Current Genomics - Volume 1, Issue 3, 2000

While many wild animal species are relatively uniformly coloured, a wide variety of coat colours are found in domestic animals. Shift from natural selection towards criterias that are based on human preferences is most likely to account for the observed increase in coat colour variation. This makes domestic animals unique for studying gene function and gene regulation with regards to loci affecting pigmentation. Following an initial evolutionary discussion, this review will focus on two aspects of mammalian pigmentation; regulation of pigment synthesis and distribution of pigment producing cells. Molecular interaction between the G-protein coupled receptor MC1-R (melanocyte stimulating hormone receptor) and the agouti protein is the main regulatory system known to control the synthesis of eumelanin (brown or black pigment) versus phaeomelanin (red or yellow pigment). For both genes, mutations that explain phenotypical variants are characterised in several species. This includes numerous dominant-acting mutations of the MC1-R gene a constitutively activated receptor, and subsequently synthesis of black pigment. Additionally, it has been shown that the agouti gene, which is known to antagonise the MC1-R, is able to modify the expression of a wild-type MC1-R, as well as a semi-dominant variant of this receptor. Whereas agouti and extension often cause pigment switches, the distribution of pigment depends on proliferation and migration of neural crest derived melanocytes. Several genes, including the tyrosine kinase c-kit receptor and its ligand steel factor, regulate these processes. Functional mutations within the c-kit gene or variants of the ligand have been identified, and both loci are documented to influence the level of spotting.

The muscle disease field has benefited enormously from the increasing availability of genomic resources derived from the human genome mapping and allied projects. Although a number of skeletal and cardiac disorders are still at the linkage or candidate gene analysis stage, genes have been identified for the most common ones. The increasing variety of genes involved makes genetic screens an essential tool for more precise diagnosis and better classification of these disorders. The mouse represents the system of choice for the study of muscular dystrophies and cardiomyopathies but, not surprisingly, many murine models often show phenotypic differences between human and mouse. Only a handful of spontaneous or targeted mouse mutants are available within the field of muscle diseases compared to the increasing genetic complexity of myopathies and cardiomyopathies identified in humans. This shortage has been identified in other inherited diseases and has contributed to the revival of ENU (ethylnitrosourea) mutagenesis. Several large-scale ENU mutagenesis programs set up worldwide should provide allelic collections of mutants for pathologically interesting genes and uncover new gene functions. An effective integration between high throughput production of mutants, DNA-chip based expression analysis and the comprehensive maps derived from the human and mouse genome projects will make possible systematic studies of mammalian gene function, facilitating the identification of better mouse models.

Mutagenesis has been the foundation of genetics in most model organisms, from prokaryotes to the fruit flies. The simplicity of mutagenizing and propagating these creatures is critical for projects designed to isolate mutations affecting most any imaginable biological process. Not only has mutagenesis been exploited for the identification of phenotypic mutants, but also for the derivation of chromosomal aberrations, such as deletions and inversions, that are powerful genetic tools for many sorts of experiments. The laboratory mouse, which serves as the most important and powerful animal model for human genetics and disease, is only recently being widely exploited by classical phenotype-driven mutagenesis. The limitation has been (and still remains) related to the biology and life cycle of the mouse, which renders large-scale mutagenesis projects rather cumbersome and expensive. Is classical chemical mutagenesis really worthwhile, given the powerful germline manipulation technologies available for mice Are there new technologies that will render classical mutagenesis obsolete In this review, I shall discuss the tools of mutagenesis that are available for mice, and consider emerging and potential future technologies that will ultimately allow us to investigate, in an unprecedented way, the in vivo function of all mammalian genes.

Familial Exudative Vitreoretinopathy (FEVR) is a hereditary eye disorder, first reported in 1969 by Criswick and Schepens. It affects both the retina and the vitreous body, and is characterized by an abnormal vascularization of the peripheral retina. In the majority of cases, it is inherited in an autosomal dominant manner, but recently, a series of cases with an X-linked recessive and a few families with an autosomal recessive inheritance have also been reported. While linkage analysis has not been reported for the autosomal recessive form, the gene for the autosomal dominant form has been localized to the long arm of chromosome 11 (11q13 -q23). DNA linkage analysis of X-linked families has mapped the FEVR gene to Xp11.3 - p11.4. This is also a locus for Norrie disease (ND) which is a bilateral X-linked recessive disorder, characterized by ocular dysgenesis, progressive mental retardation and deafness. The cloning of the ND gene has made it possible to investigate the etiology of ND, as well as several other clinically similar conditions. The ND gene product is ubiquitously expressed in tissues, including the brain, retina and cochlea, but not the liver. Mutational analysis of the ND gene identified the entire spectrum of segregating mutations in ND, as well as in some X-linked FEVR families, implying that ND and X-linked FEVR are allelic disorders. However, in some other X-linked FEVR families, no disease-causing mutations in the ND gene have been identified, indicating that X-linked FEVR is a genetically heterogeneous disorder. Although X-linked recessive disorders generally do not affect females, it has been shown that ND and X-linked FEVR can occur in female carriers, likely due to an unfavorable X-inactivation. The above studies have greatly improved our understanding of the retinal degeneration in ND and X-linked FEVR at the molecular level. The availability of an animal model should assist in developing a therapeutic approach, either to delay or to prevent these devastating disorders in the future.

Genetic instability often leads to tumourogenesis. Genomic alterations such as deletions of a chromosome region containing a tumour suppresser gene or amplification of a region containing an oncogene have been frequently found to be associated with the initiation and the progression of cancer. Therefore identification of chromosomal regions amplified or deleted in tumour cells may reveal the presence of such genes. Amplification of 20q13 for instance is frequently observed in breast cancer cells. This region contains a gene encoding a protein kinase that belongs to the Aurora/Ipl1p-related kinase family involved in microtubule dependent mitotic events that control chromosome segregation. Deregulation of these kinases perturbs the ploidy of the cells. The human genome encodes at least three different kinases that have been found to be overexpressed in different tumour cells. But only the ectopic overexpression of the kinase encoded by the gene located at 20q13 is capable to transform cultured cells and induce the apparition of tumours in nude mouse. In this manuscript we describe the function of the three human Aurora/Ipl1p-related kinases, and review the genomic alterations reported for the chromosome region where the kinase genes localise. But we first discuss the impact of the human genome sequence project for the identification of new kinases in the context of cancer research.

Cancer biology as seen from chromosome 11 involves a plethora of mechanisms for chromosomal changes. The high frequency of repeated elements, the presence of active retrotransposons, the appearance of fragile sites, and the presence (and amplification) of drug resistance genes are all expected to destabilize the integrity of this chromosome. Thus, it is not unexpected that chromosome 11 is often mutated in a variety of tumors. Here, we review genes relevant to lung carcinogenesis and progression. Numerous loci and genes will be omitted since their role appears to be restricted to organ sites other than lung (i.e., the KAI gene at 11p11.2 which is involved in metastatic prostate cancer; the EXT2 gene at 11p11.2, which is one of the genes responsible for hereditary multiple exostoses; the WT1 gene at 11p13, which is frequently mutated in nephroblastoma; the TSG101 gene at 11p15.1-2, which may play a role in breast cancer; the ST5 (HTS1) gene at 11p15.3-4, which may be responsible for suppression of HeLa cell somatic cell hybrids). These genes may represent tissue-specific alterations that push certain types of cells into uncontrolled growth. In contrast, chromosome 11 also has genes for basic metabolic processes that are integral to the proliferation of cells (i.e., RRM1) and these are expected to be involved in a broad range of tumors. This review specifically focuses on HRAS, RRM1, MEN1, PPP2R1B, and ATM. Studies of the chromosomal abnormalities that underly cancer has produced a greater understanding of the normal patterns of gene regulation in healthy cells. Imprinting is one example of this, and the future promises to reveal much more.

Environmental pressures can direct genomes from a normal to a more or less pronounced imbalance in the base composition. These pressures seem to occur relatively often since genomes with a deviation from a normal base composition are widespread throughout lower eukaryotes. These genomes show altered codon usage and enrichment for the preferred bases in intron and intergenic regions. Techniques designed for large scale sequencing and assembly of genomes with normal base composition will fail with these unusual genomes. Additionally, the currently available analysis tools are mainly suitable for gene finding in genomes with normal base composition. In recent years some large scale genome analysis projects involving species with a skew directed to a very high AT content were initiated. These projects are encountered with sequencing, assembly, and gap closure problems due to the high AT content. These problems can only be overcome with additional techniques, which partly were developed and used in the ongoing projects. In this review some characteristic aspects of AT rich genomes, the progress of the Dictyostelium discoideum and the Plasmodium falciparum projects, as well as techniques specifically used for the sequencing of these genomes are highlighted.