Mouse mutants and phenotypes: accessing information for the study of mammalian gene function

Recent advances in high-throughput gene targeting and conditional mutagenesis are creating new and powerful resources to study the in vivo function of mammalian genes using the mouse as an experimental model. Mutant ES cells and mice are being generated at a rapid rate to study the molecular and phenotypic consequences of genetic mutations, and to correlate these study results with human disease conditions. Likewise, classical genetics approaches to identify mutations in the mouse genome that cause specific phenotypes have become more effective. Here, we describe methods to quickly obtain information on what mutant ES cells and mice are available, including recombinase driver lines for the generation of conditional mutants. Further, we describe means to access genetic and phenotypic data that identify mouse models for specific human diseases.     

Identification and quantification of disease-related gene clusters

MOTIVATION: DNA microarray technology and the completion of human and mouse genome sequencing programs are now offering new avenues for the investigation of complex genetic diseases. In particular, this makes possible the study of the spatial distribution of disease-related genes within the genome. We report on the first systematic search for clustering of genes associated with a polygenic autoimmune disease. RESULTS: Using a set of cDNA microarray chip experiments in two mouse models of rheumatoid arthritis, we have identified approximately 200 genes based on their expression in inflamed joints and mapped them into the genome. We compute the spatial autocorrelation function of the selected genes and find that they tend to cluster over scales of a few megabase pairs. We then identify significant gene clusters using a friends-of-friends algorithm. This approach should aid in discovering functionally related gene clusters in the mammalian genome.     

Mutagenesis strategies for identifying novel loci associated with disease phenotypes

The systematic identification of the function of all the genes in the mammalian genome is one of the major scientific challenges for the 21st century. A comprehensive insight into mammalian gene function will illuminate our understanding of the genetic bases of disease. Mouse mutagenesis is a powerful tool for the study of mammalian gene function. Most recently, a number of approaches employing the chemical mutagen ethylnitrosourea (ENU) have been utilised by mouse geneticists to deliver a substantial new collection of mouse disease models. The growing mouse mutant archive provides a powerful resource for the identification of novel genes involved with human genetic disease.     

Gene transfer and gene mapping in mammalian cells in culture

The ability to transfer mammalian genes parasexually has opened new possibilities for gene mapping and fine structure mapping and offers great potential for contributing to several aspects of mammalian biology, including gene expression and genetic engineering. The DNA transferred has ranged from whole genomes to single genes and smaller segments of DNA. The transfer of whole genomes by cell fusion forms cell hybrids, which has promoted the extensive mapping of human and mouse genes. Transfer, by cell fusion, of rearranged chromosomes has contributed significantly to determining close linkage and the assignment of genes to specific chromosomal regions. Transfer of single chromosomes has been achieved utilizing microcells fused to recipient cells. Metaphase chromosomes have been isolated and used to transfer single-to-multigenic DNA segments. DNA-mediated gene transfer, simulating bacterial transformation, has achieved transfer of single-copy genes. By utilizing DNA cleaved with restriction endonucleases, gene transfer is being empolyed as a bioassay for the purification of genes. Gene mapping and the fate of transferred genes can be examined now at the molecular level using sequence-specific probles. Recently, single genes have been cloned into eucaryotic and procaryotic vectors for transfer into mammalian cells. Moreover, recombinant libraries in which entire mammalian genomes are represented collectively are a rich new source of transferable genes. Methodology for transferring mammalian genetic information and applications for mapping mammalian genes is presented and prospects for the future discussed.     

Towards a molecular-genetic analysis of mammalian development

The mouse has been a slower starter than many other organisms in the race to unravel the genetic control of embryonic development. Recent cloning of putative developmental genes combined with new approaches to manipulating the mouse genome seem set, however, to allow the mammalian embryo to move towards the front of the field.     

Animal cloning by nuclear transfer: state-of-the-art and future perspectives

Model organisms are essential to study the genetic basis of human diseases. Transgenic mammalian models, especially genetic knock-out mice have catalysed the progress in this area. To continue the advancement, further sophisticated and refined models are crucially needed to study the genetic basis and manifestations of numerous human diseases. Coinciding with the start of the new era of post-genomic research, new tools for establishment of transgenesis, such as nuclear transfer and gene targeting in somatic cells, have become available, offering a unique opportunity for the generation of transgenic animal models. The new technology provides important tools for comparative functional genomics to promote the interpretation and increase the practical value of the data generated in numerous mouse models. This paper discusses the state-of-the-art of the nuclear replacement technology and presents future perspectives.     

Identification of 18 mouse ABC genes and characterization of the ABC superfamily in Mus musculus

ATP-binding cassette (ABC) genes encode a family of transport proteins known to be involved in a number of human genetic diseases. In this study, we characterized the ABC superfamily in Mus musculus through in silico gene identification and mapping and phylogenetic analysis of mouse and human ABC genes. By querying dbEST with amino acid sequences from the conserved ATP-binding domains, we identified and partially sequenced 18 new mouse ABC genes, bringing the total number of mouse ABC genes to 34. Twelve of the new ABC genes were mapped in the mouse genome to the X chromosome and to 10 of the 19 autosomes. Phylogenetic relationships of mouse and human ABC genes were examined with maximum parsimony and neighbor-joining analyses that demonstrated that mouse and human ABC orthologs are more closely related than are mouse paralogs. The mouse ABC genes could be grouped into the seven previously described human ABC subfamilies. Three mouse ABC genes mapped to regions implicated in cholesterol gallstone susceptibility.     

Gene transfer and gene mapping in mammalian cells in culture

Summary The ability to transfer mammalian genes parasexually has opened new possibilities for gene mapping and fine structure mapping and offers great potential for contributing to several aspects of mammalian biology, including gene expression and genetic engineering. The DNA transferred has ranged from whole genomes to single genes and smaller segments of DNA. The transfer of whole genomes by cell fusion forms cell hybrids, which has promoted the extensive mapping of human and mouse genes. Transfer, by cell fusion, of rearranged chromosomes has contributed significantly to determining close linkage and the assignment of genes to specific chromosomal regions. Transfer of single chromosomes has been achieved utilizing microcells fused to recipient cells. Metaphase chromosomes have been isolated and used to transfer single-to-multigenic DNA segments. DNA-mediated gene transfer, simulating bacterial transformation, has achieved transfer of single-copy genes. By utilizing DNA cleaved with restriction endonucleases, gene transfer is being employed as a bioassay for the purification of genes. Gene mapping and the fate of transferred genes can be examined now at the molecular level using sequence-specific probes. Recently, single genes have been clones into eucaryotic and procaryotic vectors for transfer into mammalian cells. Moreover, recombinant libraries in which entire mammalian genomes are represented collectively are a rich new source of transferable genes. Methodology for transferring mammalian genetic information and applications for mapping mammalian genes is presented and prospects for the future discussed. Presented in the symposium on Gene Transfer, Differentiation and Neoplasia in Plant and Animal Cells at the 30th Annual Meeting of the Tissue Culture Association, Seattle, Washington, June 10–14, 1979. This symposium was supported in part by Grant CA 26748 from the National Cancer Institute, DHEW, and Grant RD-67 from the American Cancer Society. Supported by NIH grants HD 05196 and GM 20454 and by MOD grants 1-485 and 1-692.     

Mouse models of type 1 and type 2 diabetes derived from the same closed colony: genetic susceptibility shared between two types of diabetes

Except for rare subtypes of diabetes, both type 1 and type 2 diabetes are multifactorial diseases in which genetic factors consisting of multiple susceptibility genes and environmental factors contribute to the disease development. Due to complex interaction among multiple susceptibility genes and between genetic and environmental factors, genetic analysis of multifactorial diseases is difficult in humans. Inbred animal models, in which the genetic background is homogeneous and environmental factors can be controlled, are therefore valuable in genetic dissection of multifactorial diseases. We are fortunate to have excellent animal models for both type 1 and type 2 diabetes--the nonobese diabetic (NOD) mouse and the Nagoya-Shibata-Yasuda (NSY) mouse, respectively. Congenic mapping of susceptibility genes for type 1 diabetes in the NOD mouse has revealed that susceptibility initially mapped as a single locus often consists of multiple components on the same chromosome, indicating the importance of congenic mapping in defining genes responsible for polygenic diseases. The NSY mouse is an inbred animal model of type 2 diabetes established from Jcl:ICR, from which the NOD mouse was also derived. We have recently mapped three major loci contributing to type 2 diabetes in the NSY mouse. Interestingly, support intervals where type 2 diabetes susceptibility genes were mapped in the NSY mouse overlapped the regions where type 1 diabetes susceptibility genes have been mapped in the NOD mouse. Although additional evidence is needed, it may be possible that some of the genes predisposing to diabetes are derived from a common ancestor contained in the original closed colony, contributing to type 1 diabetes in the NOD mouse and type 2 diabetes in the NSY mouse. Such genes, if they exist, will provide valuable information on etiological pathways common to both forms of diabetes, for the establishment of effective methods for prediction, prevention, and intervention in both type 1 and type 2 diabetes.     

Using standard nomenclature to adequately name transgenes,knockout gene alleles and any mutation associated to a genetically modified mouse strain

Mice provide an unlimited source of animal models to study mammalian gene function and human diseases. The powerful genetic modification toolbox existing for the mouse genome enables the creation of, literally, thousands of genetically modified mouse strains, carrying spontaneous or induced mutations, transgenes or knock-out/knock-in alleles which, in addition, can exist in hundreds of different genetic backgrounds. Such an immense diversity of individuals needs to be adequately annotated, to ensure that the most relevant information is kept associated with the name of each mouse line, and hence, the scientific community can correctly interpret and benefit from the reported animal model. Therefore, rules and guidelines for correctly naming genes, alleles and mouse strains are required. The Mouse Genome Informatics Database is the authoritative source of official names for mouse genes, alleles, and strains. Nomenclature follows the rules and guidelines established by the International Committee on Standardized Genetic Nomenclature for Mice. Herewith, both from the International Society for Transgenic Technologies (ISTT) and from the scientific journal Transgenic Research, we would like to encourage all our colleagues to adhere and follow adequately the standard nomenclature rules when describing mouse models. The entire scientific community using genetically modified mice in experiments will benefit.     

Gene therapy

Summary A number of techniques are available for insertion of new genetic information into mammalian cells. Some of these have been used successfully for genetic modification of germ line cells and somatic cells of living animals. Some of these techniques may be applicable to treatment of some of the genetic diseases of man, once problems related to the control of expression of introduced genes are solved.     

The expanding role of mouse genetics for understanding human biology and disease

It has taken about 100 years since the mouse first captured our imagination as an intriguing animal for it to become the premier genetic model organism. An expanding repertoire of genetic technology, together with sequencing of the genome and biological conservation, place the mouse at the foremost position as a model to decipher mechanisms underlying biological and disease processes. The combined approaches of embryonic stem cell-based technologies, chemical and insertional mutagenesis have enabled the systematic interrogation of the mouse genome with the aim of creating, for the first time, a library of mutants in which every gene is disrupted. The hope is that phenotyping the mutants will reveal novel and interesting phenotypes that correlate with genes, to define the first functional map of a mammalian genome. This new milestone will have a great impact on our understanding of mammalian biology, and could significantly change the future of medical diagnosis and therapeutic development, where databases can be queried in silico for potential drug targets or underlying genetic causes of illnesses. Emerging innovative genetic strategies, such as somatic genetics, modifier screens and humanized mice, in combination with whole-genome mutagenesis will dramatically broaden the utility of the mouse. More significantly, allowing genome-wide genetic interrogations in the laboratory, will liberate the creativity of individual investigators and transform the mouse as a model for making original discoveries and establishing novel paradigms for understanding human biology and disease.     

Finding the genes that direct mammalian development : ENU mutagenesis in the mouse

The genetic control of mammalian embryogenesis is not well understood. N-ethyl-N-nitrosourea (ENU) mutagenesis screens in the mouse provide a route to identify more of the genes that are required for mammalian development. The characterization of ENU-induced mutations can build on the resources provided by the mouse and human genome projects to help define the tissue interactions and signaling pathways that direct early mammalian development.     

The mouse ascending: perspectives for human-disease models

The laboratory mouse is widely considered the model organism of choice for studying the diseases of humans, with whom they share 99% of their genes. A distinguished history of mouse genetic experimentation has been further advanced by the development of powerful new tools to manipulate the mouse genome. The recent launch of several international initiatives to analyse the function of all mouse genes through mutagenesis, molecular analysis and phenotyping underscores the utility of the mouse for translating the information stored in the human genome into increasingly accurate models of human disease.     

The thankless task of playing genetics with mammalian mitochondrial DNA: a 30-year review

The advances obtained through the genetic tools available in yeast for studying the oxidative phosphorylation (OXPHOS) biogenesis and in particular the role of the mtDNA encoded genes, strongly contrast with the very limited benefits that similar approaches have generated for the study of mammalian mtDNA. Here we review the use of the genetic manipulation in mammalian mtDNA, its difficulty and the main types of mutants accumulated in the past 30 years and the information derived from them. We also point out the need for a substantial improvement in this field in order to obtain new tools for functional genetic studies and for the generation of animal models of mtDNA-linked diseases.     

Genomics meets genetics: towards a mutant map of the mouse

Phenotype-driven mutagenesis approaches in the mouse will deliver a vastly expanded mouse mutant resource and can be expected to lead to the identification of novel genes and pathways, enabling the emergence of new insights into mammalian gene function. In order for this goal to be realized, developments in genomics need to be harnessed to progress in mouse mutagenesis. We need firstly to generate a mutant map of the mouse, devising and employing rapid methods for the genetic mapping of the growing mouse mutant resource. Secondly, we need to be able to rapidly identify and assess candidate genes in the vicinity of the mapped mutations. Developments in mapping and genotyping technology are described that will potentially speed the construction of a rich mutant map of the mouse. In addition, the benefits of comparative sequencing of the human and mouse genomes are reviewed. The availability of both human and mouse genome sequences will underpin the evolution of a comprehensive and well annotated mammalian gene map that will significantly enhance our ability to move rapidly from mapped mutation to the identification of the underlying gene. Received: 16 December 1999 / Accepted: 17 December 1999     

Mice as a mammalian model for research on the genetics of aging

Mice are an ideal mammalian model for studying the genetics of aging: considerable resources are available, the generation time is short, and the environment can be easily controlled, an important consideration when performing mapping studies to identify genes that influence lifespan and age-related diseases. In this review we highlight some salient contributions of the mouse in aging research: lifespan intervention studies in the Interventions Testing Program of the National Institute on Aging; identification of the genetic underpinnings of the effects of calorie restriction on lifespan; the Aging Phenome Project at the Jackson Laboratory, which has submitted multiple large, freely available phenotyping datasets to the Mouse Phenome Database; insights from spontaneous and engineered mouse mutants; and complex traits analyses identifying quantitative trait loci that affect lifespan. We also show that genomewide association peaks for lifespan in humans and lifespan quantitative loci for mice map to homologous locations in the genome. Thus, the vast bioinformatic and genetic resources of the mouse can be used to screen candidate genes identified in both mouse and human mapping studies, followed by functional testing, often not possible in humans, to determine their influence on aging.     

Genome Surfing: Using Internet-Based Informatic Tools toward Functional Genetic Studies in Mouse and Humans

The wealth of databases containing genomic information and the easy access via the internet can be an invaluable tool in performing genetic studies and identifying important sequences. This article provides an overview and specific methods for using these resources in both positional cloning and identifying candidate genes for diseases and phenotypes. The ability to apply information across the mouse and human species is stressed. Useful internet sites and their contents are identified and described, and some understanding of their current limitations is provided. As additional genomic definition accelerates, the use of these tools will become more essential in cutting edge research linking sequence and function in whole mammalian organisms.