Current Genomics - Volume 2, Issue 3, 2001

A growing number of dominantly inherited neurodegenerative disorders are associated with an expanded polyglutamine-encoding sequence. Alterations in gene expression have been described for several of these diseases. Many animal and cell culture models have been established. In order to generate gene expression profiles of model systems using microarray technology, the Hereditary Disease Array Group (HDAG) was formed. This collaboration helps participants to refine the design, methods, and analyses and to identify potential problem areas. The ultimate goal of HDAG is to elucidate the mechanisms by which expanded polyglutamine tracts contribute to neuropathogenesis. This conference review intends to describe this collaborative effort and highlight some of the issues relating to technical aspects, quality control and bioinformatics as well as therapeutic targets and human samples.

The Drosophila sine oculis (so) gene is a high hierarchy and essential gene in the developmental pathway of the fly visual system. so is the founder member of the SIX family, which in the fly also includes the genes D-six3 (optix) and D-six4 and in vertebrates, the SIX1, SIX2, SIX3, SIX4, SIX5 and SIX6 genes. In addition to a homeobox domain, all members of the SIX family of proteins contain a characteristic highly conserved region denoted as the SIX domain. Genes of the SIX family encode nuclear homeobox proteins that have been proposed to be the DNA binding domain of a transcription complex that also includes members of the EYA (eyes absent) gene family. A number of studies suggest important roles for the SIX genes in the development of the anterior part of the vertebrate CNS and eye, in myogenesis and perhaps also in the development of the auditory system, kidneys, digits and connective tissue. This review presents a comprehensive description of the current knowledge of the human SIX gene family, including unpublished data from our laboratories. We describe the genomic organization and structure of the human SIX genes and discuss their phylogenetic relationships in the context of the evolution of the SIX gene family. Using data mostly available from other species we discuss the developmental expression patterns and function of the SIX genes. Lastly, we present the current knowledge of the involvement of the SIX genes in human disease.

DNA sequences of protein-coding genes seem to be more effective than 16S rRNA gene sequencing for classifying the ecological diversity of bacteria. This fact, however, may be a consequence of the low evolutionary rate of 16S rRNA genes. While 16S rRNA gene sequence data are useful for placing moderately divergent populations into separate sequence clusters, protein-coding genes provide a more effective tool for distinguishing very closely related, recently evolved, ecological populations. Preliminary investigations using metabolic genes as genetic markers, such as genes coding for malate dehydrogenase or 6-phosphogluconate dehydrogenase, have been performed to study microbial communities. The sequencing of metabolic genes could enable the study of specific biochemical activities in bacteria, the identification of clones within bacterial populations, and the characterisation of specific clones within communities of pathogenic microorganisms. Multilocus sequence typing has been successfully used, e.g. for the identification of the currently circulating hypervirulent meningococcal lineages in epidemiological studies. It has also suggested that sequencing of protein-coding genes would provide a finer phylogenetic resolution when finding geovars possibly belonging to unknown species. It is expected, therefore, that sequencing of protein-coding loci, which usually show a wider sequence variations and are more rapidly evolving than the more conserved 16S rRNA encoding genes, will disclose many previously unknown ecological populations of bacteria in future population surveys.

G-protein coupled receptors (GPCRs) constitute the largest set of cell membrane proteins involved in signal transduction and more than half of all drugs currently available influence their activity. Furthermore, genomic sequencing techniques have already enabled the isolation of more than hundred genes that encode so called orphan receptors representing a fruitful resource of potential targets for cellular signaling studies and novel drug discovery. This review focuses on recent progress in molecular cloning, gene organization analysis and chromosomal localization of a new sub-family of mammalian genes encoding the GPR37 (G-Protein coupled orphan Receptor 37) and related proteins. These genes are specifically expressed in brain tissues and they are significantly homologous to endothelin- and bombesin- receptor genes. Comparative genomic analysis has identified two distinct sets of highly conserved human and rodent genes. The first group includes the ortholog genes encoding the putative human, mouse and rat GPR37 receptors, also termed ETBR-LP (Endothelin-B Receptor-Like Protein) or GPCR / CNS1 (GPCR / Central Nervous System 1), that are characterised by a relatively large putative extracellular domain (261-249 amino-acids). The second group comprises the genes of the human, mouse and rat GPR37L1 [GPR37-Like protein 1 or ET(B)R-LP-2, GPCR / CNS2] with a shorter (129 amino-acids) extracellular domain. The human and mouse GPR37 and GPR37L1 genes have been shown to contain a single intron interrupting the receptor-coding sequence within the presumed third transmembrane domain. Northern blot analysis and in situ hybridization have shown characteristic patterns of expression of GPR37 and related genes suggesting that they may exert highly specific functions in the mammalian central nervous system.

The development of methods for efficiently introducing foreign genes into living cells provides novel tools to investigate intracellular processes at the molecular level. In addition, the development of suitable delivery vehicles for in vivo gene transfer is a prerequisite for clinical application of therapeutic genes. This review will summarize the current status of the development of both viral as well as non-viral vectors for gene therapy. In addition, we also discuss novel gene-delivery vehicles based on viral envelopes containing fusogenic spike proteins originated from different myxoviruses. These recombinant viral envelopes or virosomes could be viewed as hybrid vectors combining both viral and non-viral strategies, and are well suited for a wider application in therapeutic gene and drug delivery.

Complete genomic sequences of several plant species, most notably the models Arabidopsis thaliana and rice, is now available. One way to discover the biological role of the thousands of new genes is reverse genetics. Plant molecular biologists have already developed several reverse genetics tools. The purpose of this review is to explore the technological avenues taken to address this question and to provide an update on current developments. Because gene targeting by homologous recombination is still not a commodity in plants and despite recent progress with chimeric oligonucleotides, other strategies have been implemented. The most well established routes rely on insertion mutagenesis, either via transposons or Agrobacterium T-DNA transformation. For transposons, except in a few species where highly active endogenous transposable elements exist, this requires the introduction of exogenous elements by transgenesis. The most common strategy for generating insertions relies on binary systems with a stable transposase source and an engineered non-autonomous element. These may contain gene-trap or enhancer-trap devices. This was achieved with both the maize Activator / Dissociation (Ac / Ds) and Enhancer / Inhibitor (En / I) systems in arabidopsis and rice. T-DNA may also be used as an insertion mutagen in species where transformation frequencies are high. In species where transformation is less efficient, gene silencing may prove to be an attractive solution. Finally, the advent of high throughput mutation detection techniques will allow the use of conventional chemically or physically induced mutagenesis in plant reverse genetics. This is theoretically applicable to a wide range of species.

A defined number of skeletal muscle fibers are formed in two separate waves during prenatal development, while postnatal growth is restricted to hypertrophic muscle fiber growth. The genes of the MRF (muscle regulatory factors) gene family, consisting of 4 structurally related transcription factors - myogenin, MyoD1, myf-5, and MRF4 - regulate both skeletal muscle fiber development and postnatal hypertrophic growth. In meat producing animals, skeletal muscle tissue becomes meat after slaughtering. Skeletal muscle fibers are the major cell type of meat mass. Thus, differences in the activity of the MRF gene family may be very important for the amount of meat deposited in these animals, which is of major economic importance. Therefore, the MRF genes can be considered as potential candidate genes to investigate the relation between genomic variation in these genes and skeletal muscle mass, and thus meat mass.In this review we discuss the MRF gene family in relation to meat production, and show that information of genomic variation in these functional genes, and variation in their expression provide information that can be used in commercial breeding. Furthermore, we will review experiments that show that hormones, growth factors, and specific drugs can affect the expression of these genes, thus potentially affecting skeletal muscle mass and thus meat mass, offering several potential strategies for steering of meat production, and showing the power of functional genomics. Using the genetic information available from these experiments, ways to speed up genetic improvement of livestock breeding and future research directions will be highlighted.