FIG. 3C, lane 2), most probably because of limiting-Cre activity, as increasing amounts of Cre preparation improved the yield of excision (data not shown). As expected, Cre recombinase mediated rearrangement in pFlExR (FIG. 3B), as assessed by the presence of the additional 4.9 kb EcoRV/XbaI DNA fragment recognized by probes 1 and 2 (FIGS. 3C and D, lane 4). The structure of the recombined plasmids was assessed by cloning in E. coli, followed by restriction mapping and sequencing of 20 individual colonies. All the recovered plasmids that were recombined underwent both inversion and excision (data not shown). The inverted/excised plasmid pFlExRrec (FIG. 3B; see also materials and methods) remained unchanged, when incubated in the presence of the Cre preparation (FIGS. 3C and D, compare lanes 5 and 6). As expected, this experiment indicates that Cre always mediated inversion and excision of the pFlExR construct in vitro, and that once rearrangement has taken place, it is irreversible.
To demonstrate the feasibility of this new recombination system in eukaryotic cells, the inventors transiently transfected into COS-1 cells pFlExR or pFlExRrec either alone, or together with excess of pSG5-Cre (a Cre recombinase-expressing vector), and analysed these cells for either EGFP fluorescence or β-galactosidase activity. Those cells transfected with the pFlExR reporter plasmid alone showed clearly green fluorescence (FIG. 4A), but only faint β-galactosidase activity (FIG. 4C). In contrast, the cells transfected with the pFlExR reporter plasmid together with pSG5-Cre reproducibly showed no green fluorescence (FIG. 4B), but prominent beta-galactosidase activity (FIG. 4D), indicating that Cre always mediates consecutively inversion and excision in vivo. Cells transfected with pFlExRrec alone or together with pSG5-Cre showed no green fluorescence at all, but prominent β-galactosidase activity (FIGS. 4E and F), indicating that once inversion/excision has occurred, the DNA molecule remains stable in vivo. Altogether, these experiments clearly demonstrate that the Cre-mediated recombination strategy of the invention operates in vivo, at least in transiently transfected mammalian cells.
Example 2
In Vivo Site-specific Recombination in the Context of Normal Chromatin
To develop the use of this system in living organisms, the inventors have demonstrated its functionality in the context of normal chromatin. To do this, the inventors carried out homologous recombination in ES cells, generating thereby a conditional knock-out linked to the expression of a β-galactosidase reporter gene in cells undergoing Cre-mediated recombination. The RARγ locus was chosen because: (i) its expression pattern is known (Ruberte et al., 1990); (ii) the phenotype of the knock-out is well characterised; and (iii) it is easy to target in ES cells, thus facilitating insertion of a heterologous fragment of more than 3 kb, as is required in the present method. The targeting vector used for homologous recombination (FIG. 5B) contained a 6 kb genomic fragment encompassing exons E8 to E13, in which were inserted: (i) a loxP and a lox511 in front of exon E8; (ii) a DNA module made of the natural splice acceptor of E8, the first 4 codons of E8 in frame with the NLS-LacZ-pA coding region, altogether in the antisense orientation; (iii) a loxP site in the reverse orientation, when compared to the first loxP site; (iv) a neomycin resistance (Neo) cassette; and (v) a lox511 site in the opposite orientation, when compared to the first lox511 site. The Neo cassette was flanked by FRT sites, thus allowing its excision using the FLP recombinase. The structures of the wild-type locus (A) and the recombined locus before (C; HR allele NeoR, LacZ−), and after removal of the selection cassette (D; HR allele NeoS, LacZ) are schematised in FIG. 5. Out of 234 surviving ES cell clones, 2 exhibited the expected restriction patterns for homologous recombination, as analysed by Southern blot (data not shown). Clone FK177 was injected into blastocysts, giving rise to 11 chimeras, out of which 2 transmitted the modified allele to their germline. FIG. 6 depicts the conditional RARγ allele (A), the intermediate steps (B) and (C) and the final structure of this locus after Cre treatment (D). Clone FK177 was transiently transfected with a Cre recombinase-expressing plasmid and analyzed by Southern blotting (data not shown). 2 clones were identified to be recombined (FK177.4 and FK177.18) Injection of these clones gave rise to 8 chimeric males and 1 chimeric female. Whereas the chimeric males were tested for germline transmission, the chimeric female was sampled and different organs were subjected to β-galactosidase stain. Organs that were known to express RARγ showed distinct blue staining (i.e. skin, bronchi, Harderian gland, tracheal rings; data not shown).
To further demonstrate that inversion and excision also occur in vivo, the mouse line FK177 has been crossed with a mouse strain expressing Cre recombinase very early during development (CMV-Cre). All the tissues known to express RARγ show blue straining (data not shown). Additionally, crosses with a mouse strain expressing Cre recombinase selectively in skin (K14-Cre) showed that inactivation of the RARγ gene and activation of the reporter Lac Z occurred in a conditional manner in epidermis only.
Cre recombinase can mediate inversion of any DNA fragment flanked by two loxP sites, which are in the opposite orientation. However, each DNA molecule continually undergoes rounds of recombination. In a living cell, this finally results in an equilibrium, with half of the loxP-flanked DNA being in the sense orientation, and the other half in the antisense orientation (Abremski et al., 1983). This technique was used by several groups to study particular genetic alterations in vivo, but its applications are limited (Lam et Rajewsky, 1998; Kano et al., 1998). One attempt to stabilize the intervening DNA in the inverted orientation has been made using modified loxP sites, which can efficiently undergo one round of recombination, but are impaired for the subsequent rounds. Nevertheless, this system cannot provide a tight control of recombination, due to the residual activity of these loxP sequences (Araki et al., 1997). Here the inventors have devised a novel approach to invert, upon Cre-mediated rearrangements, any DNA fragment in a stable, irreversible way. They have demonstrated the feasibility of this method by switching over irreversibly the transcription of the EGFP gene to the transcription of the lacZ gene, in transiently transfected COS cells.
The power of recombinase-based strategies to achieve conditional genomic alterations relies upon a collection of particular transgenic mice, in which specific Cre expression patterns must be carefully evaluated. The existence of anti-Cre antibodies permits the detection of Cre protein by immunohistochemistry (Schwenk et al., 1997). However, functional characterization of Cre activity is the ultimate test for the suitability of a given transgenic line for its use in conditional knockout experiments. This is usually performed by using additional transgenic lines, in which Cre-mediated recombination is used to control the activity of a reporter gene in individual cells. Several such loxP-flanked lacZ or EGFP reporter lines have been generated (Akagi et al., 1997; Mao et al., 1999; Soriano et al., 1999; Kawamoto et al., 2000). However, the reporter genes may either be silent in a Cre-target tissue (Brocard et al., 1997), or occasionally lie in a chromatin configuration inaccessible to recombination by Cre, even if it is expressed (Kellendonk et al., 1999). To distinguish between the two possibilities accounting for the failure of a reporter gene to produce a functional protein (no transcription versus no recombination), dual reporter systems have been constructed (Lobe et al., 1999; Novak et al., 2000) (Z/AP or Z/EG mice). Such cassettes express the first reporter (lacZ), or the second one (alkaline phosphatase or EGFP), or none of them, depending on whether the cassette is transcribed but not recombined, transcribed and recombined, or untranscribed, respectively. Although attractive, these strategies require multiple time-consuming animal breedings to obtain, within a single mouse, the desired constellation of transgenes (e.g. the Cre, the reporter, the loxP-flanked alleles . . . ). Furthermore, the Cre-mediated recombination frequency may vary between genomic target locations. Thus, the excision pattern for a conditional allele cannot be accurately inferred from that of a reporter gene. There is an obvious need for a direct approach that allows one to identify individual cells recombined at a given gene locus. Applied to gene targeting in ES cells, the present method should result in conditional knockout mice, in which Cre-mediated recombination at a given locus will be necessarily associated with expression of a reporter gene (FIG. 7A). This will allow easy detection of individual cells that have undergone Cre-mediated recombination (i.e. replacement of the normal gene product by the reporter protein gene, in other words a gene knockout/knock-in of the reporter gene).
The inventors' approach has also been tested in the context of normal chromatin environment. However, to generate conditional genetic alterations, care has to be taken during vector design that the distance between the compatible loxP sites, once inversion has taken place (asterisks, FIGS. 2B and C), allows excision, i.e. at least 82-bp using Cre/loxP (Hœss et al., 1985). Additionally, one should keep in mind that modifying the genome of eukaryotic cells in such a way may have some drawbacks. The presence of prokaryotic sequences in the antisense orientation (e.g. lacZ reporter gene) carries the risk of gene silencing (Cohen-Tannoudji et al., 2000). The repeat of an endogenous splicing site, and possibly of a poly-adenylation signal in the antisense orientation, may induce the occurrence of aberrantly spliced or poly-adenylated mRNA. In fact, this may not be a problem as antiparallel coupling of two genes (i.e. overlap of two genes transcribed in opposite orientations) has been shown to occur in mammalian cells; in the case of the overlapping thyroid hormone receptor alpha and Rev-erbA alpha genes, aberrant splicing or polyadenylation of mRNA have not been reported (Chawla et Lazar, 1993). In any case, DNA repeats, which are unavoidable, should be reduced as much as possible. The occurrence and frequency of such drawbacks will have to be directly estimated by further studies.
It is known that Cre recombinase can mediate exchange of a loxP-flanked genomic fragment by any other loxP-flanked DNA present in a circular vector, promoting consistent insertion of different exogenous sequences into the same locus of the genome (cassette exchange) (Araki et al., 1999; Feng et al., 1999). If one applies the present method to gene targeting in ES cells, firstly single loxP and lox511 sites would be left in the gene upon Cre-mediated inversion/excision, but the most attractive feature is that this loxP/lox511-flanked fragment would stay in position, even when an active Cre recombinase remains in the cells. Therefore, it becomes possible to integrate, by cassette exchange, the gene for Cre recombinase itself into the targeted locus of the genome (“easier knock-in”, because exchange occurs in 50% of the cells expressing Cre) (Feng et al., 1999), expanding the collection of lineage/cell-type specific Cre-expressing mouse lines and circumventing time-consuming experiments such as transgenesis (FIG. 7B). Using the present strategy to target a given gene in ES cells would then provide, at once, a conditional knockout, a reporter for monitoring excision at the locus, and a target for multiple knock-in using Cre-directed cassette exchange. Finally, the invention should also allow more sophisticated genetic rearrangements to be done, namely those genetic alterations that are considered “impossible” to achieve (Nagy et al., 2000): (i) accurate conditional rescue of a gene knockout (FIG. 7C), (ii) conditional point-mutations (FIG. 7D), and (iii) conditional replacement of a given gene product by another one (FIG. 7E).
Example 3
Generation of Conditional Reporter Alleles by Trapping Genes in ES Cells Using a poly-A Trap Approach
To date, only a few reporter lines have been described (Akagi et al., 1997; Lobe et al., 1999; Mao et al., 1999; Soriano, 1999; Kawamoto et al., 2000; Novak et al., 2000), which are not always functional in all tissues. The method of the invention proposed in Example 2 provides a reporter allele directly at the Cre-inactivated locus. However, it needs to be done for each individual locus, a procedure which requires time-consuming homologous recombination experiments. Gene traps provide a general strategy to target any gene locus in a given cell type, among which one can choose genes exhibiting discrete patterns of expression during either development or differentiation (Hill et al., 1993; Friedrich et al., 1993). The vectors used to date can be divided into two main classes: (i) Vectors that trap genes active in the chosen cell line, using a promoterless Neo as a selectable marker. Thus, they require an integration into a transcriptionally active gene to provide resistance to the selective drug G418. (ii) Vectors in which the selectable Neo is under the control of its own promoter (Skarnes et al., 1992; Salminen et al., 1998) lacking its poly A signal but instead containing a splice donor site. They require an integration in front of a poly A signal from the mouse genome to produce a stable mRNA (Niwa et al., 1993). These latter vectors permit the trapping of all genes, whether they are active or inactive in the given cell line.
The inventors disclose a new system to generate cells harbouring a conditional reporter allele knocked-into endogeneous genes by combining a poly A trap-based method with the Cre/loxP-lox511 method (Schnütgen et al., 2001). The rapid amplification of cDNA ends (RACE) allows one to search databanks and, thereby to identify the trapped gene. When applied to embryonic stem cells, injection of the gene-trapped clones into blastocysts may provide a library of conditional reporter mouse lines for analysis of Cre-mediated recombination patterns. Furthermore, recombinase-mediated cassette exchange (RCME) will make it possible to generate a library of mouse strains harbouring any other conditional construct at the trapped loci, including the Cre gene itself. This approach will allow a large-scale screen of gene-trapped containing clones, which may be used for the generation of a zoo of mouse lines expressing Cre (or FLP recombinase) in any given tissue or cell type.
The gene trap construct is schematised in FIG. 8. It is made of two DNA fragments of which the first one contains the conditional reporter cassette (LacZ), whereas the second one contains the poly-A based gene trap elements (FIG. 8A). In detail, the reporter cassette is in the antisense orientation and contains the splice acceptor site from the rabbit β-globin intron (SA) linked to an internal ribosomal entry site (IRES) and the nls-LacZ cDNA followed by a polyadenylation signal (Bonnerot et al., 1987). This fragment is flanked on the 5′ side with a loxP and a lox511 sequence in the sense orientation, and on the 3′ side with a loxP sequence in the antisense orientation. The gene trap cassette contains a phosphoglycerate kinase (PGK) promoter driving expression of a neomycin phosphotransferase (Neo) cDNA linked to a synthetic splice donor site (SD; Zambrowicz et al., 1998). This fragment is followed by a lox511 site in the antisense orientation. Cre-mediated recombination may initially induce the inversion of the intervening DNA at either the loxP sites (FIG. 8B) or the lox511 sites (FIG. 8C). Both reactions lead to constructs in which either the lox511 sites (FIG. 8B, asterisks) or the loxP sites (FIG. 8C, asterisks) form a direct repeat, allowing Cre recombinase to mediate excision (FIG. 8D). To further allow recombinase-mediated cassette exchange (RCME) according to Schlake et al. (1994) at the trapped loci, the whole construct is flanked by a wild type FRT sequence on its 5′ side and a mutated FRT (FRTm) sequence on its 3′ side.
To test the construct for feasability of Cre-mediated rearrangements, an in vitro Cre reaction was carried out following Schnütgen et al. (2001). The plasmids (FIG. 9A) were incubated either with the Cre preparation (FIG. 9B; lanes 2, 4, 6 and 8) or with a heat-inactivated Cre preparation (FIG. 9B; lanes 1, 3, 5 and 7; see Materials and Methods). They were digested with HindIII and analysed by Southern blotting using a probe located in the rabbit β-globin splice acceptor site (FIG. 9A). To check the activity of the Cre preparation, a loxP-flanked LacZ containing plasmid (FIG. 9B; ploxlacZlox) was used (see also Schnütgen et al., 2001). As expected, Cre recombinase mediated rearrangement in pJMG (FIG. 9A) to produce the intermediate (pJMG-f), as assessed by the presence of the additional 4.9 kb and 3.5 kb HindIII fragments (FIGS. 9B and C, lane 4). The other intermediate (pJMG-fm) cannot be distinguished from pJMG using this digest. However, it was also evidenced using another restriction mapping (data not shown). Cre recombinase also mediated excision of the inverted plasmids to produce pJMG-fx, as assessed by the presence of the 6.9 kb HindIII fragment (FIGS. 9B and C; lanes 4). The structure of the recombined plasmids was assessed by cloning in E. coli, followed by restriction mapping and sequencing. Additionally, upon Cre-mediated recombination, intermediate plasmid pJMG-f (and pJMG-fm; data not shown) was not only reverted to pJMG, as assessed by the presence of the 2.2 kb HindIII fragment, but also excised to produce pJMG-fx (FIGS. 9B and C, lane 6). Some unexcised plasmids were left in lanes 2, 4 and 6, most probably because of limiting Cre activity, as increasing amounts of Cre preparation improved the yield of excision (data not shown). The plasmid pJMG-fx cannot undergo any recombination event (FIGS. 9B and C, lane 8), as was demonstrated (Schnütgen et al., 2001).
The inventors anticipated that random integration of the NotI-excised fragment of pJMG into the genome would lead to expression of a stable mRNA encoding for Neo phosphotransferase only upon trapping of a gene that provide a polyadenylation sequence. Using this strategy, a gene does not need to be transcribed to be trapped. Furthermore, the sequence of the trapped gene can be easily identified by rapid amplification of cDNA ends (3′-RACE; Frohman, 1988). The sequence of the fusion transcript is likely to contain coding regions, allowing identification of the trapped gene in database searches. At the trapped locus, the wildtype mRNA should still be expressed, as the splice acceptor site which is in the antisense orientation, should not interfere with normal transcription of the gene (FIG. 10B). After Cre-mediated recombination the endogeneous promoter of the trapped gene will drive the expression of the LacZ reporter (FIG. 10C). Additionally, due to the presence of the LacZ cassette in the sense orientation, the 3′ end of the endogenous trapped message will be replaced by the IRES-LacZ sequence. Thus, expression of the trapped gene is likely to be abrogated, or at least its gene product will be truncated.
To test for functionality of the splice acceptor site as well as of the IRES and LacZ sequences, the NotI fragment from the intermediate plasmid pJMG-f, which contains the LacZ cassette in the sense orientation (FIG. 8B; see also Materials and Methods) was used for electroporation of F9 cells. After selection with G418, F9 clones were selected and tested for LacZ expression (FIGS. 11A to I). As expected, each clone exhibited a different lacZ expression pattern reflecting the activity of the trapped gene in F9 cells, ranging from no expression at all (FIGS. 11 C,E,G) to strong expression (FIG. 11A). Twenty-four clones were randomly picked and amplified for RNA isolation. Two of them were subsequently used for 3′ RACE-PCR analysis. In clone 21 the early transposon Etn (accession number AB033515) was trapped, whereas in clone 24 the locus RPCI-23-70D11 (accession number AZ235091) was trapped. This experiment demonstrated (i) the functionality of the synthetic splice donor site downstream of Neo, that can splice into an endogeneous poly-A signal, as Neo resistant clones were obtained; (ii) the functionality of the rabbit β-globin splice acceptor site and of the IRES-LacZ fusion, as blue clones were obtained, independently of G418 resistance. This clearly indicates that unexpressed genes were efficiently trapped; (iii) identification of the trapped loci can be easily performed by 3′ RACE PCR.
Gene trapping was then performed in mouse embryonic stem cells which were electroporated with the NotI fragment of pJMG and selected against G418 for 2 weeks. One hundred resistant clones were amplified and frozen. DNA was isolated for analysis of multi-sites targeting. RNA isolation and RACE-PCR analysis was done, and three clones have been chosen to be injected into mouse blastocysts.
The inventors devised a novel approach to generate conditional reporters by trapping genes in cells. they make use of the poly-A trap based method rather than the use of promoter-based trap methods as, in the latter case, only expressed genes are trapped. Indeed, using the poly-A based trap method the inventors may target genes which are not expressed in ES cells, but which are expressed later in a tissue- or cell-specific manner, not only during early development but also in the adult mouse. The loxP and lox511 sites may allow Cre-mediated RCME, to replace the reporter cassette by another one. In this approach, the addition of two incompatible FLP recombinase recognition sites (FRT and FRTm) may allow a subsequent FLP-mediated RCME (FIG. 12A). The inventors may use this system to generate a number of mouse lines, expressing for example the inducible recombinase CreERT under the control of the trapped promoters. Furthermore, RCME using FLP may allow the inventors to insert at the trapped locus a conditional allele for Cre (FIG. 12B); whereas RCME using Cre may allow the inventors to reintroduce at the trapped locus a conditional allele for FLP (FIG. 12C).
The present application of the invention in gene trapping furnishes a highly powerful system that allows (i) generation of conditional reporter alleles at any gene locus; (ii) possibly generation of conditional knock-out alleles and (iii) generation of targets for RCME via Cre or FLP recombinases to produce a library of Cre- or FLP-expressing lines (a Cre- or a FLP-Zoo) or to insert conditional alleles for Cre or FLP.
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## Claims

1. An isolated DNA molecule comprising a sequence A flanked by site specific recombinase targeting sequences (SSRTS) L1 and a sequence B flanked by site specific recombinase targeting sequences (SSRTS) L2, said SSRTS L1 and SSRTS L2 being unable to recombine with one another, wherein:
i) sequences L1 are in an orientation opposite one another, wherein said sequences point towards each other or away from each other,
ii) sequences L2 are in an orientation opposite to each other, wherein said sequences point towards each other or away from each other,
iii) the order of the sequences in said isolated DNA molecule is 5′-L1-L2-sequence A-sequence B-L1-L2-3′, and
iv) at least one of sequence A or sequence B encodes a protein.

2. The isolated DNA molecule according of claim 1 wherein the same recombinase recognizes SSRTS L1 and SSRTS L2.

3. The isolated DNA molecule of claim 2 wherein the recombinase specific for the SSRTS is selected from the group consisting of Cre recombinase of bacteriophage P1, the FLP recombinase of Saccharomyces cerevisiae, the R recombinase of Zygosaccharomyces rouxii pSR1, the A recombinase of Kluyveromyces drosophilarium pKD1, the A recombinase of Kluyveromyces waltii pKW1, the integrase λ Int, the recombinase of the GIN recombination system of Mu phage, and bacterial β recombinase.

4. The isolated DNA molecule according to claim 3, wherein said recombinase is said Cre recombinase of bacteriophage P1.

5. The isolated DNA molecule according to claim 4, wherein each of said SSRTS L1 and SSRTS L2, specific for Cre recombinase is selected from the group consisting of Lox P1, Lox 66, Lox 71, Lox 511, Lox 512, Lox 514, and a mutated Lox P1 sequence, wherein said mutated Lox P1 sequence comprises at least one point mutation in the spacer sequence.

6. The isolated DNA molecule according to claim 5, wherein either SSRTS L1 comprises the Lox P1 sequence (SEQ ID NO: 52) and SSRTS L2 comprises the Lox 511 sequence (SEQ ID NO: 53) or SSRTS L1 comprises the Lox 511 sequence and SSRTS L2 comprises the Lox P1 sequence.

7. The isolated DNA molecule according to claim 3 wherein the recombinase is the FLP recombinase of Saccharomyces cerevisiae.

8. The isolated DNA molecule according to claim 7, wherein said SSRTS L1 and/or SSRTS L2 specific for said FLP recombinase are chosen from the group consisting of FRT-S and FRT-F30.88.

9. The isolated DNA molecule according to claim 1, wherein sequences A and/or B encode at least one exon.

10. The isolated DNA molecule according to claim 1, wherein an IRES sequence is inserted 5′, 3′, or 5′ and 3′ to the at least one of sequence A or sequence B that encodes a protein.

11. The isolated DNA molecule according to claim 1, wherein said protein is selected from the group consisting of a reporter protein and a selection marker.

12. The isolated DNA molecule according to claim 11, wherein said reporter protein is selected from the group consisting of an autofluorescence protein and an enzyme detectable histochemically.

13. The isolated DNA molecule of claim 12, wherein said autofluorescence protein is selected from the group consisting of the green fluorescent protein (GFP), the enhanced green fluorescent protein (EGFP), the red fluorescent protein (RFP), the blue fluorescent protein (BFP), and the yellow fluorescent protein (YFP).

14. The isolated DNA molecule according to claim 12 wherein said enzyme detectable histochemically is selected from the group consisting of β-galactosidase, β-glucoronidase, alkaline phosphatase, luciferase, alcohol dehydrogenase, and chloramphenicol-acetyl transferase.

15. A vector comprising the isolated DNA molecule according to claim 1.