Methods of modifying eukaryotic cells

Description of the invention

The invention relates to a method of genetically modifying an endogenous gene or chromosomal locus in eukaryotic cells and a method of genetically modifying an endogenous gene or chromosomal locus in mouse embryonic stem cells.

Field of the Invention

The field of this invention is a method of constructing and using DNA macromolecular vectors for targeting, by homologous recombination, and for modifying, in any desired manner, endogenous genes and chromosomal loci in eukaryotic cells. These macromolecular DNA target vectors for eukaryotic cells, referred to as LTVECs ( large DNA targeting vector for eukaryotic cells), are obtained from larger fragments of cloned genomic DNA than are commonly used in other approaches to carry out homologous exchange in eukaryotic cells. The field of this invention further provides a fast and convenient method of detecting eukaryotic cells in which the LTVEC has correctly targeted and modified the desired endogenous gene (s) or chromosomal locus (s). The field also covers the use of these cells to produce genetically engineered organisms, the organisms themselves, and the methods of their use.

Introduction

The use of LTVECs provides significant advantages over the currently used methods. For example, as they are derived from DNA fragments larger than those currently used to generate targeting vectors, LTVECs can be made faster and more conveniently from available libraries of large genomic DNA fragments (such as BAC and PAC libraries) than target vectors constructed with currently available technologies. Additionally, larger modifications as well as modifications involving larger regions of the genome can be more conveniently performed than with the technologies currently available.

In addition, the present invention uses long regions of homology to increase the frequency of homologous exchange of "hard-to-target" loci, and also reduces the advantage, if any, of using isogenic DNA in these target vectors.

The present invention thus provides a fast, convenient and efficient method for systematically modifying virtually all endogenous genes and chromosomal loci of an organism.

State of the art

It has been proven that gene targeting using homologous recombination between exogenous homologous DNA and endogenous chromosomal sequences is an extremely valuable way to create deletions, insertions, engineered mutations, repair gene mutations, introduce transgenes or carry out other genetic modifications in mice. Currently available methods use the use of standard target vectors, with regions of homology to endogenous DNA typically less than 10-20 kb in total, to introduce the desired genetic modification into mouse embryonic stem (ES) cells, and then inject altered ES cells into mouse embryos to transfer of these genetically engineered modifications into the germline of mice (Smithies et al., Nature, 317: 230-234, 1985; Thomas et al., Cell, 51: 503-512, 1987; Koller et al., Proc Natl Acad Sci USA, 86: 8927-8931,1989; Kuhn et al., Science, 254: 707-710,1991; Thomas et al., Nature, 346: 847-850,1990; Schwartzberg et al., Science, 246: 799-803, 1989; Doetschman et al., Nature, 330: 576-578, 1987; Thomson et al., Cell, 5: 313-321, 1989; DeChiara et al., Nature, 345: 78-80,1990; United States Patent No. 5,789,215, issued Aug 4, 1998 to GenPharm International). In those currently available methods for detecting rare ES cells in which standard target vectors have correctly targeted and modified the desired endogenous gene (s) or chromosomal locus (loci), knowledge of sequences beyond the homologous targeting sequences contained in the target vector is required. Assays to detect successful homologous exchange use standard Southern blotting or long PCR reactions (Cheng, et al., Nature, 369: 684-5, 1994; Foord and Rose, PCR Methods Appl, 3: 3149-61, 1994; Ponce and Micol , Nucleic Adds Res, 20: 623,1992; US Patent No. 5,436,149 to Takara Shuzo Co., Ltd.) with sequences beyond the target vector and encompassing an entire arm of homology (see Definitions); therefore

Since these methods are limited in size, the size of the homology arms must not exceed 10-20 kb (Joyner, The Practical Approach Series, 293, 1999).

It would be extremely valuable to be able to use target vectors with homology arms larger than the methods currently used. For example, such target vectors could be more conveniently and faster constructed from available libraries containing large genomic inserts (e.g., BAC or PAC libraries) than target vectors constructed with currently available technologies in which such genomic inserts must be broadly characterized and ordered prior to use. Moreover, larger modifications and modifications involving larger regions of the genome could be carried out more conveniently and would require fewer steps than currently available technologies. In addition, the use of long regions of homology could increase the frequency of homologous exchange of "hard-to-target" loci in eukaryotic cells, since homologous exchange using homologous recombination in eukaryotic cells seems to be related to the overall homology contained within the target vector (Deng and Capecchi, Mol Cell Biol , 12: 3365-71,1992). Additionally, the increased frequency of homologous exchange achieved using the long homology arms could reduce any potential benefit of using isogenic DNA in these target vectors.

The use of homologous recombination in bacteria has largely resolved the problem of performing fine modifications on large genomic fragments, such as those cloned in BAC libraries (Zhang, et al., Nat Genet, 20: 123-8, 1998; Yang, et al., Nat Biotechnol, 15: 859-65, 1997; Angrand, et al., Nucleic Acids Res, 27: el6, 1999; Muyrers, et al., Nucleic Acids Res; 27: 1555-7, 1999; Narayanan, et al., Gene Ther, 6: 442-7, 1999), allowing the construction of vectors that contain large regions of homology to endogenous eukaryotic genes and chromosomal loci. However, when produced, they were found not to be typically useful for modifying endogenous genes and chromosomal loci by homologous recombination where the homology arms are larger than 10-20 kb due to difficulties in detecting the rare events of normal homologous exchange ( Joyner, The Practical Approach Series, 293, 1999). Consequently, vectors constructed using bacterial homologous recombination from genomic BAC fragments still need to be broadly ordered before being used as target vectors (Hill et al., Genomics, 64: 111-3, 2000). Therefore, there is still a need for a quick and convenient methodology that allows the use of target vectors containing large regions of homology to modify endogenous genes or chromosomal loci in eukaryotic cells.

In accordance with the present invention, the inventors have provided methods that allow the use of target vectors containing large regions of homology so as to modify endogenous genes or chromosomal loci in eukaryotic cells by homologous recombination. Such methods overcome the above-mentioned limitations of currently available technologies. Moreover, one of ordinary skill in the art will readily appreciate that the methods of the present invention can readily be adapted for use with any genomic DNA of a eukaryotic organism including, but not limited to, animals such as a mouse, rat, other rodent, or human, as well as plants such as soybeans, corn and wheat.

Summary of the invention

The present invention relates to a method of genetically modifying an endogenous gene or chromosomal locus of interest in eukaryotic cells, comprising:

a) a large cloned genomic fragment larger than 20 kb is obtained containing the DNA sequence of interest;

b) using bacterial homologous recombination to genetically modify the large cloned genomic fragment according to a) to generate a large target vector for use in eukaryotic cells (LTVEC), the LTVEC having homology arms which are overall larger than 20 kb;

c) introducing the LTVEC according to b) into eukaryotic cells to modify an endogenous gene or chromosomal locus in the cells; and

d) quantification is used to detect allele modification (MOA) in eukaryotic cells according to c) to identify those eukaryotic cells in which the endogenous gene or locus has been genetically modified.

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Preferably, a cloned large genomic fragment containing a DNA sequence that is homologous to the endogenous gene or chromosomal locus of interest is used as the large cloned genomic fragment.

Preferably, the genetic modification of an endogenous gene or chromosomal locus comprises the deletion of a coding sequence, gene segment, or regulatory element; alteration of a coding sequence, gene segment, or regulatory element; insertion of a new coding sequence, gene segment, or regulatory element; creating a conditional allele; or the replacement of a coding sequence or gene segment from one species with a homologous or orthological coding sequence from the same or a different species.

More preferably, the alteration of the coding sequence, gene segment, or regulatory element comprises a substitution, addition or fusion.

Even more preferably, the fusion comprises an epitope tag or a bi-functional protein.

Preferably, the quantification is a quantification that includes quantitative PCR, FISH, comparative genomic hybridization, isothermal DNA amplification, or quantitative hybridization with an immobilized probe.

Preferably, a non-human mammal embryonic stem cell is used as the eukaryotic cell.

More preferably, a mouse, rat or other rodent embryonic stem cell is used as the embryonic stem cell.

Preferably, the endogenous gene or chromosomal locus is an endogenous gene or chromosomal locus of a mammal.

More preferably, the endogenous gene or chromosomal locus is an endogenous human gene or chromosomal locus.

More preferably, the endogenous gene or chromosomal locus is an endogenous gene or chromosomal locus from a mouse, rat or other rodent.

Preferably, an LTVEC vector capable of accepting large DNA fragments greater than 100 kb is used as the LTVEC vector.

The invention further relates to a method of genetically modifying an endogenous gene or chromosomal locus of interest in mouse embryonic stem cells, comprising:

a) a cloned large genomic fragment larger than 20 kb is obtained which contains the DNA sequence of interest, wherein the large cloned DNA fragment is homologous to the endogenous gene or chromosomal locus;

b) using bacterial homologous recombination to genetically modify the large cloned genomic fragment according to a) to produce a macromolecular target vector for use in mouse embryonic stem cells, the macromolecular target vector having homology arms entirely greater than 20 kb, and wherein the genetic modification endogenous gene or chromosomal locus is a deletion of a coding sequence, a gene segment or regulatory element;

c) introducing a macromolecular target vector according to

b) to mouse embryonic stem cells to modify an endogenous gene or chromosomal locus in the cells; and

d) quantification is used to detect allele modification (MOA) in mouse embryonic stem cells according to c) to identify those mouse embryonic stem cells in which the endogenous gene or chromosomal locus has been genetically modified, the quantification being quantified by PCR.

Preferably, in the methods described above, about 1-5 μg of the macromolecular target vector according to c) are introduced to about 1 x 10⁷ cells.

In accordance with the present invention, the inventors have developed a fast, efficient, and efficient method of creating and searching for eukaryotic cells that contain modified endogenous genes or chromosomal loci. For the first time, these new methods combine:

1. Bacterial homologous recombination to accurately carry out genetic modifications within the large cloned fragment, thereby creating large target vectors for use in eukaryotic cells (LTVEC);

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2. Direct introduction of these LTVECs into eukaryotic cells to modify the endogenous chromosomal locus of interest in these cells; and

3. An analysis for the determination of rare eukaryotic cells in which the target allele has been modified as desired, including an allele modification (MOA) assay of the starting allele that requires no sequence information other than the targeting sequence, such as, for example, a quantitative response PCR.

The invention provides a method of genetically modifying an endogenous gene or chromosomal loci in eukaryotic cells comprising: a) obtaining a large cloned genomic fragment containing a DNA sequence of interest; b) using homologous recombination to genetically modify the large cloned genomic fragment according to a) in order to construct a large target vector for use in eukaryotic cells (LTVEC); c) introducing the LTVEC according to b) into eukaryotic cells in order to modify an endogenous gene or a chromosomal locus in these cells; and d) using a quantitative assay to detect allele modification (MOA) in eukaryotic cells according to c) to identify those eukaryotic cells in which the endogenous gene or chromosomal locus has been genetically modified.

Another embodiment of the invention is a method wherein the genetic modification of an endogenous gene or chromosomal locus comprises the deletion of a coding sequence, gene segment or regulatory element; alteration of a coding sequence, gene segment, or regulatory element; insertion of a new coding sequence, gene segment, or regulatory element; creating a conditional allele; or the replacement of a coding sequence or gene segment derived from one species with a homologous or orthological coding sequence from another species.

Another possible embodiment of the invention is a method wherein the alteration of a coding sequence, gene segment or regulatory element comprises a substitution, addition or fusion, wherein the fusion comprises an epitope tag or a bi-functional protein.

Yet another embodiment of the invention is a method wherein the quantitative test is quantitative PCR, comparative genomic hybridization, isothermal DNA amplification, quantitative hybridization with an immobilized probe. Invader Probes® or MMP® assays can also be used, with the quantitative PCR reaction including TaqMan®, Molecular Beacon or Eclipse ™ probe technology.

Another preferred embodiment of the invention is a method wherein the eukaryotic cell is a non-human mammal embryonic stem cell, wherein the embryonic stem cell is in particular a mouse, rat or other rodent embryonic stem cell.

Another preferred embodiment of the invention is a method wherein the endogenous chromosomal gene or locus is an endogenous mammalian chromosomal gene or locus, preferably a human chromosomal gene or locus, or a mouse, rat or other rodent chromosomal gene or locus.

An additional preferred embodiment is a method in which the LTVEC vector is capable of accepting large DNA fragments greater than 20 kb and especially large DNA fragments greater than 100 kb.

According to the method of the invention, a genetically modified endogenous gene or chromosomal locus can be obtained.

According to the method of the invention, a genetically modified eukaryotic cell can be obtained.

According to the method of the invention, a non-human organism containing a genetically modified endogenous gene or chromosomal locus produced by the method of the invention can be obtained.

According to the method of the invention, also a non-human organism produced from genetically modified eukaryotic cells or embryonic stem cells produced according to the method of the invention can be obtained.

According to the method of the invention, a non-human organism containing a genetically modified endogenous gene or chromosomal locus can be obtained by a method comprising the steps of: a) obtaining large cloned genomic fragments containing a DNA sequence of interest; b) using bacterial recombination

Homologously to genetically modify large cloned genomic fragments according to a) in order to construct a large target vector (LTVEC) for use in embryonic stem cells; c) introducing the LTVEC according to b) into embryonic stem cells in order to modify an endogenous gene or a chromosomal locus in these cells; d) using a quantitation to detect allele modification ( modification of alleles (MOA) in the embryonic stem cells according to c) to identify those embryonic stem cells in which the endogenous gene or chromosomal locus has been genetically modified; e) introducing the embryonic stem cell according to d) into the blastocyst; and introducing the blastocyst according to e) into the surrogate mother to develop the pregnancy.

According to the method of the invention, a non-human organism containing a genetically modified endogenous gene or chromosomal locus can be obtained by a method comprising the steps of: a) obtaining large cloned genomic fragments containing a DNA sequence of interest; b) using bacterial homologous recombination to genetically modify large cloned genomic fragments according to a) in order to construct a large target vector (LTVEC) for use in eukaryotic cells; c) introducing the LTVEC according to b) into eukaryotic cells in order to modify the endogenous gene or chromosomal locus in these cells; d) using a quantitative assay to detect allele modification (MOA) in eukaryotic cells according to c) to identify those eukaryotic cells in which the endogenous gene or chromosomal locus has been genetically modified; e) removing the nucleus from the eukaryotic cell according to d); f) introduction of the cell nucleus according to e) into the oocyte; and g) introducing an oocyte into a surrogate mother to develop pregnancy.

According to the method of the invention, a non-human organism containing a genetically modified endogenous gene or chromosomal locus can be obtained by a method comprising the steps of: a) obtaining large cloned genomic fragments containing a DNA sequence of interest; b) using bacterial homologous recombination to genetically modify large cloned genomic fragments according to a) in order to construct a large target vector (LTVEC) for use in eukaryotic cells; c) to guide the LTVEC according to b) into eukaryotic cells in order to modify an endogenous gene or chromosomal locus in these cells; d) using a quantitative assay to detect allele modification (MOA) in eukaryotic cells according to c) to identify those eukaryotic cells in which the endogenous gene or chromosomal locus has been genetically modified; e) fusing a eukaryotic cell according to d) with another eukaryotic cell; f) introducing the eukaryotic fusion cell into the surrogate mother for the development of pregnancy.

The non-human organism is a mouse, rat, or other rodent; the blastocyst is a mouse, rat or other rodent blastocyst; the oocyte is a mouse, rat, or other rodent oocyte; and the surrogate mother is a mouse, rat, or other rodent.

Another preferred embodiment is where the embryonic stem cell is a non-human mammal embryonic stem cell, preferably a mouse, rat or other rodent embryonic stem cell.

The genetically modified eukaryotic cells according to the invention, and in particular the genetically modified embryonic stem cells, can be used for the production of a non-human organism.

A method of genetically modifying an endogenous gene or chromosomal locus of interest in a mouse embryonic stem cell of the invention comprises: a) obtaining a large cloned genomic fragment larger than 20 kb, which contains the DNA sequence of interest, wherein the large cloned genomic fragment is homologous to the endogenous a gene or chromosomal locus; b) using bacterial homologous recombination to genetically modify the large cloned genomic fragment according to a) in order to construct a large target vector for use in mouse embryonic stem cells, the genetic modification being a deletion of a coding sequence, gene segment or regulatory element; c) introducing the macromolecular target vector according to b) into mouse embryonic stem cells in order to modify an endogenous gene or a chromosomal locus in these cells; d) using a quantitative assay to detect allele modification (MOA)

In mouse embryonic stem cells according to gc) to identify those embryonic stem cells in which the endogenous gene or chromosomal locus has been genetically modified, the quantitative test being a quantitative PCR reaction.

According to the invention, it is possible to use the genetically modified mouse embryonic stem cell described above to generate a mouse.

In the methods according to the invention, preferably about 1 - 5 μg of the large molecule target vector are introduced to about 1 x 10⁷ eukaryotic cells.

Brief description of the figures

Figure 1: Schematic diagram of the production of a typical LTVEC using homologous recombination.

(hb1 = homology box 1; hb2 = homology box 2; RE = restriction enzyme cleavage site).

Figure 2: Schematic diagram of the donor fragment and LTVEC vector for mouse OCR10.

(hb1 = homology box 1; lacZ = β-galactosidase ORF; SV40 poly-A = simian virus 40 (SV40) DNA fragment containing polyadenylation site and signal sequence; PGKp = mouse phosphoglycerate kinase (PGK) promoter; EM7 = promoter bacterial; neo = neomycin phosphotransferase; PGKpoly-A = 3 'untranslated region derived from the PGK gene and containing a polyadenylation site and signal; hb2 = homology box 2).

Figure 3A - 3D: Mouse OCR10 cDNA sequence; hb1 = Homology Box 1 (hb1); hb2 = homology box 2 (hb2); and TaqMan® probes and primers used in the quantitative PCR assay to detect allele modification (MOA) in ES cells targeted with the mOCR10 LTVEC.

hb1: bp 1 to 211 hb2: bp 1586 to 1801 TaqMan® probe and corresponding PCR primer kit derived from exon 3 mOCR10: TaqMan® probe: nucleotides 413 to 439 - upper strand primer ex3-5 ': nucleotides 390 to 410 - upper strand ex3-3 'primer: nucleotides 445 to 461 - lower strand TaqMan® probe and corresponding PCR primer set derived from mOCR10 exon 4:

TaqMan® probe: nucleotides 608 to 639 - upper strand ex4-5 'primer: nucleotides 586 to 605 - upper strand ex4-3' primer: nucleotides 642 to 662 - lower strand

Definitions A "target vector" is a DNA construct that contains sequences "homologous" to the endogenous chromosomal nucleic acid sequences flanking the desired genetic modification (desired genetic modification). Flanking homology sequences, referred to herein as "homology arms" direct the target vector to a specific chromosomal location within the genome on the basis of the homology between the homology arms and the corresponding endogenous sequence, and introduce the desired genetic modification by a process referred to herein as "homologous recombination".

"Homologous" means two or more nucleic acid sequences that are either identical or sufficiently similar to be capable of hybridising to each other or undergoing intermolecular exchange.

"Gene targeting" is the modification of an endogenous chromosomal locus by insertion, deletion, or replacement of an endogenous sequence by homologous recombination using a target vector.

A "knockout" is a genetic modification resulting from the disruption of the genetic information encoded in a chromosomal locus.

A "knockin" is a genetic modification resulting from the replacement of the genetic information encoded in a chromosomal locus with another DNA sequence.

A "knockout organism" is an organism in which a significant number of the organism's cells contain a knockout organism.

A "knockout organism" is an organism in which a significant number of the organism's cells contain a knockout.

A "marker" or "selectable marker" is a selectable marker that allows the isolation of rare transfected cells expressing the marker from the majority of treated cells in a population. Such a selectable marker gene includes, but is not limited to, neomycin phosphotransferase and hygromycin B phosphotransferase, or fluorescent proteins such as GFP.

An "ES cell" is an embryonic stem cell. This cell usually comes from the internal cell mass of an embryo in the blastocyst phase.

An "ES cell clone" is a sub-population of cells derived from a single cell of the ES cell population following DNA introduction and subsequent selection.

A "flanking DNA" is a segment of DNA that is collinear and immediately adjacent to a specific point of reference.

"LTVECs" are macromolecular (large) eukaryotic target vectors that are derived from cloned genomic DNA fragments larger than those conventionally used in other approaches to achieve homologous gene exchange in eukaryotic cells.

A "non-human organism" is an organism that is not normally recognized as being human by the public.

"Allele modification" (MOA) refers to the modification of a specific DNA sequence of one gene allele (s) or chromosomal locus (loci) in the genome. This allele modification (MOA) includes, but is not limited to, single nucleotide or multi-kbase deletions, substitutions, or insertions involving the chromosomal gene (s) or locus (loci) of interest, as well as any and all possible modifications therebetween. extremes.

An "orthological" sequence refers to a sequence from one species that is functionally equivalent to that sequence in another species.

The following description and examples are provided to illustrate the subject matter of the invention. One skilled in the art will recognize that these examples are provided for illustration only and are not included to limit the invention.

Detailed Description of the Invention

The inventors have developed a new, fast, efficient and efficient method of creating and searching for eukaryotic cells that contain modified endogenous genes or chromosomal loci. In these cells, the modification can be gene (s) shutdowns, gene (s) integrations, point mutations, or large genomic insertions or deletions, or other modifications. By way of non-limiting example, the cells may be embryonic stem cells, which are useful for the production of organisms with the gene (s) being switched off or on, and in particular mice with a switched off or on gene (s), to determine the function of that gene (s) that are have been changed, deleted and / or inserted.

For the first time, the new methods described here combine:

1. Bacterial homologous recombination to precisely create the desired genetic modification within a large cloned genomic DNA fragment, thereby creating macromolecular target vectors for use in eukaryotic cells (LTVEC);

2. Directly introducing these LTVECs into eukaryotic cells to modify the corresponding endogenous gene (s) or chromosomal locus (loci) of interest in these cells; and

3. Analysis for determination of those rare eukaryotic cells in which the target alleles have been modified as desired, using a quantitative allele modification (MOA) assay of the starting allele.

It should be emphasized that the previous methods for determining successful homologous recombination in eukaryotic cells cannot be used in combination with the LTVEC vectors of the invention due to the long homology arms present in the LTVEC vectors. The use of LTVECs to purposefully modify endogenous genes or chromosomal loci in eukaryotic cells by homologous recombination has been made possible by the new application of the assay to identify rare eukaryotic cells in which the target allele has been modified as desired, using the quantitative allele modification assay ( MOA) of the starting allele by using, for example, quantification of PCR or other appropriate quantification of MOA.

The ability to use target vectors in homology arms longer than those used in currently available methods is extremely valuable for the following reasons:

1. It is faster and more convenient to produce target vectors from available libraries containing large genomic inserts (e.g. BAC or PAC libraries) than vectors produced using previous technologies, in which the genomic inserts must be carefully characterized before use

And "truncated" (explained in detail below). In addition, only minimal sequence information for the locus of interest is required, i.e. it is necessary to know about 80-100 nucleotides which are required to create homology cassettes (explained in detail below) and to generate probes that can be used in quantitative MOA determinations. .

2. Larger modifications and modifications involving larger genomic regions are carried out more conveniently and in fewer steps than with previous technologies. For example, the method of the invention allows fine modifications to be made to large loci that cannot be accommodated by traditional plasmid-based target vectors due to their size limitations. It also allows you to modify any given locus at various points (e.g. introducing specific mutations in different exons of a multizon gene) in one step, reducing the need to generate complex target vectors and perform multiple rounds of homologous exchange and search for homologous recombination in ES cells.

3. The use of long homology regions (long homology arms) increases the frequency of homologous exchange of "hard to target" loci in eukaryotic cells, which is in line with previous reports that targeting homologous recombination in eukaryotic cells seems to be related to the complete homology contained in the vector destination.

4. The increased homologous exchange frequency achieved with the long homology arms apparently diminishes the benefit, if any, of using isogenic DNA in these target vectors.

5. The use of quantitative MOAs to search for homologous recombination in eukaryotic cells not only increases the benefits of using LTVECs as target vectors (the advantages are outlined above), but also reduces the time needed to identify correctly modified eukaryotic cells from typically seven days to several hours . In addition, the use of quantitative MOA does not require the use of probes located outside the endogenous gene (s) or the chromosomal locus (chromosomal loci) that are modified, so there is no need to know the gene (s) or locus (loci) targeting the modified gene (s). This represents a significant improvement over the past method of performing the search and makes this approach to finding homologous recombination events less laborious and much cheaper.

Methods

Many of the techniques used to construct DNA vectors described herein are standard molecular biology techniques known to those skilled in the art (see, e.g., Sambrook, J., EF Fritsch, and T. Maniatis. Molecular cloning: A Laboratory Manual, Second Edition, Volumes 1, 2 and 3, 1989; Current Protocols in Molecular Biology, Ed. Ausubel et al., Greene Publ. Assoc., Wiley Interscience, New York). All DNA sequencing was performed using standard techniques using the ABI 373A DNA sequencer and the Taq Dideoxy Terminator Cycle Sequencing Kit (Applied Biosystems, Inc., Foster City, CA).

Step 1. Obtaining a large genomic DNA clone containing the gene (s) or locus (loci) of interest.

The gene (s) or locus (loci) of interest may be selected on the basis of specific criteria, such as structural or functional details, or may be selected in the absence of such details, as potential genes or gene fragments may be predicted by various efforts. genome sequencing projects. Importantly, it should be noted that it is not necessary to know the complete sequence and structure of the gene (s) of interest in order to use the method of the present invention to generate LTVECs. Indeed, the only sequence information required is approximately 80-100 nucleotides to obtain a genomic clone of interest as well as to generate homology cassettes used in the generation of the LTVEC vector (detailed below) and to prepare probes for use in quantitative MOA assays.

After selecting the gene (s) or locus (s) of interest, a large genomic clone containing that gene (s) or locus (loci) is obtained. This clone (s) can be obtained by several methods including, but not limited to, searching for appropriate DNA libraries

(E.g., BAC, PAC, YAC, or cosmid) using standard hybridization and PCR techniques, or by any other method known to one of skill in the art.

Step 2. Attach homology cassettes 1 and 2 to the modification cassette and generate the LTVEC vector.

Homology boxes mark the sites of bacterial homologous recombination that are used to generate LTVECs from large cloned genomic fragments (Figure 1). Homology boxes are short segments of DNA, usually double-stranded and at least 40 nucleotides in length, that are homologous to the regions within the large cloned regions flanking the "region to be modified". The homology cassettes are attached to the modification cassette such that after homologous recombination in bacteria, the modification cassette replaces the region to be modified (Figure 1). The technique of constructing a target vector using homologous recombination can be performed in a variety of systems (Yang et al., Nat Biotechnol, 15: 859-65, 1997; Muyrers et al., Nucleic Acids Res, 27: 1555-7, 1999; Angrand et al., et al., Nucleic Acids Res, 27: el6, 1999; Narayanan et al., Gene Ther, 6: 442-7, 1999; Yu et al., Proc Natl Acad Sci USA, 97: 5978-83, 2000). One of the more preferred technologies in use today is ET cloning (Zhang et al., Nat Genet, 20: 123-8, 1998; Narayanan et al., Gene Ther, 6: 442-7, 1999) and variants of this technology (Yu, i. et al., Proc Natl Acad Sci USA, 97: 5978-83,2000). ET refers to the proteins recE (Hall and Kolodner, Proc Natl Acad Sci USA, 91: 3205-9, 1994) and recT (Kusano et al., Gene, 138: 17-25, 1994) that perform a homologous recombination reaction. RecE is an exonuclease that truncates one strand of a linear double-stranded DNA (essentially the donor DNA fragment described below) 5 'to 3', thus leaving behind a linear double-stranded fragment with a 3 'single-stranded overhang. This single-stranded overhang is coated with the recT protein, which has single-stranded DNA (ssDNA) binding activity (Kovall and Matthews, Science, 277: 1824-7, 1997). Cloning of ETs is performed using E. coli in which the E.coli gene products are transiently expressed. coli recE and recT (Hall and Kolodner, Proc Natl Acad Sci USA, 91: 3205-9, 1994; Clark et al., Cold Spring Harb Symp Quant Biol, 49: 453-62, 1984; Noirot and Kolodner, J Biol Chem , 273: 12274-80, 1998; Thresher et al., J Mol Biol, 254: 364-71, 1995; Kolodner et al., Mol Microbiol, 11: 23-30, 1994; Hall et al., J Bacteriol, 175: 277-87, 1993) and the bacteriophage lambda (λ) λ gam protein (Murphy, J Bacteriol, 173: 5808-21, 1991; Poteete et al., J Bacteriol, 170: 2012-21, 1988). The λ gam protein is required to protect the donor DNA fragment from degradation by the recBC exonuclease system (Myers and Stahl, Annu Rev Genet, 28: 49-70, 1994) and is required for efficient ET cloning in recBC hosts⁺such as the frequently used E. coli DH10b strain.

The region to be modified and replaced using bacterial homologous recombination can vary in length from zero nucleotides (creating insertions inside the original locus) to many tens of kilobases (creating deletions and / or replacing the original locus). Depending on the modification cartridge, the following effects may occur:

a) deletion of coding sequences, gene segments or regulatory elements:

b) alteration (s) of coding sequences, gene segments or regulatory elements including (e) substitutions, additions and fusions (e.g. epitope tags or the formation of bifunctional proteins such as those with GFP);

c) insertion of new coding regions, gene segments or regulatory elements; such as those for selectable marker genes or reporter genes or insertion of new genes under endogenous transcriptional control;

d) formation of conditional alleles, e.g. insertion of loxP sites flanking the region to be excised by Cre recombinase (Arembski and Hoess, J Biol Chem, 259: 1509-14, 1984) or FRT sites flanking the region to be excised by the Flp recombinase (Adrews and et al., Cell, 40: 795-803, 1985; Meyer-Leon et al., Cold Spring harb Symp Quant Biol, 49: 797-804, 1984; Cox, Proc Natl Acad Sci USA, 80: 4223-7, 1983 ); or

e) replacement of coding sequences, gene segments, or regulatory elements from one species with orthological coding sequences from another species, eg replacement of a mouse genetic locus with a human orthological genetic locus to generate a mouse in which a specific locus has been "humanized".

Any or all of these modifications can be introduced into the LTVEC. Example 1 below provides a specific, non-limiting example in which the endogenous coding sequence has been completely removed and simultaneously replaced with both a reporter gene and a selectable marker, demonstrating the advantages of the method of the invention over previous technologies.

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Stage 3 (optional). Confirmation that each LTVEC has been correctly constructed.

Verifying that each LTVEC has been correctly constructed by:

a. Diagnostic PCR to check for new junctions created by inserting a donor fragment into the gene (s) or chromosomal locus (loci) of interest. The thus obtained fragments can be sequenced to further verify new junctions formed by introducing a donor fragment into the gene (s) or chromosomal locus (loci) of interest.

b. Diagnostic restriction enzyme digestion to verify that only the desired modifications were introduced into the LTVEC during the bacterial homologous recombination process.

c. Direct sequencing of the LTVEC, especially of the regions containing the site of modification, to check for new junctions created by introducing a donor fragment into the gene (s) or chromosomal locus (loci) of interest.

Stage 4. Purification, preparation and linearization of LTVEC vector DNA for introduction into eukaryotic cells,

a. Preparation of LTVEC DNA

Small Scale (Miniprep) DNA Preparation of Selected LTVEC (Sambrook, J., E.R. Fritsch and T. Maniatis. Molecular Cloning: A Laboratory Manual, Second Edition, Volumes 1, 2, and 3, 1989; Tillett and Neilan, Biotechniques , 24: 568-70,572,1998;

http://www.qiagen.com/literature/handbooks/plkmini/plm_3 99.pdf and retransformation of LTVEC vector DNA miniprep to E. coli by electroporation (Sambrook, J., EF Fritsch and T. Maniatis, Molecular Cloning: A Laboratory Manual, Second Edition, Volumes 1, 2, and 3, 1989). This step is necessary to get rid of the plasmid encoding the recombinogenic proteins used in the bacterial homologous recombination stage (Zhang et al., Nat Genet, 20: 123-8, 1998; Narayanan et al., Gene Ther, 6: 442-7, 1999) . Getting rid of this plasmid is useful: a) because it is a multi-copy plasmid and may reduce the yield of large-scale LTVEC vector preparations; b) to eliminate the possibility of inducing expression of recombinogenic proteins; and c) as this may obscure the physical LTVEC vector mapping. Prior to introducing the LTVEC into eukaryotic cells, larger amounts of LTVEC DNA are prepared using standard methodologies (http://www.qiagen.com/literature/handbooks/plk/plklow.pdf; Sambrook, J., EF Fritsch and T. Maniatis. Molecular Cloning: A Laboratory Manual, Second Edition, Volumes 1, 2 & 3, 1989; Tillett and Neilan, Biotechniques, 24: 568-70,572, 1998). However, this step may be omitted if the method of bacterial homologous recombination using recombinogenic prophage is used, i.e. which uses genes encoding recombinogenic proteins that are integrated into a bacterial chromosome (Yu, et al., Proc Natl Acad Sci USA, 97: 5978 -83, 2000).

b. LTVEC vector DNA linearization:

In order to prepare the LTVEC for introduction into eukaryotic cells, the LTVECs are conveniently linearized such that the endogenous gene (s) or chromosomal locus (loci) remain flanked by the long arms of homology. This can be achieved by linearization of the LTVEC, preferably within the vector backbone, using any suitable, rarely cutting restriction enzyme.

Examples of suitable restriction enzymes include NotI, PacI, Sfil, Srfl, Swal, Fsel etc. The selection of the restriction enzyme can be made experimentally (i.e. by testing several different candidate rare-cleaving enzymes) or, if the sequence of the LTVEC vector is known, by sequence analysis and selecting an appropriate restriction enzyme on the basis of this analysis. Where the LTVEC vector has a backbone containing uncommon cleavage sites, such as CosN sites, it can be cleaved with enzymes that recognize such sites, for example, the λ terminase (Shizuya et al., Proc Natl Acad Sci USA, 8 9: 8794-7, 1992; Becker and Gold, Proc Natl Acad Sci USA, 75: 4199-203,1978; Rackwitz et al., Gene, 40: 259-66, 1985).

Step 5. Introducing the LTVEC into eukaryotic cells and selecting those cells for which LTVEC was successfully introduced.

LTVEC vector DNA can be introduced into eukaryotic cells using standard methodology (Sambrook, J., EF Fritsch and T. Maniatis. Molecular Cloning: A Laboratory Manual, Second Edition, Volumes 1/2 and 3, 1989). Cells in which the introduction of LTVEC was successful, i.e. the introduction of LTVEC into them, can be selected by subjecting them to selection factors depending on the selectable marker gene that has been

Inserted into the LTVEC. As a non-limiting example, when the selectable marker is the neomycin phosphotransferase (neo) gene (Beck, et al., Gene, 19: 327-36, 1982), then cells that have adopted the LTVEC vector can be selected on media containing G418; cells that lack the LTVEC will die and cells that adopt the LTVEC will survive (Santerre, et al., Gene, 30: 147-56, 1984). Other suitable selectable markers are any drugs that show activity in eukaryotic cells (Joyner, The Practical Approach Series, 293, 1999), such as Hygromycin B (Santerre, et al., Gene, 30: 147-56, 1984). ; Bernard, et al., Exp Cell Res, 158: 237-43, 1985; Giordano and McAllister, Gene, 88: 285-8, 1990), blasticidin S (Izumi, et al., Exp Cell Res, 197: 229 -33, 1991) and others known to those skilled in the art.

Step 6. Search for homologous recombination events in eukaryotic cells using quantitative allele modification (MOA) assay.

Eukaryotic cells that have been successfully modified by targeting the LTVEC to the chromosomal locus of interest can be identified using a variety of approaches that are capable of detecting allele modification within the locus of interest but are not based on whole arm (s) testing homology. Such approaches include, but are not limited to:

(a) quantitative PCR using TaqMan® (Lie and Petropoulos, Curr Opin Biotechnol, 9: 43-8,

1998);

(b) quantification of MOA using nonlinear fluorescent markers (Molecular Beacon) (Tan, et al., Chemistry, 6: 1107-11, 2000) (c) fluorescent in situ hybridization, FISH (Laan, et al., Hum Genet , 96: 275-80, 1995) or comparative genomic hybridization (CGH) (Forozan, et al., Trends Genet, 13: 405-9, 1997; Thompson and Gray, J Cell Biochem Suppl, 139-43, 1993; Houldsworth and Chaganti, Am J Pathol, 145: 1253-60,1994);

(d) isothermal DNA amplification (Lizardi, et al., Nat Genet, 19: 225-32, 1998; Mitra and Church, Nucleic Acids Res, 27: e34, 1999);

(e) quantitative hybridization to the immobilized probe (s) (Southern, J.Mol.Biol. 98: 503, 1975; Kafatos FC; Jones CW; Efstratiadis A, Nucleic Acids Res 7 (6): 1541-52, 1979);

(f) Invader Probes® (Third Wave Technologies);

(g) Eclipse ™ probes and Molecular Beacon (Synthetic Genetics); and (h) MMP (High Throughput Genomics) tests.

Here, the inventors provide an example that uses TaqMan® quantitative PCR to search for successfully targeted eukaryotic cells. In this non-limiting example, TaqMan® is used to identify those cells that have undergone homologous recombination in which part of one of the two endogenous alleles of the diploid genome is replaced with a different sequence. Unlike traditional methods, where a difference in the length of the restriction fragment spanning the entire homology arm (s) indicates a modification of one of the two alleles, the quantitative TaqMan® method will detect modification of one allele by measuring the reduction in the copy number of the unmodified allele (by half ). More specifically, the probe detects no modified allele, only the unmodified allele. For this reason, the method is independent of the type of modification and is not limited to the sequence replacement described in the example. TaqMan® is used to quantify the copy number of template DNA in a genomic DNA sample, especially by comparison with a reference gene (Lie and Petropoulos, Curr Opin Biotechnol, 9: 43-3, 1998). The quantification of the reference gene is performed on the same genomic DNA as the target gene (s) or locus (loci). Therefore, two TaqMan® DNA amplifications (each with an appropriate probe) are performed. One TaqMan® probe represents the "Ct" (threshold cycle) of the reference gene, while the other probe represents the Ct of the target gene region (s) or locus (loci) replaced during a successful homologous exchange. Ct is the amount reflecting the amount of starting DNA for each TaqMan® probe, i.e. a smaller sequence requires more PCR cycles to reach the threshold cycle. In the cynic of halving the copy number of the template sequence for the TaqMan® reaction, there will be an increase of approximately one Ct unit. In cells where one of the alleles of the target gene (s) or locus (loci) has been replaced during nomological recombination, the TaqMan® reaction will result in an increase of one Ct for the target TaqMan® reaction without an increase in Ct for the reference gene, compared to DNA from the cells with no homologous replacement. This allows for direct

Detecting the modification of one allele of the gene (s) of interest in eukaryotic cells using the LTVEC vector.

As stated above, allele modification screening is the use of any method that detects a modification of one allele to identify those cells that have undergone homologous recombination. The target alleles are not required to be identical (homologous), and in fact may contain polymorphic regions, as is the case in offspring that are crossbred between two different strains of mice. Moreover, a specific situation that is also covered by MOA searches is the homologous exchange of genes that usually occur as a single copy in a cell, such as some located on the sex chromosomes and in particular on the Y chromosome. In this case, methods may be used to detect the occurrence of homologous exchange. that will detect single target allele modification such as quantitative PCR, southern hybridization etc. It will be clear that the method of the invention can be used to produce modified eukaryotic cells even when the alleles are polymorphic or when they exist as a single copy in the target cells.

Step 8. Applications of modified eukaryotic cells.

(a) The genetically modified eukaryotic cells produced by the methods described in steps 1 to 7 can be used in any in vitro or in vivo assay where it is desired to alter the phenotype of the cell.

(b) The genetically modified eukaryotic cells produced by the methods described in steps 1 to 7 can also be used to generate an organism carrying the genetic modification. Genetically modified organisms can be produced by several different techniques including, but not limited to:

1. Modified stem (ES) cells such as the frequently used rat or mouse ES cells. ES cells can be used to produce genetically modified rats or mice using standard blastocyst injection technology or aggregation techniques (Robertson, Practical Approach Series, 254, 1987; Wood, et al., Nature, 365: 87-9, 1993; Joyner , The Practical Approach Series, 293, 1999), injection into a tetraploid blastocyst (Wang, et al., Mech Dev, 62: 137-45, 1997), or nuclear transfer and cloning (Wakayama, et al., Proc Natl Acad Sci USA, 96: 14984-9,1999). ES cells from other organisms such as rabbits (Wang, et al., Mech Dev, 62: 137-45, 1997; Schoonjans, et al., Mol Reprod Dev, 45: 439-43, 1996) or chickens (Pain, et al., Development, 122: 2339-48, 1996) or other species should also be amenable to genetic modification (s) using the methods of the invention.

2. Modified protoplasts can be used to produce genetically modified plants (for example, see US Patent No. 5,350,689 "Corn Plants and Transgenic Corn Plants Regenerated from Protoplasts or Protoplast-Derived Cells" and the US Patent No. 5,350,689. No. 5,508,189 "Regeneration of Plants from Cultivated Controlled Cell Protoplasts" and references therein).

3. Transfer of cell nuclei from modified eukaryotic cells into oocytes to generate cloned allele-modified organisms (Wakayama, et al., Proc Natl Acad Sci USA, 96: 14984-9, 1999; Baguisi, et al., Nat Biotechnol, 17: 456 -61,1999; Wilmut, et al., Reprod Fertil Dev, 10: 639-43,1998; Wilmut, et al., Nature, 385: 810-3,1997; Wakayama, et al., Nat Ganet, 24: 108-9, 2000; Wakayama, et al., Nature, 394: 369-74, 1998; Rideout, et al., Nat Genet, 24: 109-10,2000; Campbell, et al., Nature, 380: 64-6, 1996).

4. Fusion of cells to transfer the modified allele to another cell, involving the transfer of the altered chromosome (s) and the use of the cell (s) to produce organisms that bear the altered allele or altered chromosome (Kuroiwa, et al., Nat Biotechnol, 18: 1086- 1090, 2000).

5. The method of the invention is applicable to any other approach either used or yet undiscovered.

While many of the techniques used in the practice of the individual steps of the methods of the invention are known to those skilled in the art, the inventors believe that the novelty of the method of the invention lies in the unique combination of these steps and techniques in combination with a never-before-described method of introducing LTVEC directly into eukaryotic cells for modification. chromosomal locus and the use of quantitative MOA to identify eukaryotic cells, which have been appropriately modified. This new combination

The PL 204 759 B1 represents a significant improvement over previously used technologies for producing organisms having modifications of endogenous genes or chromosomal loci.

Examples

Example 1:

Construction of mouse ES cells with OCR10 gene deletion.

a. Selection of a large genomic DNA clone containing mOCR10.

A bacterial artificial chromosome (BAC) clone carrying a large genomic DNA fragment containing the coding sequence of the mouse OCR10 gene (mOCR10) was obtained by screening a template genomic DNA BAC library (Incyte Genomics) using PCR. The primers used to screen this library were derived from the mOCR10 gene cDNA sequence.

Two pairs of primers were used:

(a) OCR10.RAA (5'-AGCTACCAGCTGCAGATGCGGGCAG -3 ') and OCR10.PVIrc (5'-CTCCCCAGCCTGGGTCTGAAAGATGACG-3') which amplifies a 102 bp fragment of DNA; and (b) OCR10.TDY (5-GACCTCACTTGCTACACTGACTAC-3 ') and OCR10.OETrc (5-ACTTGTGTAGGCTGCAGAAGGTCTCTTG-3') which amplifies a 1500 bp fragment of DNA

This mOCR10 BAC contained approximately 180 kb of genomic DNA covering the entire mOCR10 coding sequence. This BAC clone was used to construct the LTVEC vector, which was then used to remove part of the mOCR10 coding sequence while introducing a reporter gene whose start codon precisely replaces the mOCR10 start codon, as well as inserting a selectable marker gene useful for selection in both E. coli and in mammalian cells depending on the reporter gene (Figure 2). The reporter gene (in this non-limiting example, LacZ, the sequence of which is readily available to one of skill in the art) encodes the enzyme E. coli β-galactosidase. Due to the site of LacZ insertion (its start codon is in the same position as the mOCR10 start codon), LacZ expression should mimic mOCR10 expression as observed in other examples where similar LacZ substitutions were performed using previous technologies (see Gene trap strategies in ES cells ”by W. Wurst and A. Gossler, Joyner, The Practical Approach Series, 293, 1999). The LacZ gene allows a quick and standardized assay to be carried out to determine its in situ expression patterns, thus providing a surrogate test that reflects the normal expression patterns of the replaced gene or chromosomal locus (replaced genes or chromosomal loci).

b. Construction of the donor fragment and generation of the LTVEC vector.

The modification cassette used in the construction of the mOCR10 LTVEC vector is the lacZ-SV-40 poly-A-PGKp-EM7-neo-PGK poly-A cassette, in which lacZ is a selectable marker gene as described above, SV40 poly-A is a monkey-derived fragment Virus 40 (SV40) (Subramanian, et al., Prog Nucleic Acid Res Mol Biol, 19: 157-64, 1976; Thimmappaya, et al., J Biol Chem, 253: 1613-8, 1978; Dhar et al., Proc Natl Acad Sci USA, 71: 371-5, 1974; Reddy, et al., Science, 200: 494-502, 1978) and containing a polyadenylation site and signal sequence (Subramanian, et al., Prog Nucleic Acid Res Mol Biol, 19: 157-64, 1976; Thimmappaya, et al. , J Biol Chem, 253: 1613-8, 1978; Dhar, et al., Proc Natl Acad Sci USA, 71: 371-5, 1974; Reddy, et al., Science, 200: 494-502, 1978), PGKp is the mouse phosphoglycerate kinase (PGK) promoter (Adra, et al., Gene, 60: 65-74, 1987) (which has been widely used to target expression of drug resistance genes in mammalian cells), EM7 stands for a strong bacterial promoter which is preferred in allowing positive selection in bacteria of the complete LTVEC vector construct by directing the expression of the neomycin phosphotransferase (neo) gene. neo is a selectable marker that confers kanamycin resistance in prokaryotic cells and G418 resistance in eukaryotic cells (Beck, et al., Gene, 19: 327-36, 1982), and PGK polyA is a 3 'untranslated region derived from from the PGK gene and containing a polyadenylation site and a signal sequence (Boer, et al., Biochem Genet, 28: 299-308, 1990).

For the construction of the mOCR10 LTVEC vector, first, a donor fragment consisting of the mOCR10 1 homology box (hb1) upstream of the LacZ gene in the modification cassette and the mOCR10 2 homology box (hb2) appended downstream of the neo-PGK polyA sequence in the modification cassette (Figure 2) was constructed (Figure 2). standard technology of recombinant genetic engineering. Homology cassette 1 consists of 211 bp the untranslated sequence immediately upstream of the start methionine of the mOCR10 open reading frame (mOCR10 ORF) (Figure 3A-3D). Homology box 2 (hb2) consists of the 216 bp mOCR10 ORF and terminates with a stop codon (Figure 3A-3D).

PL 204 759 B1

Then using bacterial homologous recombination (Zhang, et al., Nat Genet, 20: 123-8, 1998; Angrand, et al., Nucleic Acids Res, 27: el6, 1999; Muyrers, et al., Nucleic Acids Res, 27: 1555-7,1999; Narayanan, et al., Gene Ther, 6: 442-7,1999; Yu, et al., Proc Natl Acad Sci USA, 97: 5978-83, 2000) this donor fragment was used to accurately replace the mOCR10 coding region (from the start codon - methionine to the stop codon) with an insertion cassette, resulting in the LTVEC vector mOCR10 (Figure 2). Thus, in this mOCR10 LTVEC vector, the mOCR10 coding sequence was replaced with an insertion cassette creating an approximately 20 kb deletion in the mOCR10 locus leaving approximately 130 kb of homology above (homology arm above) and 32 kb of homology below (homology arm below).

It should be noted that LTVEC vectors can be generated from available BAC libraries more conveniently and faster than target vectors produced using previous technologies, since only a single step of bacterial homologous recombination is required, with the only sequence information being that needed to generate homology cassettes. In contrast, previous approaches to producing target vectors using bacterial homologous recombination require that the macromolecular target vectors be "truncated" prior to their introduction into ES cells (Hill et al., Genomics, 64: 111-3, 2000). This truncation is necessary due to the need to produce homology arms short enough to accommodate the search methods used in previous approaches. One major drawback of the method of Hill et al. it is that two steps of homologous recombination are required only for shortening (one to shorten the region above the modified locus and one to shorten the region below the modified locus). To do so, more sequence information is needed, including information about the sequence including the truncation sites. Furthermore, another obvious advantage, illustrated in the example above, is that a very large deletion including the mOCR10 gene (approximately 20 kb) can be easily produced in a single step. In contrast, the use of previously available technologies to achieve the same goal requires several steps and may require labeling of regions upstream and downstream of the coding sequences with loxP sites to remove the sequence flanking these sites with Cre recombinase after introducing the modified locus into eukaryotic cells. This may not be achievable in one step and thus may require the construction of two target vectors using two different selection markers and two consecutive homologous swap events, one to introduce a loxP site in the region upstream of the coding sequence and the other to introduce a loxP site in the region below the coding sequence. It should also be noted that the generation of large deletions using previously available homologous exchange technologies in eukaryotic cells often occurs with low efficiency because the frequency of homologous recombination may be low when using target vectors containing large deletions flanked by relatively short homology arms. The high yield obtained with the method of the invention (see below) is due to the use of very long homology arms present in the LTVEC which increase the frequency of homologous recombination in eukaryotic cells.

c. Verification, preparation and introduction of LTVEC mOCR10 DNA into ES cells.

The sequence surrounding the junction of the insertion cassette and the homology sequence was verified by DNA sequencing. The size of the mOCR10 LTVEC was verified by restriction analysis followed by pulsed electric field gel electrophoresis (PFGE) (Cantor, et al., Annu Rev Biophys Biophys Chem, 17: 287-304, 1988; Schwartz and Cantor, Cell, 37: 67-75 , 1984). Standard large-scale plasmid preparation of the mOCR10 LTVEC vector was performed, the plasmid DNA was digested with the restriction enzyme NotI, which cuts inside the mOCR10 LTVEC vector backbone, to linearize the DNA. The linearized DNA was then introduced into mouse ES cells by electroporation (Robertson, Practical Approach Series, 254, 1987; Joyner, The Practical Approach Series, 293, 1999; Sambrook, et al., Sambrook, J., EF Fritsch, and T. Maniatis . Molecular Cloning: A Laboratory Manual, Second Edition, Volumes 1, 2 & 3, 1989). Successfully transfected cells were selected by standard selection methods in G418 containing media (Robertson, Practical Approach Series, 254, 1987; Joyner, The Practical Approach Series, 293, 1999).

d. Identification of homologously exchanged ES cell clones using quantitative allele modification (MOA) assay.

In order to identify those ES cells in which one of the two endogenous mOCR10 genes had been replaced with a modification cassette sequence, DNA from individual ES cell clones was analyzed.

PL 204 759 B1 by quantitative PCR using standard TaqMan® methodology as described (Applied Biosystems, TaqMan® Universal PCR Master Mix, catalog number P / N 4304437; see also http://www.pebiodocs.com/pebiodocs/04304449. pdf). The primers and Taq-Man® probes were used as described in Figure 3A-3D. 69 independent ES cell clones were screened and 3 were identified as positive, i.e. as clones in which one of the endogenous mOCR10 coding sequences has been replaced with the modification cassette described above.

Several advantages of the MOA approach are visible:

(i) it does not require the use of a probe outside the modified locus, thus making the knowledge of the flanking sequence of the modified locus unnecessary.

(ii) compared to the conventional Southern blot methodology, which was the previous method of choice, requires little time to run (Robertson, Practical Approach Series, 254, 1987, Joyner, The Practical Approach Series, 293, 1999), thus reducing the identification time correctly modified cells from usually a few days to only a few hours.

This represents a significant improvement to the screening method used in the past and makes it a less time consuming and costly approach to search for homologous recombination events in eukaryotic cells.

Yet another advantage of the method of the invention is that it is also superior to previous technologies due to its ability to target difficult loci. It has been shown that, using previous technologies, the frequency of successful homologous exchange for certain loci can be as low as 1 in 2,000 integration events, perhaps even lower. Using the method of the invention, the inventors have demonstrated that such difficult loci can be targeted much more efficiently using LTVEC vectors that contain long homology arms. (ie larger than previous technologies allowed). As the non-limiting example presented above shows, the inventors have tracked the mOCR10 locus, a locus whose difficult homologous replacement with the use of previous technologies has been proven. Using the method of the invention, the inventors have shown that they achieved successful homologous exchange in 3 out of 69 ES cell clones integrating the LTVEC mOCR10 vector (containing more than 160 kb of homology arms and introducing a 20 kb deletion) while using previous technologies for homology in ES cells (Joyner, The Practical Approach Series, 293, 1999) using vectors based on plasmids with homology arms shorter than 10-20 kb and also introducing a deletion of less than 15 kb, no homologous exchange events were detected among 600 vector integrations. These data show conclusively the advantages of the method according to the invention over previous technologies.

Example 2:

Increased frequency of homologous exchange and eliminating the need to use isogenic DNA when LTVEC vectors are used as target vectors.

As noted above, the increased homologous exchange frequency achieved using long homology arms should reduce the benefit, if any, of using genomic DNA in the construction of an LTVEC vector that is isogenic (i.e., sequence identical) to the DNA of targeted eukaryotic cells. In order to test this hypothesis, the inventors constructed several LTVEC vectors using genomic DNA from the same mouse substrain as the eukaryotic cell to target (possibly isogenic) and a large number of LTVEC vectors using genomic DNA derived from mouse strains different from the eukaryotic cell for targeting (possibly non-isogenic). Non-isogenic DNA showed a homologous exchange frequency averaging 6% (ranging from 1 to 20%, Table 1), while isogenic LTVEC vectors showed an average targeting frequency of 3% (ranging from 2 to 5%, indicating that the rate of successful exchange homology with LTVEC vectors does not depend on isogeneity.

PL 204 759 B1

<td rowspan="2">NON-ISOGENIC Gene target</td><td rowspan="2">Description</td><td rowspan="2">Origin GOUT</td><td rowspan="2">Cell ES</td><td colspan="5">Approximate size (kb)</td><td rowspan="2">% Targeting</td>

<td>Size BAC</td><td>Arm 1</td><td>Arm 2</td><td>Deletion</td><td>Clones positive</td>

<td>OGH</td><td>LacZ-ATG merger</td><td>SvJ</td><td>CJ7</td><td> 148</td><td> 50</td><td> 90</td><td> 5'</td><td> 4</td><td> 4</td>

<td>OCR10 (A)</td><td>LacZ-ATG merger</td><td>SvJ</td><td>CJ7</td><td> 165</td><td> 135</td><td> 8</td><td> 20</td><td> 1</td><td> 1.4</td>

<td>OCR10 (B)</td><td>LacZ-ATG merger</td><td>SvJ</td><td>CJ7</td><td> 160</td><td> 130</td><td> 32</td><td> 20</td><td> 3</td><td> 4.3</td>

<td>MA61</td><td>LacZ-ATG merger</td><td>SvJ</td><td>CJ7</td><td> 95</td><td>N / A</td><td>N / A</td><td> 30</td><td> 3</td><td> 4.6</td>

<td>MA16</td><td>LacZ-ATG merger</td><td>SvJ</td><td>CJ7</td><td> 120</td><td>N / A</td><td>N / A</td><td> 8</td><td> 8</td><td> 13</td>

<td>AGRP</td><td>LacZ-ATG merger</td><td>SvJ</td><td>CJ7</td><td> 189</td><td> 147</td><td> 32</td><td> 8</td><td> 1</td><td> 1.1</td>

<td>SHIP-2</td><td>LacZ-ATG merger</td><td>SvJ</td><td>CJ7</td><td> 136</td><td> 30</td><td> 90</td><td> 11</td><td> 7</td><td> 15</td>

<td>Sm22</td><td>LacZ-ATG merger</td><td>SvJ</td><td>CJ7</td><td> 70</td><td> 35</td><td> 35</td><td> 0.9</td><td> 18</td><td> 20</td>

<td>LGR7L</td><td>LacZ-ATG merger</td><td>SvJ</td><td>CJ7</td><td> 200</td><td>N / A</td><td>N / A</td><td> 1</td><td> 3</td><td> 3.2</td>

<td>C5aR</td><td>LacZ-ATG merger</td><td>SvJ</td><td>CJ7</td><td> 160</td><td> 80</td><td> 25</td><td> 1</td><td> 4</td><td> 4.2</td>

<td>IL18</td><td>LacZ-ATG merger</td><td>SvJ</td><td>CJ7</td><td> 120</td><td> 50</td><td> 65</td><td> 10</td><td> 7</td><td> 7.3</td>

<td>PLGF</td><td>LacZ-ATG merger</td><td>SvJ</td><td>CJ7</td><td> 130</td><td> 40</td><td> 20</td><td> 8</td><td> 1</td><td> 1</td>

<td>NaDC-1</td><td>LacZ-ATG merger</td><td>SvJ</td><td>CJ7</td><td> 180</td><td> 30</td><td> 45</td><td> 25</td><td> 4</td><td> 2.1</td>

<td>ISOGENIC</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td>

<td>ROR1</td><td>IntracellLacZ fusion</td><td>CJ7</td><td>CJ7</td><td> 55</td><td> 14</td><td> 14</td><td> 20</td><td> 5</td><td> 5</td>

<td>ROR1</td><td>Intracell fusion- 3xmyc</td><td>CJ7</td><td>CJ7</td><td> 55</td><td> 14</td><td> 14</td><td> 20</td><td> 2</td><td> 2</td>

<td>ROR2</td><td>Mutation Brachydactyly and a Myc tag</td><td>CJ7</td><td>CJ7</td><td> 45</td><td> 11</td><td> 24</td><td> 0.5</td><td> 2</td><td> 2</td>

Example 3:

A detailed description of the TaqMan® based MOA assay for identifying the targeted ES clones.

ES cell clones that took the LTVEC vector and incorporated it into their genome at the targeted locus via homologous recombination were identified by the allele modification (MOA) assay, which uses quantitative real-time PCR to distinguish between targeted ES cell clones (with homologous exchange). in which one of the two alleles targeted is modified and homologously exchanged with ES cell clones, in which both alleles remained unmodified. The MOA determination consists of a primary search and a secondary search. The primary screening consists of the following steps: (1) culturing LTVEC transfected ES cell clones in 96-well gelatin coated plates; (2) isolation of genomic DNA from each ES cell clone; (3) using each genomic DNA sample as a template in 8 separate quantitative PCR reactions on two 384-well plates, with 2 of the PCR reactions using a set of target-specific primers that hybridize to the DNA sequence at one end of the genomic fragment targeted to deletions ("PCR reaction above"), and 2 of the PCR reactions use a set of target-specific primers, which hybridize to the DNA sequence at the other end of the genomic fragment targeted for deletion ("PCR below"), 4 of the reactions use a set of primers that recognize 4 non-targeted loci ("reference PCR") and each PCR reaction contains a fluorescent probe (for example a TaqMan® [ABI], Eclipse ™, or Molecular Beacon [Synthetic Genetics] probe, which recognizes the amplified sequence and whose fluorescence signal is directly proportional to the amount of PCR product; (4) performing the reaction in a device that is a combination of a thermocycler and a fluorescence detector (e.g. ABI 7900HT) that quantifies the accumulation of products

PL 204 759 B1 amplification during the PCR reaction and determines the threshold cycle (CT0, the point at which a fluorescence signal is detected above background noise; (5) calculating for each sample of ES cell clone DNA the difference in CT values ​​(Δ CT) between PCR reactions above and each of the four reference reactions

PCR and between the PCR reactions below and each of the four reference PCR reactions to create 8 tables with 96 ACT values; (6) normalizing the ACT values ​​to positive values, (7) calculating the median value for each comparison table for target and reference sequences;

(8) determination of the confidence interval using a computer program that examines eight ACT tables and determines how many times a given ES cell clone DNA sample generates an ACT value within the tolerance ranges of 0.5 to 1.5, 0.25 to 1.5, 0, 5 to 2.0, 0.25 to 2.0, 0.5 to 3.0, and 0.25 to 3.0 cycles greater than the median of ACT (examples of computer programming languages ​​to create or write such a program include visual basics, Java or any other computer programming language known to one skilled in the art); (9) plotting the values ​​and their medians for each of the 8 ACT tables as histograms; and (10) identifying correctly targeted ES cell clone candidates from checking the confidence intervals of the ACT histograms. In a preferred example, the ACT value for the candidate target clone is 0.5 to 1.5 cycles greater than the median of 8 of the 8 reference comparisons.

Candidate clones identified by the primary screening in the MOA assay are confirmed or rejected by a secondary screening which includes the steps of: (1) use of genomic DNA from each of the positive candidate ES cell clones from more negative clones and from mouse genomic DNA copy number standards that carry one or two copies of the LacZ-Neo cassette onto the diploid genome as templates in two quantitative PCR reactions 384-well plates, with one reaction being the PCR above (as in the original screening), 4 reactions being the reference PCR reactions with two reference loci, which are different from those used in the primary screening, one reaction is with primers and probe that are specific for the LacZ gene from the LTVEC vector and one reaction is with primers and probe that are specific for the Neo gene from the LTVEC vector; (2) performing the PCR in a quantitative PCR apparatus, as in the primary screening;

(3) Calculating, as in the original screening, the values ​​of the difference in ACT between the PCR above and each of the two reference PCR reactions, between the PCR below and each of the two reference PCR reactions, between the LacZ PCR and each of the two reference PCR reactions, and between Neo PCR and each of the two reference PCR reactions to create 8 ACT tables;

(4) normalizing the ACT values ​​to positive values; (5) calculating the median value for each of the ACT tables; (6) calculating the confidence intervals as in the original scan; and (7) plotting the values ​​and their medians for each of the eight ACT tables as a histogram.

Based on the examination of the results of the evaluation of the confidence intervals and ACT histograms for the primary and secondary screening, candidate ES clones with correct homologous exchange are either confirmed or rejected. In the preferred example, the ACT value for the homologously displaced candidate clone is in the range of 0.5 to 1.5 cycles above the median in 12 of the 12 reference comparisons from the primary and secondary screenings combined.

To calculate the number of LTVEC copies per diploid genome in validated, correctly targeted ES clones, their ACT values ​​from the LacZ and Neo PCR comparisons are compared with the two reference PCR reactions with the ACT values ​​for the LacZ-Neo copy quantity standards.

Each ES cell clone is scored as having 1, 2, or more than 2 copies of the LTVEC. For each modified allele design, ES cell clones are screened in groups of 96 (typically less than 288 total clones) until 3 positive MOA clones are identified that contain a single LacZ-Neo cassette.

Example 4:

Use of FISH for the detection of correctly targeted LTVEC vectors in ES cells.

Using the LTVEC technology described herein, the inventors switched off the SM22alpha gene in ES cells. SM22alpha is a limited-origin 22-kDa smooth muscle protein (SMC) that physically associates with cytoskeleton actin filament bundles in contractile smooth muscle. The homologously exchanged ES cells were then subjected to standard fluorescence in situ hybridization (FISH) performed on stretched metaphase chromosomes to verify that the gene underwent proper homologous replacement. The experiment was performed with two probes: 1) the probe for the SM2alpha gene containing the unmodified BAC clone used to create the LTVEC vector and 2) the DNA probe for LacZ and Neomycin, which only detects

A gene modification resulting from a homologous exchange (insertion of the LacZ and Neo gene cassettes). These stretched metaphase chromosomes were prepared from the cells and hybridization was performed simultaneously with both probes, which were labeled with different fluorophores to allow detection of hybridization of each probe on the same stretched chromosome. The ES cell line without homologous exchange was analyzed in parallel as a control. As expected, the controls detected two SM22alpha alleles on homologous chromosomal arms, but no hybridization of the LacZ-Neo probe occurred. As in the control, two alleles in the same chromosomal locus and on homologous chromosomes were detected in extended chromosomes with homologous replacement, but double labeling with LacZ-Neo probe occurred on one of the two chromosomes indicating co-localization of the LacZ-Neo and SM22alpha DNA sequences in the allele SM22alpha. Importantly, no LacZ-Neo and SM22alpha gene sequences were detected in the wrong locations on the stretched chromosome. The lack of additional integration of the SM2alpha gene sequences and the co-localization of LacZ-Neo with SM22alpha in one chromosome of the homologous pair strongly suggest that correct targeting (homologous gene exchange) of LacZ to one of the SM22alpha alleles by homologous recombination occurred.

Example 5:

Lowering the amount of DNA used for electroporation of ES cells improves the efficiency of homologous exchange.

Typically, standard methods for modification by homologous gene exchange use 20 to 40 µg of the target vector in the electroporation procedure. The inventors found that with LTVEC vectors, electroporation using much lower amounts of DNA - in the range of about 1 to 5 μg per 1X10⁷ cells - doubles the frequency of correctly targeted homologous recombination events, while the number of secondary, non-homologous insertion events is greatly reduced. This marked improvement in the efficiency of homologous exchange is significant because it significantly reduces the number of ES cell clones that need to be screened to find several positive clones with a correctly targeted single copy modification. Additional benefits are reduced costs and increased capacity and processing capacity.

Example 6:

Use of the method of the invention to create gene knockout mice for the study of muscle atrophy.

MA61, also referred to as MAFbx, is a recently discovered ubiquitin ligase that is activated in various forms of muscle atrophy (see Provisional Application US No. 60 / 264,926, filed August 10, 2001, and US Provisional Application of North America. (serial number not yet known), filed October 22, 2001, all assigned to Regeneron Pharmaceuticals Inc., which are hereby incorporated by reference in their entirety). In order to further investigate the biological importance of this gene in muscle atrophy, knockout mice were created using the following method of the invention.

First, to obtain a large cloned genomic fragment containing the MA61 gene, a Bacterial Artificial Chromosome (BAC) library was screened with primers derived from the MA61 cDNA sequence. The thus obtained BAC clone was then used to create a Large Target Vector for Eukaryotic Cells (LTVEC) as follows. A modification cassette containing a 5 'homology box / lacZ gene / polyA / PGK promoter / neo / polyA / 3' homology box was constructed. Homology boxes were included to mark the sites of bacterial homologous recombination during the production of the LTVEC. The LacZ gene is a reporter gene that has been positioned so that its initiation codon is at the same position as the MA61 initiation codon. As a result of homologous recombination in bacteria, the modification cassette replaced the MA61 gene. Thus, an LTVEC MA61 vector was constructed in which the MA61 coding sequences in the BAC clone were replaced with a modification cassette constructed as described above. The LTVEC vector DNA was then prepared, purified and linearized for insertion into eukaryotic cells as described above.

Small-scale LTVEC MA61 vector DNA preparation was performed ((Sambrook, J., EF Fritsch and T. Maniatis. Molecular Cloning: A Laboratory Manual, Second Edition, Volumes 1, 2 and 3, 1989; Tillett and Neilan, Biotechniques, 24: 568-70,572,1998;

http: //www.qiagen.xom/literature/handbooks/plkmini/plm_399.pdf) and retransformed to E. coli using electroporation (Sambrook, J., EF Fritsch and T. Maniatis, Molecular Cloning: A Laboratory Manual, Edition Drugie, Volumes 1, 2 and 3, 1989) to remove the plasmid encoding the recombinogenic proteins

PL 204 759 B1 used in the bacterial homologous recombination step (Zhang et al., Nat Genet, 20: 123-8, 1998;

Narayanan et al., Gene Ther, 6: 442-7,1999). Prior to introducing the LTVEC MA61 into eukaryotic cells, larger amounts of the LTVEC were prepared using standard methodology (http://www.qiagen.com/literature/handbooks/plk/plklow.pdf; Sambrook, J., EF Fritsch and T. Maniatis. Molecular Cloning: A Laboratory Manual, Second Edition, Volumes 1, 2 &amp; 3, 1989; Tillett and Neilan, Biotechniques, 24: 568-70,572, 1998).

The LTVEC MA61 vector was then linearized to prepare the LTVEC MA61 for introduction into eukaryotic cells. This was achieved by digesting with the restriction enzyme NotI, which leaves a modified gene (s) or a chromosomal locus (loci) flanked by long homology arms.

The LTVEC MA61 vector was then introduced into eukaryotic cells using standard electroporation methodology (Sambrook, J., EF Fritsch and T. Maniatis. Molecular Cloning: A Laboratory Manual, Second Edition, Volumes 1, 2 and 3, 1989). Cells into which the LTVEC MA61 vector was successfully introduced were selected by exposure to a selection agent. Since the neomycin phosphotransferase (neo) gene was used as a selectable marker in the modification cassette (Beck, et al., Gene, 19: 327-36, 1982), cells that took up the LTVEC MA61 vector were selected in G418 containing medium; cells that lacked the LTVEC MA61 vector died, while cells that took the LTVEC MA61 vector survived (Santerre, et al., Gene, 30: 147-56, 1984).

Eukaryotic cells that had been successfully modified by targeting the MA61 LTVEC vector to the MA61 locus were identified using TaqMan® quantitative PCR (Lie and Petropoulos, Curr Opin Biotechnol, 9: 43-8, 1998).

Ultimately, the genetically modified ES cells were used to generate genetically engineered, in this case knockout, mice using standard blastocyst injection technology. Thus, mice with knockouts of the MA61 gene, mice in which the MA61 gene has been deleted, were created.

Both these gene knockout and wild-type (WT) mice were exposed to atrophy-inducing conditions created by denervation of the mice and the levels of atrophy were compared. First, the sciatic nerve in the middle thigh of the hind limb was isolated and cut in mice. Cutting the sciatic nerve leads to innervation shutdown and, within 14 days, atrophy of the muscles of the lower limb, more specifically the tibial anterior and gastrocnemius muscles, over a 14-day period. 7 to 14 days after the innervation was turned off, the animals were sacrificed by carbon dioxide inhalation. The tibialis anterior muscle (TA) and gastrocnemius complex (GA) were then removed from the right (denervated) and left (intact) hind limbs and weighed, frozen at a fixed length in isopentane cooled liquid nitrogen. The degree of atrophy was assessed by comparing the muscle weight of the denervated limb with the muscle weight of the non-denervated limb.

Muscular atrophy was assessed 7 and 14 days after cutting the right sciatic nerve. The wet masses of the right, denervated muscles were compared with the wet masses of the left, non-denervated muscles. The comparisons between right and left are given in table 2.

<td>7 days</td><td colspan="3">Gastrocnemius Complex</td><td colspan="3">M. anterior tibial</td>

<td>Genotype</td><td>Sample size</td><td>Average</td><td>SD</td><td>Sample size</td><td>Average</td><td>SD</td>

<td>TUE</td><td> 7</td><td> 0,76</td><td> 0,016</td><td> 11</td><td> 0,68</td><td> 0,033</td>

<td>KO</td><td> 6</td><td> 0,84</td><td> 0,022</td><td> 11</td><td> 0,80</td><td> 0,015</td>

<td>14 days</td><td colspan="3">Gastrocnemius Complex</td><td colspan="3">M. anterior tibial</td>

<td>Genotype</td><td>Sample size</td><td>Average</td><td>SD</td><td>Sample size</td><td>Average</td><td>SD</td>

<td>TUE</td><td> 5</td><td> 0,55</td><td> 0,024</td><td> 5</td><td> 0,62</td><td> 0,023</td>

<td>KO</td><td> 5</td><td> 0,80</td><td> 0,019</td><td> 5</td><td> 0,80</td><td> 0,012</td>

and on day 14 the muscles of the knockout mice showed significantly (p &lt;0.001) less atrophy than the muscles of the wild-type mice. The difference between the non-wild type and the non-wild type mice was

On day 14 than on day 7. While the wild-type mice atrophied, the mice did not show additional atrophy.

Taken together, the approach using the generation of LTVECs and directly using them as target vectors combined with MOA screening for homologous recombination events in ES cells creates a new way to construct genetically altered loci that is fast, inexpensive, and a significant improvement over the onerous, time-consuming methods previously used in use. Thus, it opens the possibility to perform rapid in vivo functional genomic analysis on a large scale of substantially any and all genes in the genome of an organism, requiring only a fraction of the time and cost required by previous technologies.