Production of chimeras by blastocyst and morula injection of targeted ES cells

The ability of mammalian embryos to incorporate foreign cells and develop as chimeras has been exploited for a variety of purposes including the elucidation of cell lineages, the investigation of cell potential, the perpetuation of mutations produced in embryonic stem (ES) cells by gene targeting, and the subsequent analysis of these mutations. The extent of contribution of the foreign cells depends on their developmental synchrony with the host embryo and their mitotic and developmental potential, which may be severely restricted if the cells bear mutations. If the goal in making chimeras is the transmission of a mutation produced by gene targeting to the next generation, the mutant ES cells must have the capacity to undergo meiosis and gametogenesis. Cells from two different mammalian embryos were first combined experimentally to produce a composite animal, dubbed a chimera, nearly four decades ago. Pairs of cleaving, pre-implantation embryos were mechanically associated in vitro until they aggregated together to make single large morulae; these in turn resulted in chimeric offspring (1). Genetic markers were used to distinguish the contributions of the two embryos in these animals. Since then, various methods for making chimeras have been explored to address different types of questions (2). In 1972 it was reported that highly asynchronous embryonic cells, which had been cultured in vitro, could contribute to chimeras upon re-introduction into pre-implantation embryos (3). Not long afterward, several groups working with teratocarcinomas, tumours derived from germ cells of the gonad, discovered that stem cells from these tumours, known as embryonal carcinoma cells, could contribute to an embryo if introduced into pre-implantation stages (4-6). It appeared that the undifferentiated stem cells of the tumour had enough features in common with early embryonic cells that they could respond to the embryonic environment, differentiating in a normal manner, even after long periods in vitro. Their embryonic potential was limited, however, and many teratocarcinoma cell lines made only meagre contributions to the developing fetus or even produced tumours in chimeras (7). Either their derivation from tumours or their extended sojourn in vitro rendered these cells so dissimilar from early embryonic cells that they rarely, if ever, had full embryonic potential.

Classical genetics and gene targeting

Gene targeting has provided considerable insight into the functions of numerous genes since it was developed a decade ago (1-4). A listing of the diversity of targeted genes and breadth of mutant phenotypes characterized to date can be obtained through mouse mutation databases (http://www.bis.med. jhmi.edu/Dan/tbase.html and http://biomednet.com/cgi-bin/ mko/mkohome.pl) (5, 6). However, in order to take full advantage of this technology, classical genetic methods should be utilized to extend our knowledge of individual genes to genetic pathways. In this chapter, the significance of genetics in gene targeting and phenotype interpretation are discussed. We describe how Mendelian and quantitative genetics can be exploited to map modifier loci or generate animals carrying mutations in two or more genes. We also discuss the development and application of classical genetic approaches towards elucidating gene function such as generation of allelic series and creation of deletion complexes throughout the genome in ES cells and mice. Several genetic considerations should be taken into account during the initial stages of a gene targeting experiment. In order to maximize homologous recombination efficiency, both arms of a targeting vector should be isolated from the same strain of mice as that of the ES cells (see Chapter 1 for details). Although most ES cell lines have been isolated from 129 strains of mice, significant genetic variation exists among the different substrains, which is sometimes evident by pronounced differences in coat colour (see Chapter 4, Table 1) (7, 8). For instance, 129/Sv mice (Aw/Aw, +c-Tyr +p/+c-Tyr +p ) have a white-bellied agouti (Aw) phenotype, whereas 129/SvJ mice (Aw/Aw, Tyrc p/T yrc-ch p) have a cream colour owing to the effect of mutant tyrosinase (Tyr) and pink-eyed dilution (p) alleles which are epistatic to Aw (9). Molecular analysis of different 129 substrains using microsatellite markers has provided insight into their genetic differences and revealed that 129/SvJ is particularly divergent and actually contaminated with genomic regions of non-129 origin (7, 8). Before the significance of this heterogeneity was appreciated, many targeting vectors were constructed from 129/SvJ DNA for use in 129/Sv ES cell lines.

Production and analysis of ES cell aggregation chimeras

Embryonic stem (ES) cells behave like normal embryonic cells when returned to the embryonic environment after injection into a host blastocyst or after aggregation with earlier blastomere stage embryos. In such chimeras, ES cells behave like primitive ectoderm or epiblast cells (1), in that they contribute to all lineages of the resulting fetus itself, as well as to extraembryonic tissues derived from the gastrulating embryo, namely the yolk sac mesoderm, the amnion, and the allantois. However, even when aggregated with preblastocyst stage embryos, ES cells do not contribute to derivatives of the first two lineages to arise in development, namely, the extraembryonic lineages: trophoblast and primitive endoderm (2). The pluripotency of ES cells within the embryonic lineages is critical to their use in introducing new genetic alterations into mice, because truly pluripotent ES cells can contribute to the germline of chimeras, as well as all somatic lineages. However, the ability of ES cells to co-mingle with host embryonic cells, specifically in the embryonic, but not the major extraembryonic lineages, opens up a variety of possibilities for analysing gene function by genetic mosaics rather than by germline mutant analysis alone (3). There are two basic methods for generating pre-implantation chimeras in mice, whether it be embryo ↔ embryo or ES cell ↔ embryo chimeras. Blastocyst injection, in which cells are introduced into the blastocoele cavity using microinjection pipettes and micromanipulators, has been the method of choice for most ES cell chimera work (see Chapter 4). However, the original method for generating chimeras in mice, embryo aggregation, is considerably simpler and cheaper to establish in the laboratory. Aggregation chimeras are made by aggregating cleavage stage embryos together, or inner cell mass (ICM) or ES cells with cleavage stage embryos, growing them in culture to the blastocyst stage, and then transferring them to the uterus of pseudopregnant recipients to complete development. This procedure can be performed very rapidly by hand under the dissecting microscope, thus making possible high throughput production with minimal technical skill (4). In this chapter we describe some of the uses of pre-implantation chimeras, whether made by aggregation or blastocyst injection, but focus on the technical aspects of aggregation chimera generation. We also discuss the advantages and disadvantages of aggregation versus blastocyst injection for chimera production.

Site-specific recombination in cells and mice

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

Gene trap strategies in ES cells

Gene trap (GT) strategies in mouse embryonic stem (ES) cells are increasingly being used for detecting patterns of gene expression (1-4, isolating and mutating endogenous genes (5-7), and identifying targets of signalling molecules and transcription factors (3, 8-10). The general term gene trap refers to the random integration of a reporter gene construct (called entrapment vector) (11, 12) into the genome such that ‘productive’ integration events bring the reporter gene under the transcriptional regulation of an endogenous gene. In some cases this also simultaneously generates an insertional mutation. Entrapment vectors were originally developed in bacteria (13), and applied in Drosophila to identify novel developmental genes and/or regulatory sequences (14-17). Subsequently, a modified strategy was developed for mouse in which the reporter gene mRNA becomes fused to an endogenous transcript. Such ‘gene trap’ vectors were initially used primarily as a tool to discover genes involved in development (1, 2,18). In the last five years there has been a significant shift of GT approaches in mouse to much broader, large scale applications in the context of the analysis of mammalian genomes and ‘functional genomics’. Sequencing and physical mapping of both the human and mouse genomes is expected to be completed within the next five years. Already, a large number of mouse and human genes have been identified as expressed sequence tags (ESTs), and very likely the majority of genes will be discovered as ESTs shortly. This vast sequence information contrasts with a rather limited understanding of the in vivo functions of these genes. Whereas DNA sequence can provide some indication of the potential functions of these genes and their products, their physiological roles in the organism have to be determined by mutational analysis. Thus, the sequencing effort of the human genome project has to be complemented by efficient functional analyses of the identified genes. One potentially powerful complementation to the efforts of the human genome project would be a strategy whereby large scale random mutagenesis in mouse is combined with the rapid identification of the mutated genes (6,7,19, and German gene trap consortium, W. W. unpublished data).

Production of targeted embryonic stem cell clones

The discovery that cloned DNA introduced into tissue culture cells can undergo homologous recombination at specific chromosomal loci has revolutionized our ability to study gene function in cell culture and in vivo. In theory, this technique, termed gene targeting, allows one to generate any type of mutation in any cloned gene. The kinds of mutations that can be created include null mutations, point mutations, deletions of specific functional domains, exchanges of functional domains from related genes, and gain-of-function mutations in which exogenous cDNA sequences are inserted adjacent to endogenous regulatory sequences. In principle, such specific genetic alterations can be made in any cell line growing in culture. However, not all cell types can be maintained in culture under the conditions necessary for transfection and selection. Over ten years ago, pluripotent embryonic stem (ES) cells derived from the inner cell mass (ICM) of mouse blastocyst stage embryos were isolated and conditions defined for their propogation and maintenance in culture (1, 2). ES cells resemble ICM cells in many respects, including their ability to contribute to all embryonic tissues in chimeric mice. Using stringent culture conditions, the embryonic developmental potential of ES cells can be maintained following genetic manipulations and after many passages in vitro. Furthermore, permanent mouse lines carrying genetic alterations introduced into ES cells can be obtained by transmitting the mutation through the germline by generating ES cell chimeras (described in Chapters 4 and 5). Thus, applying gene targeting technology to ES cells in culture affords researchers the opportunity to modify endogenous genes and study their function in vivo. In initial studies, one of the main challenges of gene targeting was to distinguish the rare homologous recombination events from more commonly occurring random integrations (discussed in Chapter 1). However, advances in cell culture and in selection schemes, in vector construction using isogenic DNA, and in the application of rapid screening procedures have made it possible to identify homologous recombination events efficiently. Since there are numerous publications available that describe basic tissue culture techniques in this chapter we will only describe techniques specific for ES cells.

Gene targeting, principles, and practice in mammalian cells

When a fragment of genomic DNA is introduced into a mammalian cell it can locate and recombine with the endogenous homologous sequences. This type of homologous recombination, known as gene targeting, is the subject of this chapter. Gene targeting has been widely used, particularly in mouse embryonic stem (ES) cells, to make a variety of mutations in many different loci so that the phenotypic consequences of specific genetic modifications can be assessed in the organism. The first experimental evidence for the occurrence of gene targeting in mammalian cells was made using a fibroblast cell line with a selectable artificial locus by Lin et al. (1), and was subsequently demonstrated to occur at the endogenous β-globin gene by Smithies et al. in erythroleukaemia cells (2). In general, the frequencies of gene targeting in mammalian cells are relatively low compared to yeast cells and this is probably related to, at least in part, a competing pathway: efficient integration of the transfected DNA into a random chromosomal site. The relative ratio of targeted to random integration events will determine the ease with which targeted clones are identified in a gene targeting experiment. This chapter details aspects of vector design which can determine the efficiency of recombination, the type of mutation that may be generated in the target locus, as well as the selection and screening strategies which can be used to identify clones of ES cells with the desired targeted modification. Since the most common experimental strategy is to ablate the function of a target gene (null allele) by introducing a selectable marker gene, we initially describe the vectors and the selection schemes which are helpful in the identification of recombinant clones (Sections 2-5). In Section 6, we describe the vectors and additional considerations for generating subtle mutations in a target locus devoid of any exogenous sequences. Finally, Section 7 is dedicated to the use of gene targeting as a method to express exogenous genes from specific endogenous regulatory elements in vivo, also known as ‘knock-in’ strategies. A targeting vector is designed to recombine with and mutate a specific chromosomal locus.