A whole-genome assembly of Drosophila

Assembly of the working draft of the human genome with GigAssembler

The data for the public working draft of the human genome contains roughly 400,000 initial sequence contigs in approximately 30,000 large insert clones. Many of these initial sequence contigs overlap. A program, GigAssembler, was built to merge them and to order and orient the resulting larger sequence contigs based on mRNA, paired plasmid ends, EST, BAC end pairs, and other information. This program produced the first publicly available assembly of the human genome, a working draft containing roughly 2.7 billion base pairs and covering an estimated 88% of the genome that has been used for several recent studies of the genome. Here we describe the algorithm used by GigAssembler.

Http://C. elegans: mining the functional genomic landscape

Caenorhabditis elegans is a powerful animal model for the study of functional genomics. The completed and well-annotated DNA sequence is available and a systematic study of gene function by RNA-interference-mediated knockdown of every gene is in progress. Full-genome DNA microarrays and DNA chips can be used to determine expression changes at different stages of development and in different mutant backgrounds, and a protein-interaction map based on the yeast two-hybrid approach is in progress. These high-capacity approaches to studying gene function will provide new insights into invertebrate and vertebrate biology.

An Eulerian path approach to DNA fragment assembly

For the last 20 years, fragment assembly in DNA sequencing followed the "overlap-layout-consensus" paradigm that is used in all currently available assembly tools. Although this approach proved useful in assembling clones, it faces difficulties in genomic shotgun assembly. We abandon the classical "overlap-layout-consensus" approach in favor of a new euler algorithm that, for the first time, resolves the 20-year-old "repeat problem" in fragment assembly. Our main result is the reduction of the fragment assembly to a variation of the classical Eulerian path problem that allows one to generate accurate solutions of large-scale sequencing problems. euler, in contrast to the celera assembler, does not mask such repeats but uses them instead as a powerful fragment assembly tool.

Selenium metabolism in Drosophila: selenoproteins, selenoprotein mRNA expression, fertility, and mortality

Selenocysteine is a rare amino acid in protein that is encoded by UGA with the requirement of a downstream mRNA stem-loop structure, the selenocysteine insertion sequence element. To detect selenoproteins in Drosophila, the entire genome was analyzed with a novel program that searches for selenocysteine insertion sequence elements, followed by selenoprotein gene signature analyses. This computational screen and subsequent metabolic labeling with (75)Se and characterization of selenoprotein mRNA expression resulted in identification of three selenoproteins: selenophosphate synthetase 2 and novel G-rich and BthD selenoproteins that had no homology to known proteins. To assess a biological role for these proteins, a simple chemically defined medium that supports growth of adult Drosophila and requires selenium supplementation for optimal survival was devised. Flies survived on this medium supplemented with 10(-8) to 10(-6) m selenium or on the commonly used yeast-based complete medium at about twice the rate as those on a medium without selenium or with >10(-6) m selenium. This effect correlated with changes in selenoprotein mRNA expression. The number of eggs laid by Drosophila was reduced approximately in half in the chemically defined medium compared with the same medium supplemented with selenium. The data provide evidence that dietary selenium deficiency shortens, while supplementation of the diet with selenium normalizes the Drosophila life span by a process that may involve the newly identified selenoproteins.

Strategies for the systematic sequencing of complex genomes

Recent spectacular advances in the technologies and strategies for DNA sequencing have profoundly accelerated the detailed analysis of genomes from myriad organisms. The past few years alone have seen the publication of near-complete or draft versions of the genome sequence of several well-studied, multicellular organisms - most notably, the human. As well as providing data of fundamental biological significance, these landmark accomplishments have yielded important strategic insights that are guiding current and future genome-sequencing projects.

Microarray analysis of trophoblast differentiation: gene expression reprogramming in key gene function categories

Placental development results from a highly dynamic differentiation program. We used DNA microarray analysis to characterize the process by which human cytotrophoblast cells differentiate into syncytiotrophoblast cells in a purified cell culture system. Of 6,918 genes analyzed, 141 genes were induced and 256 were downregulated by more than 2-fold. Dynamically regulated genes were divided by the K-means algorithm into 9 kinetic pattern groups, then by biologic classification into 6 overall functional categories: cell and tissue structural dynamics, cell cycle and apoptosis, intercellular communication, metabolism, regulation of gene expression, and expressed sequence tag (EST) and function unknown. Gene expression changes within key functional categories were tightly coupled to morphological changes. In several key gene function categories, such as cell and tissue structure, many gene members of the category were strongly activated while others were strongly repressed. These findings suggest that differentiation is augmented by "categorical reprogramming" in which the function of induced genes is enhanced by preventing the further synthesis of categorically related gene products.

The human ATP-binding cassette (ABC) transporter superfamily

The ATP-binding cassette (ABC) transporter superfamily contains membrane proteins that translocate a variety of substrates across extra- and intra-cellular membranes. Genetic variation in these genes is the cause of or contributor to a wide variety of human disorders with Mendelian and complex inheritance, including cystic fibrosis, neurological disease, retinal degeneration, cholesterol and bile transport defects, anemia, and drug response. Conservation of the ATP-binding domains of these genes has allowed the identification of new members of the superfamily based on nucleotide and protein sequence homology. Phylogenetic analysis is used to divide all 48 known ABC transporters into seven distinct subfamilies of proteins. For each gene, the precise map location on human chromosomes, expression data, and localization within the superfamily has been determined. These data allow predictions to be made as to potential functions or disease phenotypes associated with each protein. In this paper, we review the current state of knowledge on all human ABC genes in inherited disease and drug resistance. In addition, the availability of the complete Drosophila genome sequence allows the comparison of the known human ABC genes with those in the fly genome. The combined data enable an evolutionary analysis of the superfamily. Complete characterization of all ABC from the human genome and from model organisms will lead to important insights into the physiology and the molecular basis of many human disorders.

Genome annotation: from sequence to biology

The genome sequence of an organism is an information resource unlike any that biologists have previously had access to. But the value of the genome is only as good as its annotation. It is the annotation that bridges the gap from the sequence to the biology of the organism. The aim of high-quality annotation is to identify the key features of the genome - in particular, the genes and their products. The tools and resources for annotation are developing rapidly, and the scientific community is becoming increasingly reliant on this information for all aspects of biological research.

Functional genomics and the study of development, variation and evolution

It has rarely been possible to connect the developmental and evolutionary branches of genetics, particularly with regard to the precise changes in the molecular control of development that are responsible for phenotypic variation and evolution. Making such connections will require a high-resolution molecular description of the genetic networks that underlie development and an understanding of their responses to genetic and environmental variation. Functional genomics approaches to development and evolution promise to accelerate the research necessary to accomplish these goals.

Spatial and temporal control of RNA stability

Maternally encoded RNAs and proteins program the early development of all animals. A subset of the maternal transcripts is eliminated from the embryo before the midblastula transition. In certain cases, transcripts are protected from degradation in a subregion of the embryonic cytoplasm, thus resulting in transcript localization. Maternal factors are sufficient for both the degradation and protection components of transcript localization. Cis-acting elements in the RNAs convert transcripts progressively (i) from inherently stable to unstable and (ii) from uniformly degraded to locally protected. Similar mechanisms are likely to act later in development to restrict certain classes of transcripts to particular cell types within somatic cell lineages. Functions of transcript degradation and protection are discussed.

DNA sequencing with transposons

The use of transposons offers the possibility of a directed approach to DNA sequencing, where a target DNA up to about 6kb in length can be sequenced quickly and with minimal redundancy. Transposons are mobile DNA elements which can be inserted in a reasonably random fashion into the target DNA. An important part of this process is the location of the transposon insertions (known as mapping) and the selection of a sensible subset of transposons to use as priming sites for sequencing reactions. This paper presents a probabilistic method of scoring selected subsets of transposons and a graph-theoretic algorithm for selection of a subset of maximal score.

Whole-genome analysis: annotations and updates

The most important advances in the field of genome annotation over the past two years involve the use of cDNA sequences, protein structures and gene expression data to predict genes. These types of information not only improve gene identification, but they also give insights into variation in gene structure and function.

Characterization of the flamenco region of the Drosophila melanogaster genome

The flamenco gene, located at 20A1-3 in the beta-heterochromatin of the Drosophila X chromosome, is a major regulator of the gypsy/mdg4 endogenous retrovirus. As a first step to characterize this gene, approximately 100 kb of genomic DNA flanking a P-element-induced mutation of flamenco was isolated. This DNA is located in a sequencing gap of the Celera Genomics project, i.e., one of those parts of the genome in which the "shotgun" sequence could not be assembled, probably because it contains long stretches of repetitive DNA, especially on the proximal side of the P insertion point. Deficiency mapping indicated that sequences required for the normal flamenco function are located >130 kb proximal to the insertion site. The distal part of the cloned DNA does, nevertheless, contain several unique sequences, including at least four different transcription units. Dip1, the closest one to the P-element insertion point, might be a good candidate for a gypsy regulator, since it putatively encodes a nuclear protein containing two double-stranded RNA-binding domains. However, transgenes containing dip1 genomic DNA were not able to rescue flamenco mutant flies. The possible nature of the missing flamenco sequences is discussed.

From first base: the sequence of the tip of the X chromosome of Drosophila melanogaster, a comparison of two sequencing strategies

We present the sequence of a contiguous 2.63 Mb of DNA extending from the tip of the X chromosome of Drosophila melanogaster. Within this sequence, we predict 277 protein coding genes, of which 94 had been sequenced already in the course of studying the biology of their gene products, and examples of 12 different transposable elements. We show that an interval between bands 3A2 and 3C2, believed in the 1970s to show a correlation between the number of bands on the polytene chromosomes and the 20 genes identified by conventional genetics, is predicted to contain 45 genes from its DNA sequence. We have determined the insertion sites of P-elements from 111 mutant lines, about half of which are in a position likely to affect the expression of novel predicted genes, thus representing a resource for subsequent functional genomic analysis. We compare the European Drosophila Genome Project sequence with the corresponding part of the independently assembled and annotated Joint Sequence determined through "shotgun" sequencing. Discounting differences in the distribution of known transposable elements between the strains sequenced in the two projects, we detected three major sequence differences, two of which are probably explained by errors in assembly; the origin of the third major difference is unclear. In addition there are eight sequence gaps within the Joint Sequence. At least six of these eight gaps are likely to be sites of transposable elements; the other two are complex. Of the 275 genes in common to both projects, 60% are identical within 1% of their predicted amino-acid sequence and 31% show minor differences such as in choice of translation initiation or termination codons; the remaining 9% show major differences in interpretation.

Bonus, a Drosophila homolog of TIF1 proteins, interacts with nuclear receptors and can inhibit betaFTZ-F1-dependent transcription

The Drosophila bonus (bon) gene encodes a homolog of the vertebrate TIF1 transcriptional cofactors. bon is required for male viability, molting, and numerous events in metamorphosis including leg elongation, bristle development, and pigmentation. Most of these processes are associated with genes that have been implicated in the ecdysone pathway, a nuclear hormone receptor pathway required throughout Drosophila development. Bon is associated with sites on the polytene chromosomes and can interact with numerous Drosophila nuclear receptor proteins. Bon binds via an LxxLL motif to the AF-2 activation domain present in the ligand binding domain of betaFTZ-F1 and behaves as a transcriptional inhibitor in vivo.

Identification of muscle specific ring finger proteins as potential regulators of the titin kinase domain

The giant myofibrillar protein titin contains within its C-terminal region a serine-threonine kinase of unknown function. We have identified a novel muscle specific RING finger protein, referred to as MURF-1, that binds in vitro to the titin repeats A168/A169 adjacent to the titin kinase domain. In myofibrils, MURF-1 is present within the periphery of the M-line lattice in close proximity to titin's catalytic kinase domain, within the Z-line lattice, and also in soluble form within the cytoplasm. Yeast two-hybrid screens with MURF-1 as a bait identified two other highly homologous MURF proteins, MURF-2 and MURF-3. MURF-1,2,3 proteins are encoded by distinct genes, share highly conserved N-terminal RING domains and in vitro form dimers/heterodimers by shared coiled-coil motifs. Of the MURF family, only MURF-1 interacts with titin repeats A168/A169, whereas MURF-3 has been reported to affect microtubule stability. Association of MURF-1 with M-line titin may potentially modulate titin's kinase activity similar to other known kinase-associated proteins, whereas differential expression and heterodimerization of MURF1, 2 and 3 may link together titin kinase and microtubule-dependent signal pathways in striated muscles.

Impact of human genome sequencing for in silico target discovery

The year 2000 stands as a landmark in modern biology: the first draft of the human genome sequence has been completed. For the pharmaceutical industry, this achievement provides tremendous opportunities because the genomic sequence exposes all human drug targets for therapeutic intervention. The challenge for the pharmaceutical companies is to exploit this definitive resource for the identification of potential molecular targets, rapid characterization of their function and validation of their involvement in disease pathology. Bioinformatics approaches provide increasingly crucial tools to systematically support this exploratory target drug discovery activity.

The neprilysin (NEP) family of zinc metalloendopeptidases: genomics and function

Neprilysin (NEP), a thermolysin-like zinc metalloendopeptidase, plays an important role in turning off peptide signalling events at the cell surface. It is involved in the metabolism of a number of regulatory peptides of the mammalian nervous, cardiovascular, inflammatory and immune systems. Examples include enkephalins, tachykinins, natriuretic and chemotactic peptides. NEP is an integral plasma membrane ectopeptidase of the M13 family of zinc peptidases. Other related mammalian NEP-like enzymes include the endothelin-converting enzymes (ECE-1 and ECE-2), KELL and PEX. A number of novel mammalian homologues of NEP have also recently been described. NEP family members are potential therapeutic targets, for example in cardiovascular and inflammatory disorders, and potent and selective inhibitors such as phosphoramidon have contributed to understanding enzyme function. Inhibitor design should be facilitated by the recent three-dimensional structural solution of the NEP-phosphoramidon complex. For several of the family members, however, a well-defined physiological function or substrate is lacking. Knowledge of the complete genomes of Caenorhabditis elegans and Drosophila melanogaster allows the full complement of NEP-like activities to be analysed in a single organism. These model organisms also provide convenient systems for examining cell-specific expression, developmental and functional roles of this peptidase family, and reveal the power of functional genomics.

The sequence of the human genome

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

Initial sequencing and analysis of the human genome

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

Identification of Waldo-A and Waldo-B, two closely related non-LTR retrotransposons in Drosophila

We have identified two novel, closely related subfamilies of non-long-terminal-repeat (non-LTR) retrotransposons in Drosophila melanogaster, the Waldo-A and Waldo-B subfamilies, that are in the same lineage as site-specific LTR retrotransposons of the R1 clade. Both contain potentially active copies with two large open reading frames, having coding capacities for a nucleoprotein as well as endonuclease and reverse transcriptase activities. Many copies are truncated at the 5' end, and most are surrounded by target site duplications of variable lengths. Elements of both subfamilies have a nonrandom distribution in the genome, often being inserted within or very close to (CA)(n) arrays. At the DNA level, the longest elements of Waldo-A and Waldo-B are 69% identical on their entire length, except for the 5' untranslated regions, which have a mosaic organization, suggesting that one arose from the other following new promoter acquisition. This event occurred before the speciation of the D. melanogaster subgroup of species, since both Waldo-A and Waldo-B coexist in other species of this subgroup.

Evolving better brains: a need for neurotrophins?

The NGF family of neurotrophins has a crucial role in regulating neuron numbers during vertebrate development. Six years ago the prediction was made that invertebrates with simple nervous systems, such as Caenorhabditis elegans, would lack neurotrophins. Surprisingly, it now appears that not only C. elegans but also Drosophila melanogaster, lack homologs of the neurotrophins or their trk receptors. Furthermore, functional studies indicate that control of neuronal numbers in Drosophila is primarily dependent on steroids. By contrast, a recognizable trk homolog exists in molluscs, a phylum that includes species with the most complex nervous systems in the invertebrate kingdom. This suggests that neurotrophic signaling mechanisms might be one of the prerequisites for evolution of complex nervous systems. Expansion of the genome projects to other invertebrates, such as molluscs and coelenterates, should provide new insights on the molecular correlates of building complex brains.

The drosophila genome and its oncological implications

The genome of the fruit fly has recently been sequenced, prior to the release of the human genome sequence within the next few years. The fly has some 13 600 genes, compared with the estimated 80 000 genes in the human genome. Some 70% of genes appear to be broadly conserved across eukaryotic species, and some remarkable homologies have been found between 177 genes in the fly and the 289 human genes so far associated with diseases in man. The fruit fly genome is likely to prove an elegant model and a rich source of experimentation for the aetiology and regulation of human cancers.

Genetic research and nutritional individuality

Recent genetic research builds on a base established over the last century by physicians and nutritional scientists, who introduced the concept of biochemical individuality and documented its significance for understanding a wide variety of problems in human health. Current comparative genomic investigations on a variety of organisms (Haemophilus influenzae, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens) have established the existence of numerous orthologs (proteins in different organisms that show significant sequence similarities over 80% of their lengths), suggesting significant conservation of structure and probably some of function as well. At the same time, molecular comparisons among individuals within our own species show the existence of abundant molecular variants, many of which have been shown to have functional significance in nutritional and related metabolic contexts. The combination of biochemical individuality and known functional utilities of allelic variants should converge to create a situation in which nutritional optima can be specified as part of comprehensive lifestyle prescriptions tailored to the needs of each person.

The cloning, genomic organization and expression of the focal contact protein paxillin in Drosophila

Paxillin is a focal adhesion scaffolding protein, which has been proposed to play a role in focal adhesion dynamics. We have isolated a cDNA clone of the Drosophila homologue of paxillin. Comparison of the Drosophila paxillin sequence with those of vertebrate paxillins shows strong conservation of the LIM domains and LD repeats. Using the Drosophila genomic sequence we have identified two partial curated transcripts and deduced the structure of the paxillin gene. No homologues of other members of the paxillin family such as HIC-5 or leupaxin are to be found in the Drosophila genome. Surprisingly paxillin mRNA is expressed in a restricted pattern during embryogenesis. In particular it is strongly expressed in cells and tissues undergoing cell shape changes or cell migration. Many of the sites of expression are also known to be sites of integrin function or FAK expression. The data support a role for paxillin as an adapter and/or signaling protein during developmental processes involving integrin-mediated adhesion.

[Genetics and molecular medicine in cardiology]

The discoveries on molecular aspects of cellular function are changing the concepts of health and disease. All medical fields, including cardiology, have been enriched with several diagnostic test to determine predisposition and to detect molecular dysfunctions. This review on the genetic and molecular aspects of cardiovascular diseases is written at the Centenary of the rediscovery of Mendel's principles on heredity and at the time of the announcement of the end of the human genome sequencing task. The review starts with considerations on the pluricellular constitution of the human body, and the principles of genetics with their molecular bases; including a short description of the methods for gene mapping. The following sections give a historic synopsis on the concepts of medical genetics, molecular medicine, and the Human Genome Project. The review ends with a brief description of the spectrum of genetic diseases, using examples of cardiovascular diseases.

The compositional evolution of vertebrate genomes

The compositional evolution of vertebrate genomes is characterized: (i) by one predominant conservative mode, in which nucleotide changes occur, but the base composition of DNA sequences in general, and of coding sequences in particular, does not change; and (ii) by three different shifting or transitional modes, in which nucleotide changes are accompanied by changes in the base composition of sequences. Investigations on these evolutionary modes have shed new light on a central problem in molecular evolution, namely the role played by natural selection in modulating the mutational input. This review will present first the intragenomic shifts, the 'major shifts' and the 'minor shift', and then the 'whole-genome', or 'horizontal', shift. In each case, the shifts were preceded and followed by a conservative mode of evolution. This review expands on a previous one [Bernardi, Gene 241 (2000) 3-17], and summarizes the evidence that the changes of the compositional patterns of the genome and their maintenance are controlled by Darwinian natural selection.

Whole genomes: the foundation of new biology and medicine

Our genomic DNA sequence provides a unique glimpse of the provenance and evolution of our species, the migration of peoples, and the causation of disease. Understanding the genome may help resolve previously unanswerable questions, including perhaps which human characteristics are innate or acquired. Such an understanding will make it possible to study how genomic DNA sequence varies among populations and among individuals, including the role of such variation in the pathogenesis of important illnesses and responses to pharmaceuticals. The study of the genome and the associated proteomics of free-living organisms will eventually make it possible to localize and annotate every human gene, as well as the regulatory elements that control the timing, organ-site specificity, extent of gene expression, protein levels, and post-translational modifications. For any given physiological process, we will have a new paradigm for addressing its evolution, development, function, and mechanism.

The Drosophila genome

The past year has been a spectacular one for Drosophila research. The sequencing and annotation of the Drosophila melanogaster genome has allowed a comprehensive analysis of the first three eukaryotes to be sequenced-yeast, worm and fly-including an analysis of the fly's influences as a model for the study of human disease. This year has also seen the initiation of a full-length cDNA sequencing project and the first analysis of Drosophila development using high-density DNA microarrays containing several thousand Drosophila genes. For the first time homologous recombination has been demonstrated in flies and targeted gene disruptions may not be far off.

Applied genomics: integration of the technology within pharmaceutical research and development

Multiple novel technologies have recently been developed to improve the analysis of genetic sequences, to rapidly assess RNA or protein levels in relevant tissues, and to validate function of potential new drug targets. The challenge facing pharmaceutical research is one of effective integration of these new technologies in ways that can maximally affect the discovery and development pipeline. Although database mining and transcriptional profiling clearly have increased the number of putative targets, the current focus is to assign function to new gene targets in a high-throughput manner. This requires a restructuring of the classical linear progression from gene identification, functional elucidation, target validation and screen development. New approaches are called for that can make this process non-linear and high-throughput.

View of life sciences in the 21st century

As we contemplate the nature of life sciences in the 21st century, we should briefly consider the changes that have occurred in the past century. Surely, the sources of progress of this science in the next century are the advances emerging now. Furthermore, the likely pace of discovery and change in life sciences in the next century can best be estimated by a reflection on its history.

Y chromosomal fertility factors kl-2 and kl-3 of Drosophila melanogaster encode dynein heavy chain polypeptides

The molecular identity and function of the Drosophila melanogaster Y-linked fertility factors have long eluded researchers. Although the D. melanogaster genome sequence was recently completed, the fertility factors still were not identified, in part because of low cloning efficiency of heterochromatic Y sequences. Here we report a method for iterative blast searching to assemble heterochromatic genes from shotgun assemblies, and we successfully identify kl-2 and kl-3 as 1beta- and gamma-dynein heavy chains, respectively. Our conclusions are supported by formal genetics with X-Y translocation lines. Reverse transcription-PCR was successful in linking together unmapped sequence fragments from the whole-genome shotgun assembly, although some sequences were missing altogether from the shotgun effort and had to be generated de novo. We also found a previously undescribed Y gene, polycystine-related (PRY). The closest paralogs of kl-2, kl-3, and PRY (and also of kl-5) are autosomal and not X-linked, suggesting that the evolution of the Drosophila Y chromosome has been driven by an accumulation of male-related genes arising de novo from the autosomes.

Combgap relays wingless signal reception to the determination of cortical cell fate in the Drosophila visual system

The dorsoventral axis of the Drosophila visual cortex is patterned by nonautonomous signals expressed at its dorsal and ventral margins. wingless (wg) expression at the margins induces decapentaplegic (dpp), optomotor blind (omb), and aristaless in adjacent domains. We show that Combgap, a zinc finger protein, represses Wg target gene expression in the visual cortex. Wg signal reception downregulates combgap expression and derepresses target gene transcription. Combgap participates in a Hedgehog-controlled circuit in the developing wing and leg by regulating the expression of Cubitus interruptus. Combgap is thus a tissue-specific relay between Wingless and its target genes for the determination of cell fate in the visual cortex.

Cloning, expression, and mapping of hWW45, a novel human WW domain-containing gene

WW domain-containing proteins are found in all eukaryotes and play an important role in the regulation of a wide variety of cellular functions such as protein degradation, transcription, and RNA splicing. The cloning and characterization of a novel human WW domain-containing gene, hWW45, which encodes a protein of approximately 45 kDa consisting of 2 WW domains and a coiled-coil region is reported here. The murine homologue cDNA, mWW45, displays a different 3'-untranslated region and predicts a protein identity of 93% to hWW45. Northern blot and RT-PCR analysis demonstrated that both mWW45 and hWW45 transcripts are ubiquitously expressed in adult tissues. The mouse embryonic expression is first seen at 7 days post coitum in Northern blot analysis of whole embryos. Chromosomal localization by radiation hybrid mapping revealed that hWW45 is localized at chromosome 14, 10.31cR from the marker D14S269.

Modeling the feasibility of whole genome shotgun sequencing using a pairwise end strategy

In pairwise end sequencing, sequences are determined from both ends of random subclones derived from a DNA target. Sufficiently similar overlapping end sequences are identified and grouped into contigs. When a clone's paired end sequences fall in different contigs, the contigs are connected together to form scaffolds. Increasingly, the goals of pairwise strategies are large and highly repetitive genomic targets. Here, we consider large-scale pairwise strategies that employ mixtures of subclone sizes. We explore the properties of scaffold formation within a hybrid theory/simulation mathematical model of a genomic target that contains many repeat families. Using this model, we evaluate problems that may arise, such as falsely linked end sequences (due either to random matches or to homologous repeats) and scaffolds that terminate without extending the full length of the target. We illustrate our model with an exploration of a strategy for sequencing the human genome. Our results show that, for a strategy that generates 10-fold sequence coverage derived from the ends of clones ranging in length from 2 to 150 kb, using an appropriate rule for detecting overlaps, we expect few false links while obtaining a single scaffold extending the length of each chromosome.

Identification and characterization of a p53 homologue in Drosophila melanogaster

The tumor suppressor gene p53 in mammalian cells plays a critical role in safeguarding the integrity of genome. It functions as a sequence-specific transcription factor. Upon activation by a variety of cellular stresses, p53 transactivates downstream target genes, through which it regulates cell cycle and apoptosis. However, little is known about p53 in invertebrates. Here we report the identification and characterization of a Drosophila p53 homologue gene, dp53. dp53 encodes a 385-amino acid protein with significant homology to human p53 (hp53) in the region of the DNA-binding domain, and to a lesser extent the tetramerization domain. Purified dp53 DNA-binding domain protein was shown to bind to the consensus hp53-binding site by gel mobility analysis. In transient transfection assays, expression of dp53 in Schneider cells transcriptionally activated promoters that contained consensus hp53-responsive elements. Moreover, a mutant dp53 (Arg-155 to His-155), like its hp53 counterpart mutant, exerted a dominant-negative effect on transactivation. Ectopic expression of dp53 in Drosophila eye disk caused cell death and led to a rough eye phenotype. dp53 is expressed throughout the development of Drosophila with highest expression levels in early embryogenesis, which has a maternal component. Consistent with this, dp53 RNA levels were high in the nurse cells of the ovary. It appears that p53 is structurally and functionally conserved from flies to mammals. Drosophila will provide a useful genetic system to the further study of the p53 network.

Drosophila genome takes flight

In the March 24 issue of Science, a flurry of papers report on the impending completion of the Drosophila melanogaster genome sequence. This historic achievement is the result of a unique collaboration between the Berkeley Drosophila Genome Project (BDGP), led by Gerry Rubin, and the genomics company Celera, headed by Craig Venter. With its genome almost completely sequenced ahead of schedule, Drosophila is another important model organism to enter the postgenomic age, and represents the largest genome sequenced to date.

A brief history of Drosophila's contributions to genome research

The sequence of the Drosophila melanogaster genome presented in this issue of Science is the latest milestone in nine decades of research on this organism. Genetic and physical mapping, whole-genome mutational screens, and functional alteration of the genome by gene transfer were pioneered in metazoans with the use of this small fruit fly. Here we look at some of the instances in which work on Drosophila has led to major conceptual or technical breakthroughs in our understanding of animal genomes.