Characterization of differentially expressed genes in purified Drosophila follicle cells: toward a general strategy for cell type-specific developmental analysis

Genetic Programs Activated by Proneural Proteins in the Developing Drosophila PNS

Neurogenesis depends on a family of proneural transcriptional activator proteins, but the "proneural" function of these factors is poorly understood, in part because the ensemble of genes they activate, directly or indirectly, has not been identified systematically. We have taken a direct approach to this problem in Drosophila. Fluorescence-activated cell sorting was used to recover a purified population of the cells that comprise the "proneural clusters" from which sensory organ precursors of the peripheral nervous system (PNS) arise. Whole-genome microarray analysis and in situ hybridization was then used to identify and verify a set of genes that are preferentially expressed in proneural cluster cells. Genes in this set encode proteins with a diverse array of implied functions, and loss-of-function analysis of two candidate genes shows that they are indeed required for normal PNS development. Bioinformatic and reporter gene studies further illuminate the cis-regulatory codes that direct expression in proneural clusters.

Bacterial mRNA purification by magnetic capture-hybridization method

A magnetic capture-hybridization method was developed for purification of bacterial messenger RNA (mRNA) from total RNA by removing 5S, 16S and 23S ribosomal RNAs (rRNA). The quality of mRNA was evaluated by A(260 nm) / A(280 nm) value, denatured gel electrophoresis and RT-PCR. The results showed that highly purified and intact mRNA was obtained by this method. The magnetic capture-hybridization is a rapid and simple method for bacterial mRNA purification and has promising potential for improving studies using bacterial mRNA.

Genomics in obstetrics and gynaecology

With the Human Genome Project complete, and microarray technology progressing rapidly, the study of whole genomes has become a reality. The emerging field of genomics is full of promise, has become a cornerstone of commercial drug development, and looks certain to make a major contribution to clinical practice in the future. There is an increasing number of genomic studies concerned with obstetric and gynaecological conditions. Despite this, clinicians in their busy practices often lack a basic understanding of genomics and the tools involved in generating genome-based information. In the present review, we aim to provide the clinician with a basic overview of genomics--what it is, what tools it uses, and how it may benefit our patients. The existing published reports on genomic studies in the reproductive field is reviewed.

Genomic sequence of a 320-kb segment of the Z chromosome of Bombyx mori containing a kettin ortholog

The sex chromosome constitution of the silkworm, Bombyx mori, is ZW in the female and ZZ in the male. Very little molecular information is available about the Z chromosome in Lepidoptera, although the topic is interesting because of the absence of gene dosage compensation in this chromosome. We constructed a 320-kb BAC contig around the Bmkettin gene on the Z chromosome in Bombyx and determined its nucleotide sequence by the shotgun method. We found 13 novel protein-coding sequences in addition to Bmkettin. All the transposable elements detected in the region were truncated, and no LTR retrotransposons were found, in stark contrast to the situation on the W chromosome. In this 320-kb region, four genes for muscle proteins (Bmkettin, Bmtitin1, Bmtitin2, and Bmprojectin) are clustered, together with another gene (Bmmiple) on the Z chromosome in B. mori; their orthologs are also closely linked on chromosome 3 in Drosophila, suggesting a partial synteny. Real-time RT-PCR experiments demonstrated that transcripts of 13 genes of the 14 Z-linked genes found accumulated in larger amounts in males than in female moths, indicating the absence of gene dosage compensation. The implications of these findings for the evolution and function of the Z chromosome in Lepidoptera are discussed.

Transcriptional repressor functions of Drosophila E2F1 and E2F2 cooperate to inhibit genomic DNA synthesis in ovarian follicle cells

Individual members of the E2F/DP protein family control cell cycle progression by acting predominantly as an activator or repressor of transcription. In Drosophila melanogaster the E2f1, E2f2, Dp, and Rbf1 genes all contribute to replication control in ovarian follicle cells, which become 16C polyploid and subsequently undergo chorion gene amplification late in oogenesis. Mutation of E2f2, Dp, or Rbf1 causes ectopic DNA replication throughout the follicle cell genome during gene amplification cycles. Here we show by both reverse transcription-PCR and DNA microarray analysis that the transcripts of prereplication complex (pre-RC) genes are elevated compared to the wild type in E2f2, Dp, and Rbf1 mutant follicle cells. For some genes the magnitude of this transcriptional derepression is greater in Rbf1 than in E2f2 mutants. These differences correlate with differences in the magnitude of the replication defects in follicle cells, which attain an inappropriate 32C DNA content in both Rbf1 and Dp mutants but not in E2f2 mutants. The ectopic genomic replication of E2f2 mutant follicle cells can be suppressed by reducing the Orc2, Orc5, or Mcm2 gene dose by half, indicating that small changes in pre-RC gene expression can affect DNA synthesis in these cells. We conclude that RBF1 forms complexes with both E2F1/DP and E2F2/DP that cooperate to repress the expression of pre-RC genes, which helps confine DNA synthesis to sites of gene amplification. In contrast, E2F1 and E2F2 repressors function redundantly for some genes in the embryo. Thus, the relative functional contributions of E2F1 and E2F2 to gene expression and cell cycle control depends on the developmental context.

High-speed cell sorting: fundamentals and recent advances

Cell sorters have undergone dramatic technological improvements in recent years. Driven by the increased ability to differentiate between cell types, modern advances have yielded a new generation of cytometers, known as high-speed cell sorters. These instruments are capable of higher throughput than traditional sorters and can distinguish subtler differences between particles by measuring and processing more optical parameters in parallel. These advances have expanded their use to facilitate genomic and proteomic discovery, and as vehicles for many emerging cell-based therapies. High-speed cell sorting is becoming established as an essential research tool across a broad range of scientific fields and is poised to play a pivotal role in the latest therapeutic modalities.

Regulation of BMP and Activin Signaling in Drosophila

Cytokines of the TGF-beta superfamily act through an evolutionarily conserved signaling pathway to elicit a diverse range of biological responses in vertebrates as well as invertebrates. Drosophila has proved to be a powerful system to unravel the profound complexities underlying the regulation of this superficially simple signaling system for two reasons--the availability of sophisticated genetic tools and the restricted number of core signaling components compared to vertebrates. A BMP signaling pathway in Drosophila that regulates growth, differentiation and morphogenesis of the embryo and the larva has been extensively characterized. This work has provided major insights into how gradients of secreted proteins can be established and maintained in vivo, allowing a single ligand to induce multiple cell fates rather than function as an on-off switch. More recently, an activin signaling pathway has also been delineated that is required for growth and neuronal function during development. This review provides an overview of TGF-beta signaling in Drosophila with emphasis on the extensive modulation of signaling activity both within and outside the cell, that enables ligands to trigger specific and context-dependent effects.

Exploring genetic regulatory networks in metazoan development: methods and models

One of the foremost challenges of 21st century biological research will be to decipher the complex genetic regulatory networks responsible for embryonic development. The recent explosion of whole genome sequence data and of genome-wide transcriptional profiling methods, such as microarrays, coupled with the development of sophisticated computational tools for exploiting and analyzing genomic data, provide a significant starting point for regulatory network analysis. In this article we review some of the main methodological issues surrounding genome annotation, transcriptional profiling, and computational prediction of cis-regulatory elements and discuss how the power of model genetic organisms can be used to experimentally verify and extend the results of genomic research.

Genomics in pure and applied entomology

Genomics is the study of the structure and function of the genome: the set of genetic information encoded in the DNA of the nucleus and organelles of an organism. It is a dynamic field that combines traditional paths of inquiry with new approaches that would have been impossible without recent technological developments. Much of the recent focus has been on obtaining the sequence of entire genomes, determining the order and organization of the genes, and developing libraries that provide immediate physical access to any desired DNA fragment. This has enabled functional studies on a genome-wide level, including analysis of the genetic basis of complex traits, quantification of global patterns of gene expression, and systematic gene disruption projects. The successful contribution of genomics to problems in applied entomology requires the cooperation of the private and public sectors to build upon the knowledge derived from the Drosophila genome and effectively develop models for other insect Orders.

Perspective: micoarrays and differential display PCR-tools for studying transcript levels of genes in neuroendocrine systems

A central goal of neuroendocrinology is the understanding of how hormones modulate a variety of neurobiological functions including releasing factors for anterior pituitary secretions and behavior. We know that mechanisms of hormone actions clearly include the activation and repression of genes either directly through nuclear hormone receptors or indirectly, through a series of transduced signals originating from membrane receptors. Until recently, identification of the differentially expressed genes has been a "gene-at-a-time" proposition. With the advent of the completion of sequencing of several genomes including those of the human and mouse, new methods for the simultaneous assessment of many genes' expression are proving especially timely. Two such methods, differential display PCR and gene microarrays, are based on the well-established principles of DNA amplification and nucleic acid hybridization, respectively. With properly designed and well-executed experiments, these methods are powerful tools in the assessment of differentially expressed genes yielding results both expected and unanticipated.

Mechanisms of action of estrogen and progesterone

Estrogen and progesterone are steroid hormones that play a pivotal role in the regulation of mammalian reproduction. One primary action of these hormones is to regulate the development and function of the uterus. These hormones act by regulating the transcription of specific genes in the uterus. The actions of these hormones are mediated by their specific hormone receptors. These receptors are nuclear transcription factors, whose transcriptional regulatory activity is mediated by the binding of the specific steroid to these molecules. Once these receptors bind hormone, they can bind to specific cis-acting sequences in the promoter region of responsive genes and regulate transcription of these genes. In the regulation of transcription, these receptors interact with specific cofactors to activate the transcriptional machinery. A second gene family, the Steroid Receptor Coactivator (SRC) family, has been identified that serves to modulate the transcriptional activity of the hormone receptors. To date, three members of the SRC family have been identified. During the last decade, gene targeting technology has been used to identify the role of these receptors in the regulation of reproduction and uterine biology.

Dirofilaria immitis encodes Di-nhr-7, a putative orthologue of the Drosophila ecdysone-regulated E78 gene

Filarial parasites are responsible for several serious human diseases with symptoms such as lymphoedema, elephantiasis, and blindness. An understanding of how these parasites pass through developmental checkpoints may elucidate the general mechanisms of these illnesses and suggest potential targets for intervention. A useful model system for the study of human filariasis is the related nematode Dirofilaria immitis, the causative agent of dog heartworm disease. In D. immitis, molting from the third to the fourth larval stage can be induced in vitro by the insect hormone 20-OH ecdysone, suggesting that ecdysone, or some related hormone, may play a similar role in the development of D. immitis. Ecdysone has a well-characterized developmental role in insects, where it is involved in the control of molting and metamorphosis. We have identified a D. immitis orthologue of the Drosophila ecdysone response early gene E78, a member of the nuclear receptor (NR) superfamily. The D. immitis gene, Di-nhr-7 (NR1E1) encodes at least three isoforms, including two potential negative regulatory isoforms, and is expressed in a sex-specific manner. An MBP/Di-NHR-7 fusion protein is able to bind to DNA response elements that are recognized by the closely related mammalian NR Rev-erb(alpha).

Applying genomics technologies to neural development

Genomic technologies have evolved from a minority interest to a set of generally applicable, powerful tools. Recent studies have demonstrated that such tools are of great use in studies of neural development, particularly when allied to advances in data analysis and methods for analyzing gene function.

Expression profiling of Drosophila imaginal discs

BACKGROUND

In the Drosophila larva, imaginal discs are programmed to produce adult structures at metamorphosis. Although their fate is precisely determined, these organs remain largely undifferentiated in the larva. To identify genes that establish and express the different states of determination in discs and larval tissues, we used DNA microarrays to analyze mRNAs isolated from single imaginal discs.

RESULTS

Linear amplification protocols were used to generate hybridization probes for microarray analysis from poly(A)+ RNA from single imaginal discs containing between 10,000 and 60,000 cells. Probe reproducibility and degree of representation were tested using microarrays with approximately 6,000 different cDNAs. Hybridizations with probes that had been prepared separately from the same starting RNA pool had a correlation coefficient of 0.97. Expression-profile comparisons of the left and right wing imaginal discs from the same larva correlated with a coefficient of 0.99, indicating a high degree of reproducibility of independent amplifications. Using this method, we identified genes with preferential expression in the different imaginal discs using pairwise comparisons of discs and larval organs. Whereas disc-to-disc comparisons revealed only moderate differences, profiles differed substantially between imaginal discs and larval tissues, such as larval endodermal midgut and mesodermal fat body.

CONCLUSIONS

The combination of linear RNA amplification and DNA microarray hybridization allowed us to determine the expression profiles of individual imaginal discs and larval tissues and to identify genes expressed in tissue-specific patterns. These methods should be widely applicable to comparisons of expression profiles for tissues or parts of tissues that are available only in small amounts.

Have microarrays failed to deliver for developmental biology?

Comprehensive microarrays covering large numbers of the predicted expressed transcripts for some invertebrates and vertebrates have been available for some time. Despite predictions that this technology will transform biology, to date there have been few published studies using microarrays to generate novel insights in developmental biology.

Drosophila E2f2 promotes the conversion from genomic DNA replication to gene amplification in ovarian follicle cells

Drosophila contains two members of the E2F transcription factor family (E2f and E2f2), which controls the expression of genes that regulate the G1-S transition of the cell cycle. Previous genetic analyses have indicated that E2f is an essential gene that stimulates DNA replication. We show that loss of E2f2 is viable, but causes partial female sterility associated with changes in the mode of DNA replication in the follicle cells that surround the developing oocyte. Late in wild-type oogenesis, polyploid follicle cells terminate a program of asynchronous endocycles in which the euchromatin is entirely replicated, and then confine DNA synthesis to the synchronous amplification of specific loci, including two clusters of chorion genes that encode eggshell proteins. E2f2 mutant follicle cells terminate endocycles on schedule, but then fail to confine DNA synthesis to sites of gene amplification and inappropriately begin genomic DNA replication. This ectopic DNA synthesis does not represent a continuation of the endocycle program, as the cells do not complete an entire additional S phase. E2f2 mutant females display a 50% reduction in chorion gene amplification, and lay poorly viable eggs with a defective chorion. The replication proteins ORC2, CDC45L and ORC5, which in wild-type follicle cell nuclei localize to sites of gene amplification, are distributed throughout the entire follicle cell nucleus in E2f2 mutants, consistent with their use at many genomic replication origins rather than only at sites of gene amplification. RT-PCR analyses of RNA purified from E2f2 mutant follicle cells indicate an increase in the level of Orc5 mRNA relative to wild type. These data indicate that E2f2 functions to inhibit widespread genomic DNA synthesis in late stage follicle cells, and may do so by repressing the expression of specific components of the replication machinery.

Prokaryotic RNA preparation methods useful for high density array analysis: comparison of two approaches

High density oligonucleotide arrays have been used extensively for expression studies of eukaryotic organisms. We have designed a prokaryotic high density oligonucleotide array using the complete Escherichia coli genome sequence to monitor expression levels of all genes and intergenic regions in the genome. Because previously described methods for preparing labeled target nucleic acids are not useful for prokaryotic cell analysis using such arrays, a mRNA enrichment and direct labeling protocol was developed together with a cDNA synthesis protocol. The reproducibility of each labeling method was determined using high density oligonucleotide probe arrays as a read-out methodology and the expression results from direct labeling were compared to the expression results from the cDNA synthesis. About 50% of all annotated E.coli open reading frames are observed to be transcribed, as measured by both protocols, when the cells were grown in rich LB medium. Each labeling method individually showed a high degree of concordance in replica experiments (95 and 99%, respectively), but when each sample preparation method was compared to the other, approximately 32% of the genes observed to be expressed were discordant. However, both labeling methods can detect the same relative gene expression changes when RNA from IPTG-induced cells was labeled and compared to RNA from uninduced E.coli cells.

Myopodin, a synaptopodin homologue, is frequently deleted in invasive prostate cancers

Prostate cancer is one of the leading causes of cancer-related deaths for men in the United States. Like other malignancies, prostate cancer is underscored by a variety of aberrant genetic alterations during its development. Although loss of heterozygosity or allelic loss is frequently identified among prostate cancers, few genes have been identified thus far as critical to the development of invasive prostate cancers. In this report, we used the recently developed technology, the "differential subtraction chain," to perform a genome-wide search for sequences that are deleted in an aggressive prostate cancer. Among the deleted sequences, we found that one sequence was deleted in >50% of prostate cancers we tested. We mapped this sequence to chromosome 4q25 by screening the Genebridge 4 hamster radiation panel with primers specific to this probe, and subsequently identify a 54-kb minimal common deletion region that contains the sequence encoding myopodin. Sequence analysis indicates that myopodin shares significant homology with synaptopodin, a protein closely associated with podocyte and neuron differentiation. Further study shows that frequent complete or partial deletions of the myopodin gene occurred among invasive prostate cancer cases (25 of 31 cases, or 80%). Statistical analysis indicates that deletion of myopodin is highly correlated with the invasiveness of prostate cancers, and thus may hold promise as an important prognostic marker for prostate cancers.

Specific domains drive VM32E protein distribution and integration in Drosophila eggshell layers

A study was made of the localization and assembly of the VM32E protein, a putative vitelline membrane component of the Drosophila eggshell. The results highlight some unique features of this protein compared with the other proteins of the same gene family. At the time of its synthesis (stage 10), the VM32E protein is not detectable in polar follicle cells. However, it is able to move in the extracellular space around the oocyte and, by stage 11 is uniformly distributed in the vitelline membrane. During the terminal stages of oogenesis the VM32E protein is partially released from the vitelline membrane and becomes localized in the endochorion layer also. By analyzing transgenic flies carrying variously truncated VM32E proteins, we could identify the protein domains required for the proper assembly of the VM32E protein in the eggshell. The highly conserved vitelline membrane domain is implicated in the early interactions with other components and is required for cross-linking VM32E protein in the vitelline membrane. The terminal carboxylic domain is necessary for localization to the endochorion layer. Protein with the C-end domain deleted is localized solely to the vitelline membrane and cross-linked only in laid eggs, as occurs for the other vitelline membrane proteins.

Application of differential display to immunological research

The majority of immunological processes are mediated by cell-to-cell contact or receptor-ligand interactions that transmit intracellular signals and affect the regulation of transcription in the nucleus. As a consequence, precursor cells develop into their respective lineages and cells differentiate further during an immune response. In order to study changes in normal cells or even cells that have been isolated from diseased tissue, a number of approaches have been developed. One such method, differential display (DDRT-PCR), is a versatile technique for the analysis of gene expression that is based on RT-PCR and denaturing polyacrylamide gel electrophoresis. This technique is applicable to multiple samples of clonal or purified cell populations as well as to complex tissues and can be used to provide mRNA fingerprints. However, the main purpose of DDRT-PCR is to isolate differentially regulated genes in biological systems. The method is carried out without prior hypothesis as to which genes should be examined and so increases the possibility of identifying completely novel and unexpected changes in transcription. A major drawback has been the isolation of false positive clones and the need to confirm the results of analysis by another method. This makes DDRT-PCR labour intensive. A number of strategies have been recommended to reduce these problems, including reverse-northern analysis as a confirmatory step for screening putative differentials. In order to reduce the number of gel fingerprints that would be required to cover all the mRNAs in a cell, several focused approaches have been suggested. These include targeted differential display for the isolation of multigene families that have conserved protein domains or gene signatures and subtractive differential display whereby one population is subtracted from the other prior to screening. The purpose of this review is to provide some guidance to the immunologist who might wish to apply DDRT-PCR in their research. A number of examples where DDRT-PCR has been used successfully in immunological research are included.

Differential gene expression between chronic hepatitis B and C hepatic lesion

BACKGROUND & AIMS

Complementary DNA (cDNA) microarray technology allows simultaneous expression analysis of hundreds to thousands of genes. We applied the cDNA microarray technique to clarify gene expression profiles in chronic viral hepatitis tissue lesions.

METHODS

We made cDNA microarrays consisting of 1080 human cDNAs and analyzed gene expression using labeled cDNAs prepared from 6 normal, 12 chronic hepatitis B, and 14 chronic hepatitis C liver tissues. Relative expression ratios of individual genes were obtained by comparing hybridization of Cy5-labeled cDNAs from chronic hepatitis lesions and Cy3-labeled cDNA from normal liver tissue.

RESULTS

Hierarchical clustering analysis of the gene expression profiles in 26 patients showed that the patients were clustered into 2 groups with respect to similarities in differentially expressed genes. Hepatitis B and C virus infection, but not age, sex, or histology of hepatitis, were significant factors determining clustering (P < 0.05). In hepatitis B tissue lesions, genes involved in inflammation were predominant, whereas in hepatitis C, expression of anti-inflammatory response genes was relatively dominant.

CONCLUSIONS

These findings shed new light on the possible differential molecular mechanisms in the pathogenesis of hepatitis caused by hepatitis B virus and hepatitis C virus infection, from which hepatocellular carcinoma frequently develops.

DNA microarrays: raising the profile

Expression profiling using DNA microarrays is starting to come of age. The past year has seen significant advances in the number, scope and quality of studies that incorporate expression profiling experiments. Attention is starting to move on from making DNA microarrays to appropriate experimental design and sophisticated data analysis techniques.

Identification of candidate downstream genes for the homeodomain transcription factor Labial in Drosophila through oligonucleotide-array transcript imaging

BACKGROUND

Homeotic genes are key developmental regulators that are highly conserved throughout evolution. Their encoded homeoproteins function as transcription factors to control a wide range of developmental processes. Although much is known about homeodomain-DNA interactions, only a small number of genes acting downstream of homeoproteins have been identified. Here we use a functional genomic approach to identify candidate target genes of the Drosophila homeodomain transcription factor Labial.

RESULTS

High-density oligonucleotide arrays with probe sets representing 1,513 identified and sequenced genes were used to analyze differential gene expression following labial overexpression in Drosophila embryos. We find significant expression level changes for 96 genes belonging to all functional classes represented on the array. In accordance with our experimental procedure, we expect that these genes are either direct or indirect targets of labial gene action. Among these genes, 48 were upregulated and 48 were downregulated following labial overexpression. This corresponds to 6.3% of the genes represented on the array. For a selection of these genes, we show that the data obtained with the oligonucleotide arrays are consistent with data obtained using quantitative RT-PCR.

CONCLUSIONS

Our results identify a number of novel candidate downstream target genes for Labial, suggesting that this homeoprotein differentially regulates a limited and distinct set of embryonically expressed Drosophila genes.

Universal GFP reporter for the study of vascular development

We report the generation and characterization of transgenic mouse and zebrafish expressing green fluorescent protein (GFP) specifically in vascular endothelial cells in a relatively uniform fashion. These reporter lines exhibit fluorescent vessels in developing embryos and throughout adulthood, allowing visualization of the general vascular patterns with single cell resolution. Furthermore, we show the ability to purify endothelial cells from whole embryos and adult organs by a single step fluorescence activated cell sorting. We expect that these transgenic reporters will be useful tools for imaging vascular morphogenesis, global gene expression profile analysis of endothelial cells, and high throughput screening for vascular mutations.

Spatial activation and repression of the drosophila vitelline membrane gene VM32E are switched by a complex cis-regulatory system

The VM32E gene is differently expressed in the distinct cell domains composing the follicular epithelium. Our previous work on the VM32E gene defined the promoter regions required for the control of gene expression in the ventral and dorsal follicle domains. In this report, we present data from a finer dissection of each upstream regulatory region, allowing to draw the functional interactions among different regulatory elements. A 73-bp proximal region (-112/-39) contains regulatory element(s) to dictate the activation of the gene in the follicular epithelium. This region interacts with two other cis-regulatory elements and is absolutely required for their output. The first element (-206/ -113), individually unable to raise reporter expression, elicits gene activity in the ventral domain when joined to the proximal fragment; a second element (-348/-254) joined to the same proximal fragment sustains the full dorsal and ventral activity. Moreover, the ectopic expression driven by some promoter fragments in border or posterior cells uncovers the existence of specific negative regulatory elements. So, the follicular domain specificity of VM32E gene expression is achieved through the combined activities of cell-type specific positive and negative elements.

Thyroid hormone regulation of hepatic genes in vivo detected by complementary DNA microarray

The liver is an important target organ of thyroid hormone. However, only a limited number of hepatic target genes have been identified, and little is known about the pattern of their regulation by thyroid hormone. We used a quantitative fluorescent cDNA microarray to identify novel hepatic genes regulated by thyroid hormone. Fluorescent-labeled cDNA prepared from hepatic RNA of T3-treated and hypothyroid mice was hybridized to a cDNA microarray, representing 2225 different mouse genes, followed by computer analysis to compare relative changes in gene expression. Fifty five genes, 45 not previously known to be thyroid hormone-responsive genes, were found to be regulated by thyroid hormone. Among them, 14 were positively regulated by thyroid hormone, and unexpectedly, 41 were negatively regulated. The expression of 8 of these genes was confirmed by Northern blot analyses. Thyroid hormone affected gene expression for a diverse range of cellular pathways and functions, including gluconeogenesis, lipogenesis, insulin signaling, adenylate cyclase signaling, cell proliferation, and apoptosis. This is the first application of the microarray technique to study hormonal regulation of gene expression in vivo and should prove to be a powerful tool for future studies of hormone and drug action.

MTM1 mutations in X-linked myotubular myopathy

X-linked myotubular myopathy (XLMTM; MIM# 310400) is a severe congenital muscle disorder caused by mutations in the MTM1 gene. This gene encodes a dual-specificity phosphatase named myotubularin, defining a large gene family highly conserved through evolution (which includes the putative anti-phosphatase Sbf1/hMTMR5). We report 29 mutations in novel cases, including 16 mutations not described before. To date, 198 mutations have been identified in unrelated families, accounting for 133 different disease-associated mutations which are widespread throughout the gene. Most point mutations are truncating, but 26% (35/133) are missense mutations affecting residues conserved in the Drosophila ortholog and in the homologous MTMR1 gene. Three recurrent mutations affect 17% of the patients, and a total of 21 different mutations were found in several independent families. The frequency of female carriers appears higher than expected (only 17% are de novo mutations). While most truncating mutations cause the severe and early lethal phenotype, some missense mutations are associated with milder forms and prolonged survival (up to 54 years).

High throughput gene expression screening: its emerging role in drug discovery

The genetic makeup and the environment influences the health and welfare of an individual. At both the tissue and cellular level, physiological function can be correlated with the transcription of genes, whose protein products contribute and influence the activity of biological systems. In order to understand these processes, it is therefore essential to determine the temporal and spatial patterns of gene expression, and, with particular relevance to drug discovery, define changes that occur during development of disease or treatment with therapeutic agents.

Encroaching genomics: adapting large-scale science to small academic laboratories

The process of conducting biological research is undergoing a profound metamorphosis due to the technological innovations and torrent of information resulting from the execution of multiple species genome projects. The further tasks of mapping polymorphisms and characterizing genome-wide protein-protein interaction (the characterization of the proteome) will continue to garner resources, talent, and public attention. Although some elements of these whole genome size projects can only be addressed by large research groups, consortia, or industry, the impact of these projects has already begun to transform the process of research in many small laboratories. Although the impact of this transformation is generally positive, laboratories engaged in types of research destined to be dominated by the efforts of a genomic consortium may be negatively impacted if they cannot rapidly adjust strategies in the face of new large-scale competition. The focus of this report is to outline a series of strategies that have been productively utilized by a number of small academic laboratories that have attempted to integrate such genomic resources into research plans with the goal of developing novel physiological insights.

Molecular cloning and embryonic expression of dFKBP59, a novel Drosophila FK506-binding protein

A Drosophila cDNA encoding a structural homolog of mammalian FKBP59 (also identified as FKBP52), a member of the FK506-binding protein (FKBP) class of immunophilins, was isolated. The gene dFKBP59 corresponding to this cDNA has been characterized and mapped to the 30D3-4 region. The predicted amino acid sequence of this cDNA shows that the dFKBP59 protein contains one highly conserved FKBP12-like domain followed by two others with less conservation. Northern hybridization reveals that the dFKBP59 mRNA is expressed throughout the Drosophila life-cycle. In contrast to its mammalian homologs, in situ hybridization detected dFKBP59 expression in specific tissues: the lymph glands, Garland cells and oenocyte cells, which are all specialized tissues in which intensive exocytic/endocytic cycling takes place. Garland cells and oenocytes (also called Drosophila nephrocytes) function in taking up waste material from the hemolymph. Finally, I have mapped an enhancer trap element within the 5' region of dFKBP59 which may help in future studies to address the question of its function during Drosophila development.

The homeobox gene mirror links EGF signalling to embryonic dorso-ventral axis formation through notch activation

Recent studies in vertebrates and Drosophila melanogaster have revealed that Fringe-mediated activation of the Notch pathway has a role in patterning cell layers during organogenesis. In these processes, a homeobox-containing transcription factor is responsible for spatially regulating fringe (fng) expression and thus directing activation of the Notch pathway along the fng expression border. Here we show that this may be a general mechanism for patterning epithelial cell layers. At three stages in Drosophila oogenesis, mirror (mirr) and fng have complementary expression patterns in the follicle-cell epithelial layer, and at all three stages loss of mirr enlarges, and ectopic expression of mirr restricts, fng expression, with consequences for follicle-cell patterning. These morphological changes are similar to those caused by Notch mutations. Ectopic expression of mirr in the posterior follicle cells induces a stripe of rhomboid (rho) expression and represses pipe (pip), a gene with a role in the establishment of the dorsal-ventral axis, at a distance. Ectopic Notch activation has a similar long-range effect on pip. Our results suggest that Mirror and Notch induce secretion of diffusible morphogens and we have identified TGF-beta (encoded by dpp) as such a molecule in germarium. We also found that mirr expression in dorsal follicle cells is induced by the EGF-receptor (EGFR) pathway and that mirr then represses pip expression in all but the ventral follicle cells, connecting EGFR activation in the dorsal follicle cells to repression of pip in the dorsal and lateral follicle cells. Our results suggest that the differentiation of ventral follicle cells is not a direct consequence of germline signalling, but depends on long-range signals from dorsal follicle cells, and provide a link between early and late events in Drosophila embryonic dorsal-ventral axis formation.

Expression profiling of single mammalian cells--small is beautiful

Increasingly mRNA expression patterns established using a variety of molecular technologies such as cDNA microarrays, SAGE and cDNA display are being used to identify potential regulatory genes and as a means of providing valuable insights into the biological status of the starting sample. Until recently, the application of these techniques has been limited to mRNA isolated from millions or, at very best, several thousand cells thereby restricting the study of small samples and complex tissues. To overcome this limitation a variety of amplification approaches have been developed which are capable of broadly evaluating mRNA expression patterns in single cells. This review will describe approaches that have been employed to examine global gene expression patterns either in small numbers of cells or, wherever possible, in actual isolated single cells. The first half of the review will summarize the technical aspects of methods developed for single-cell analysis and the latter half of the review will describe the areas of biological research that have benefited from single-cell expression analysis.

Observing the living genome

Dynamic pictures of living genomes are now beginning to emerge from systematic studies of gene expression patterns using DNA microarrays. The rich information represented in the variation in each gene's expression provides the basis for a new kind of genomic map.