Current Genomics - Volume 6, Issue 8, 2005

Much of the knowledge in modern biology is based on studies of a handful of model organisms, such as the mouse Mus musculus, the fruit fly Drosophila melanogaster, the worm Caenorhabditis elegans and the weed Arabidopsis thaliana [1]. In the last 10 years genomic resources have revolutionized research in these organisms and provided precise knowledge of the molecular mechanisms governing fundamental biological processes: The genome sequence, expression profiling, large-scale RNA interference and yeast-two hybrid screens moved biology into the "-omics"-era. However, these fascinating developments have to be placed into an evolutionary perspective: All established model organisms represent just one of many species in a given taxa. For example, D. melanogaster is one of more than 1000 Drosophila species and one of more than one million insects [2]. Similarly, C. elegans is a nematode, but there are an estimated 1-10 million of these mostly very tiny and inconspicuous organisms [3]. Also, these organisms do not represent the tree of life in a comprehensive way. Molecular phylogeny suggests that insects and nematodes, i.e. D. melanogaster and C. elegans, represent closely related taxa and belong to a group called Ecdysozoa [4]. At the same time, the other major branch of the invertebrates, the so-called Lophotrochozoans including the molluscs and annelids, is not represented by any model organism at all. A closer look at the phylogeny reveals yet another problem. Within their groups, model organisms often belong to highly derived taxa. For example, Drosophila is a dipteran fly, C. elegans a rhabditid nematode and both do not represent all of the typical ancestral characters of insects and nematodes, respectively. Many interesting questions result from these evolutionary and phylogenetic considerations: How representative are the selected model organisms? Is what we find in D. melanogaster true for all other Drosophila species, or even for all insects? Can we use our knowledge about the model organisms to reconstruct the evolutionary history of insects, nematodes or mammals? And finally, what can we learn about humans when we study vertebrate or even invertebrate models? In the late 80th and early 90th, evolutionary developmental biology was born as a new discipline in developmental biology. "Evo-devo", as it is often called, tries to provide answers to these questions and aims for a developmental understanding of the evolution of form, morphology and biological diversity. The idea is simple: Turn away from the well-known model organisms and study organisms that look similar, but nonetheless different. With the wealth of Drosophila knowledge at hand, look into beetles and butterflies. Compare developmental patterning as known in C. elegans with other nematode species. Compare the mouse with other mammals, Xenopus with other frogs and the zebrafish with Medaka. Take the Arabidopsis data and look into other weeds, trees and non-flowering plants. Although there was a lot of skepticism initially, evolutionary developmental biology has passed the test of time and many exciting research projects are under way [5]. The idea is simple, that's true. However, the practical realization proves rather complicated, as there are many technical challenges to be faced. In many model organisms, modern research is based on genetic analysis (Drosophila, C. elegans) or gene knockout approaches (mouse), tools that are simply not available in most nonmodel organisms. Stable DNA-mediated transformation is standard in Drosophila, C. elegans, Arabidopsis and the mouse, but is still a problem in most non-model organisms. And finally, there is no genome sequence and there are no genome-dependent "-omics" approaches available in non-model species.

The homeotic gene studies of Ed Lewis [1] and the embryonic patterning studies of Christiane Nüsslein- Volhard and Eric Wieschaus [2-4] are landmarks of insect developmental genetics that continue to inspire the work of developmental geneticists today. The genes they discovered were subsequently shown to be evolutionarily conserved and are now considered to be basic components of the genetic toolkit that is deployed during development in virtually all metazoans, albeit with specific roles that vary between animal groups. Their systematic approach, which combined the power of genetics with molecular and experimental biology, established Drosophila as a premier model organism for developmental studies. Pioneering work in the field of evo-devo (evolution of development) extended the Drosophila studies to other insect and arthropod groups to determine the extent to which these genes and their regulatory networks have general applications to insect development or reflect the unique phylogenetic history of the Diptera. The systematic approach that has been so successful in Drosophila has been applied in other insects that are amenable to genetic manipulation, perhaps most successfully in the genetic analysis of homeotic genes in the red flour beetle, Tribolium castaneum. However, most non-drosophilid insects are difficult to rear in the lab or are not candidates for facile genetic analysis. As a result, comparative studies are often limited to inferring function from the expression patterns of candidate genes. There is hope, however, of narrowing the gap in technical sophistication that separates Drosophila from other insects. Recently, the reverse genetics technique of RNA interference (RNAi) has made it possible to determine gene function even in the absence of mutants. Moreover, the genomic sequence of several insects, including Tribolium, will soon be available. Here we review recent advances in the study of insect development made possible by RNAi analysis, which have whetted our appetites for the large-scale comparative genomic approaches that will soon be possible.

The genome sequence of the nematode C. elegans transformed the study of this important research organism in countless ways. In this paper, we outline the equally great impact it has had on evolutionary developmental biology, with an emphasis on sex determination. Sex determination is a compelling area for comparative studies in Caenorhabditis for two reasons. First, striking differences in reproductive mode (gonochorism vs. androdioecy) are seen even between sister species, and these depend at some level on changes in the regulation of sex determination. Second, as an early and continually active area of C. elegans research, many molecular mechanisms are known that suggest hypotheses about how these reproductive modes differ from each other. Testing these hypotheses has required development of genomic resources for several non-elegans species of Caenorhabditis. Much progress has been made on this front, and several other major projects are currently underway. With these tools in hand, both reverse genetic approaches (RNA interference, cross-species transformation, gene knockouts) and forward genetic screens can be employed in multiple species in the genus. While much remains to be learned, some major surprises have already emerged. One is that the molecular evolution of interacting sex-determining proteins is characterized by rapid compensatory evolution. Another is that outwardly similar hermaphroditic species of Caenorhabditis may have gained this important reproductive adaptation in parallel via distinct germline modifications of the ancestral sex determination pathway. These results provide insights into how nematode mating systems evolve, and important context in which to refine our understanding of the C. elegans model whose characterization made it all possible.

Ninety five percent of human genomic DNA does not code for proteins or functional RNA molecules, and is frequently referred to as "junk" or "selfish" DNA. The vast majority of this noncoding DNA has no documented role in the cell. However, according to recent analyses, three quarters of the human genome is transcriptionally active. We discuss whether the expression of non-coding genomic sequences is valuable for the cell or if it is a second-hand "junk" because of the incompleteness in transcriptional machinery organization and functioning. Introns constitute a major fraction of the noncoding DNA, representing over 40% of mammalian genomes. They are ambivalent elements that cause several problems and at the same time bring benefits to their host cells. There is a strong correspondence between the average length of introns and the size of the genome. Here we review the latest summary statistics on human introns, the evolution of introns in mammals, and the distribution of genes that encode functional RNAs within introns. We also suggest that splicing is an important filter for organisms with large genomes, serving to distinguish between functional mRNAs and arbitrary RNA transcripts generated from random loci.

The pigment epithelium-derived factor (PEDF) is a non-inhibitory serpin, which is expressed mainly in the eye, but was also reported to be present in the adult human brain, spinal cord and plasma. It is characterized as a neurotrophic/ neuroprotective factor and one of the most potent natural inhibitors of angiogenesis in the eye, where it plays a physiological regulatory role in retinal angiogenesis. In this review we describe the expression, structure-function relationships, biological activities and regulation of PEDF. In addition, we emphasize our recent findings on the role of extracellular phosphorylation in PEDF activity, and show that the neurotrophic and antiangiogenic functions of PEDF are highly influenced by its phosphorylation state. Hence, phosphorylation of PEDF may be one of the modes that determine its specific physiological outcome.

Apoptosis, the cell's intrinsic death program, plays an important role in the regulation of tissue homeostasis. Also, killing of cancer cells by various cytotoxic approaches such as anticancer drugs, γ-irradiation, suicide genes or immunotherapy, is predominantly mediated through induction of apoptosis in target cells. Understanding the molecular events that regulate apoptosis and how tumor cells evade apoptotic deletion have provided a paradigm to link cancer genetics and response to cancer therapy. Thus, insights into the mechanisms regulating drug-induced apoptosis provide rational targets for novel therapeutic interventions.

Increasing numbers of human diseases involve mutations, misexpression or malfunctioning of receptor protein tyrosine kinases (RTK). In particular, human cancers are often characterized by altered RTK function, due to different genetic causes. Identification of the gene expression program triggered by (RTKs) is essential to clarify the molecular basis of their biological activities. Intracellular signals of RTKs are initiated by specific tyrosines which, when autophosphorylated, recruit signal transducers. How the activation of different signaling pathways is translated into a certain pattern of gene expression is currently unknown. Recently, scientists have tried to answer this question applying DNA microarrays technology using wild-type and mutant RTKs transiently stimulated with their cognate growth factors. The transcriptional response to chronic stimulation of cells upon ectopic expression of oncogenic RTKs has also been investigated through DNA microarrays. The results obtained recently in this field, with their possible implication in cancer development and their impact on cancer diagnosis and treatment will be discussed.

Systematic analysis of a biological system requires elucidation of its components. However, genome sequencing is only the first step; any analysis of transcription control and further functional genomics require the identification of all transcribed transcripts. FANTOM is the international consortium for the "functional annotation of mouse" or the "functional annotation of mammals", and produces data for analyzing the human and mouse transcriptome. To gain a substantial overview, FANTOM3, which is our latest milestone, has provided not only additional mouse full-length cDNAs, but also four datasets using new or familiar technologies; 1) 102,801 fully-sequenced and annotated cDNAs, derived from 237 full-length cDNA libraries; 2) 722,642 5'-ESTs and 1,578,613 3'-ESTs; 3) 7,151,511 mapped CAGE tags from 145 mouse libraries and 3,106,472 CAGE tags mapped from 24 human libraries, for identifying not only the precise start sites of transcription, but also relative expression and promoter usage; 4) 118,594 GIS and 968,201 GSC mapped ditags from four GIS and four GSC libraries for identifying the precise transcribed regions. Mapping of these transcripts drew the outline of the complex antisense transcription network on the genome, and many putative noncoding transcripts were shown to participate in such sense-antisense paring. Both sense and antisense transcripts tended to be co-expressed, and some transcripts influenced the copy number of the opposite transcript. Several previous studies using different cDNA synthesizing methods or microarray tiling experiments achieved the same results in other species, showing that the complex transcription and regulation by antisense transcription is a common feature in higher eukaryote genomes.