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Pre-MBT patterning of early gene regulation in Xenopus: the role of the cortical rotation and mesoderm induction.

Patterning events that occur before the mid-blastula transition (MBT) and that organize the spatial pattern of gene expression in the animal hemisphere have been analyzed in Xenopus embryos. We present evidence that genes that play a role in dorsoventral specification display different modes of activation. Using early blastomere explants (16-128-cell stage) cultured until gastrula stages, we demonstrate by RT-PCR analysis that the expression of goosecoid (gsc), wnt-8 and brachyury (bra) is dependent on mesoderm induction. In contrast, nodal-related 3 (nr3) and siamois (sia) are expressed in a manner that is independent of mesoderm induction, however their spatially correct activation does require cortical rotation. The pattern of sia and nr3 expression reveals that the animal half of the 16-cell embryo is already distinctly polarized along the dorsoventral axis as a result of rearrangement of the egg structure during cortical rotation. Similar to the antagonistic activity between the ventral and the dorsal mesoderm, the ventral animal blastomeres can attenuate the expression of nr3 and sia in dorsal animal blastomeres. Our data suggest that no Nieuwkoop center activity at the blastula stage is required for the activation of nr3 and sia in vivo.

Animals↗

Preclinical applications of imaging for cancer gene therapy.

Gene therapy is a very attractive strategy in experimental cancer therapy. Ideally, the approach aims to deliver therapeutic genes selectively to cancer cells. However, progress in the improvement of gene therapy formulations has been hampered by difficulties in measuring transgene delivery and in quantifying transgene expression in vivo. In clinical trials, endpoints rely almost exclusively on the analysis of biopsies by molecular and histopathological methods, which provide limited information. Therefore, to ensure the rational development of gene therapy, a crucial issue is the utilisation of technologies for the non-invasive monitoring of spatial and temporal gene expression in vivo upon administration of a gene delivery vector. Such imaging technologies would allow the generation of quantitative information about gene expression and the assessment of cancer gene therapy efficacy. In the past decade, progress has been made in the field of in vivo molecular imaging. This review highlights the various methods currently being developed in preclinical models.

Animals↗

3' Splicing variants of ret receptor tyrosine kinase are differentially expressed in mouse embryos and in adult mice.

The RET protooncogene encodes for a transmembrane receptor tyrosine kinase and plays a crucial role in nephrogenesis and the enteric nervous system (ENS) development. Alternative splicing at the 3' end of the RET gene generates 3' splicing variants that encode RET 9, RET 51 and RET 43 isoforms. It has been hypothesized that these isoforms perform distinct functions and that their expressions are differentially regulated during mammalian development. To gain an insight into the expression patterns of various ret isoforms during embryogenesis, we investigate the temporal and spatial expressions of ret gene in mouse embryos and in adult mice. We characterized the 3' end of the mouse ret gene and localized the alternatively spliced exons. Using 3' rapid amplification of cDNA ends (3' RACE) and reverse transcription-polymerase chain reaction (RT-PCR), ret 9 and ret 51 transcripts were identified in both mouse embryos and adult mouse tissues. However, the ret 43 transcript was not. Using in situ hybridization, we showed that ret 9 was the dominant ret encoding transcript in mouse embryos. Transcripts of ret 9 were detected in all cranial ganglia; in the sensory and autonomic ganglia of the trunk; in a subset of neurons of the dorsal root ganglion (DRG); in the motor neurons of the spinal cord; in the developing lung and excretory systems; in the enteric neuroblasts of the ENS; and in the thyroid lobes. In contrast, ret 51 expression was weak and restricted to the motor column of the spinal cord, the DRG, the enteric neuroblasts, the lung bud and the kidney. In adult mice, ret 9 expression was relatively widespread in many organs while that of ret 51 was rather restricted. Our data indicated that ret isoforms are temporally and spatially regulated in mouse embryos and adult mouse.

Alternative Splicing↗

The Bearded box, a novel 3' UTR sequence motif, mediates negative post-transcriptional regulation of Bearded and Enhancer of split Complex gene expression.

During the development of the Drosophila adult peripheral nervous system (PNS), inhibitory cell-cell interactions mediated by the Notch receptor are essential for proper specification of sensory organ cell fates. We have reported previously (M. W. Leviten, E. C. Lai and J. W. Posakony (1997) Development 124, 4039-4051) that the 3' untranslated regions (UTRs) of many genes involved in Notch signalling, including Bearded (Brd) and the genes of the Enhancer of split Complex (E(spl)-C), contain (often in multiple copies) two novel heptanucleotide sequence motifs, the Brd box (AGCTTTA) and the GY box (GTCTTCC). Moreover, the molecular lesion associated with a strong gain-of-function mutant of Brd suggested that the loss of these sequence elements from its 3' UTR might be responsible for the hyperactivity of the mutant gene. We show here that the wild-type Brd 3' UTR confers negative regulatory activity on heterologous transcripts in vivo and that this activity requires its three Brd box elements and, to a lesser extent, its GY box. We find that Brd box-mediated regulation decreases both transcript and protein levels, and our results suggest that deadenylation or inhibition of polyadenylation is a component of this regulation. Though Brd and the E(spl)-C genes are expressed in spatially restricted patterns in both embryos and imaginal discs, we find that the regulatory activity that functions through the Brd box is both temporally and spatially general. A Brd genomic DNA transgene with specific mutations in its Brd and GY boxes exhibits hypermorphic activity that results in characteristic defects in PNS development, demonstrating that Brd is normally regulated by these motifs. Finally, we show that Brd boxes and GY boxes in the E(spl)m4 gene are specifically conserved between two distantly related Drosophila species, strongly suggesting that E(spl)-C genes are regulated by these elements as well.

Animals↗

Pharmacogenetic rescue in time and space of the rutabaga memory impairment by using Gene-Switch.

The GAL4-based Gene-Switch system has been engineered to regulate transgene expression in Drosophila in both time and space. We constructed a Gene-Switch transgene in which Gene-Switch expression is restricted spatially by a defined mushroom body enhancer. This system allows Gene-Switch to be active only in the mushroom bodies and only on administration of the pharmacological Gene-Switch ligand RU486. This line was used to drive the expression of a rutabaga cDNA in otherwise rutabaga mutant flies. Induction of the rutabaga cDNA in the mushroom bodies only during adulthood, or during adulthood along with the larval and pupal developmental stages, corrects the olfactory memory impairment found in rutabaga mutants. Induction of the cDNA only during the larval and pupal stages was inconsequential to performance in olfactory memory tasks. These data indicate that normal rutabaga function must be expressed in adulthood for normal memory and conclusively delimit the time and space expression requirements for correcting the rutabaga memory impairment. Such combined pharmacogenetic regulation of transgene expression now allows this time and space dissection to be made for other behavioral mutants.

Adenylyl Cyclases↗

Specification and segmentation of the paraxial mesoderm.

Somite formation in the mouse embryo begins with the recruitment of mesenchymal cells into the paraxial mesoderm. Cells destined for the paraxial mesoderm are recruited from a progenitor population found first in the embryonic ectoderm and later in the primitive streak and the tail bud. Experimental evidence suggests that the allocation of precursor cells to different mesodermal lineages may be related to the site at which the cells ingress through the primitive streak. An increasing number of genes, such as those encoding growth factor and transcription factors, are now known to be expressed in the primitive streak. It is not known whether the specification of mesodermal cell fate has any relationship with the activity of genes that are expressed in the restricted cell populations of the primitive streak. Somitomeres, which are spherical clusters of mesenchymal cells in the presomitic mesoderm, presage the segmentation of somites in the paraxial mesoderm. The somitomeric organization denotes a pre-pattern of segmentation that defines the physical boundary and the bilateral symmetry of the mesodermal segments in the body axis. The establishment of new somitomeres seems to require the interaction of a resident cell population in the presomitic mesoderm and the incoming primitive streak cells. Cell mixing, which occurs in the somitomeres prior to somite segmentation, poses problems in understanding the developmental role of the somitomere and the real significance of the partitioning of the node-derived and primitive streak-derived cells in the mesodermal segments. In the presomitic mesoderm, the expression of some genes that encode transcription factors, growth factors or tyrosine kinase receptor, and the localization of certain cell adhesion molecules are closely associated with distinct morphogenetic events, such as cell clustering in the presomitic mesoderm and the formation of epithelial somites. There is, however, very little direct relationship between the spatial pattern of gene expression and the somitomeric organization in the presomitic mesoderm. Results of somite transplantation experiments suggest that both the segmental address and the morphogenetic characteristics of the somite may be determined during somite segmentation. Regional identity of the paraxial mesodermal segment is conferred by the expression of a combination of Hox genes in the sclerotome and probably other lineage-specific genes that are subject to imprinting. Superimposed on the global metameric pattern, two orthogonal polarities of cell differentiation are endowed in each mesodermal segment. The rostro-caudal polarity is established prior to somite segmentation. This polarity is later manifested by the subdivision of the sclerotome and the alliance of the neural crest cells and motor axons with the rostral half-somite.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

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.

Drug Design↗

Multiple functions of Dlx genes.

Dlx genes comprise a highly conserved family of homeobox genes homologous to the distal-less (Dll) gene of Drosophila. They are thought to act as transcription factors. All Dlx genes are expressed in spatially and temporally restricted patterns in craniofacial primordia, basal telencephalon and diencephalon, and in distal regions of extending appendages, including the limb and the genital bud. Most of them are expressed during morphogenesis of sensory organs and during migration of neural crest cells and interneurons. In addition, Dlx5 and Dlx6 are expressed in differentiating osteoblasts. Gene targeting of Dlx1, Dlx2, Dlx3 and Dlx5 in the mouse germ-line has revealed functions in craniofacial patterning, sensory organ morphogenesis, osteogenesis and placental formation. However, no effect on limb development has yet been revealed from gene inactivation studies. A role for these genes in limb development is however suggested by the linkage of the Split Foot/Hand Malformation human syndrome to a region containing DLX5 and DLX6. As for most transcription factors, these genes seem to have multiple functions at different stages of development or in different tissues and cell types.

Amino Acid Sequence↗

A neurogenomics approach to gene expression analysis in the developing brain.

Secreted and transmembrane proteins provide critical functions in the signaling networks essential for neurogenesis. We used a genetic signal sequence gene trap approach to isolate 189 genes expressed during development in e16.5 whole head, e16.5 hippocampus and e14.5 cerebellum. Gene ontology programs were used to classify the genes into respective biological processes. Four major classes of biological processes known to be important during development were identified: cell communication, cell physiology processes, metabolism and morphogenesis. We used in situ hybridization to determine the temporal and spatial patterns of gene expression in the developing brain using this set of probes. The results demonstrate that gene expression patterns can highlight potential gene functions in specific brain regions. We propose that combining bioinformatics with the gene expression pattern is an effective strategy to identify genes that may play critical roles during brain development.

Animals↗

Identification and genetic regulation of the chalcone synthase multigene family in pea.

Chalcone synthase (CHS) is a key enzyme in the biosynthesis of diverse flavonoids involved in disease resistance, nodulation, and pigmentation in pea. We describe a multigene family encoding CHS and the effects of two regulatory loci, a and a2, on the pattern of expression of three of its member genes. Two of the genes, CHS1 and CHS3, are expressed in both petal and root tissue, whereas expression of a third gene, CHS2, is detected only in roots. The products encoded by the a and a2 loci are required for the expression of the CHS1 gene and for wild-type levels of expression of the CHS3 gene in petal tissue. In root tissue, all three CHS genes are expressed and induced by CuCl2 regardless of the genotype at the a and a2 loci. These results show that the various members of the CHS multigene family interact in diverse ways with multiple genetic signals in the plant, providing a basis for the differential expression of these genes. Spatially specific genetic regulation of distinct members of a multigene family has been clearly demonstrated.

Acyltransferases↗

Regulated expression of Arabidopsis phosphate transporters.

Phosphorus deficiency is one of the major abiotic stresses affecting plant growth. Plants respond to the persistent deficiency of phosphate (Pi) by coordinating the expression of genes involved in alleviation of the stress. The high-affinity Pi transporters are among the major molecular determinants that are activated during Pi stress. In this study, using three reporter genes (green fluorescent protein, luciferase, and beta-glucuronidase) regulated by two Pi transporter promoters, we have carried out an extensive analysis of transcriptional and spatial regulation of gene expression. Activation of the genes was rapid, repressible, and specific in response to changes in Pi availability. The phytohormones auxin and cytokinin suppressed the expression of the reporter gene driven by the AtPT1 promoter, and that of the native gene, suggesting that hormones may be involved in regulation of some component(s) of Pi starvation response pathway. These studies also provide molecular evidence for a potential role of high-affinity Pi transporters in mobilizing Pi into reproductive organs. The results suggest that members of the Pi transporter family may have similar but nonredundant functions in plants.

Arabidopsis↗

beta-lactamase as a marker for gene expression in live zebrafish embryos.

In this report we describe the development of a sensitive assay for gene expression in zebrafish embryos using beta-lactamase as a reporter gene. We show that injection of a green fluorescent substrate for beta-lactamase allows the detection of reporter gene expression in live embryos. The beta-lactamase enzyme catalyzes the hydrolysis of the substrate, thereby disrupting fluorescence resonance energy transfer from the donor to the acceptor dye in the molecule. As a result, a blue fluorescent product is produced and retained specifically in cells within which the enzyme is expressed. beta-Lactamase is therefore suitable for monitoring spatially restricted patterns of gene expression in the early embryo. We suggest that this new reporter system provides a major advancement in sensitivity over the existing methods for monitoring gene expression in vivo during early embryogenesis.

Animals↗

Effect of thyroid hormone deficiency on developmental expression of goalpha gene in the brain of neonatal rats by competitive RT-PCR and in situ hybridization histochemistry.

Goalpha is a guanine nucloetide-binding regulatory protein alpha subunit which is mainly distributed in the central nervous system, but it has not previously been reported how it is regulated by thyroid hormone in the brain of neonatal rat at transcriptional levels. In this report, we used quantitative competitive reverse transcriptional PCR to quantify the effects of TH deficiency on Goalpha gene expression in the brain of neonatal rat at mRNA levels. It was found that Goalpha mRNA levels in the brain of 14-day-old rats significantly increased over 3-fold after induction of perinatal hypothyroidism, and declined markedly after treatment of thyroxine replacement. In situ hybridization histochemistry was further employed to observe the time-course and spatial expression of Goalpha gene in the brain of neonatal rats affected by thyroid hormone deficiency during the developmental period. The data showed that perinatal hypothyroidism can enhance Goalpha mRNA levels in the temporal cortex, sensorimotor cortex, piriform cortex, amygdala, hippocampal CA1-4 subfields, dentate gyrus, arcuate nucleus (AR) and ventromedial hypothalamic nucleus (VMH) of hypothalamus, but not in the striate cortex, cingulate cortex, claustrum, caudate/putamen and thalamus in the brain of rat at 7-21 days post-partum. The results suggest that up-regulation of Goalpha gene expression may be one kind of common mechanism responsible for neurological deficits in some brain areas arising from thyroid hormone deficiency in the critical periods of neonatal rats.

Animals↗

Patterned gene expression directs bipolar planar polarity in Drosophila.

During convergent extension in Drosophila, polarized cell movements cause the germband to narrow along the dorsal-ventral (D-V) axis and more than double in length along the anterior-posterior (A-P) axis. This tissue remodeling requires the correct patterning of gene expression along the A-P axis, perpendicular to the direction of cell movement. Here, we demonstrate that A-P patterning information results in the polarized localization of cortical proteins in intercalating cells. In particular, cell fate differences conferred by striped expression of the even-skipped and runt pair-rule genes are both necessary and sufficient to orient planar polarity. This polarity consists of an enrichment of nonmuscle myosin II at A-P cell borders and Bazooka/PAR-3 protein at the reciprocal D-V cell borders. Moreover, bazooka mutants are defective for germband extension. These results indicate that spatial patterns of gene expression coordinate planar polarity across a multicellular population through the localized distribution of proteins required for cell movement.

Animals↗

Structural and functional analysis of rice genome.

Rice is an excellent system for plant genomics as it represents a modest size genome of 430 Mb. It feeds more than half the population of the world. Draft sequences of the rice genome, derived by whole-genome shotgun approach at relatively low coverage (4-6 X), were published and the International Rice Genome Sequencing Project (IRGSP) declared high quality (>10 X), genetically anchored, phase 2 level sequence in 2002. In addition, phase 3 level finished sequence of chromosomes 1, 4 and 10 (out of 12 chromosomes of rice) has already been reported by scientists from IRGSP consortium. Various estimates of genes in rice place the number at >50,000. Already, over 28,000 full-length cDNAs have been sequenced, most of which map to genetically anchored genome sequence. Such information is very useful in revealing novel features of macro- and micro-level synteny of rice genome with other cereals. Microarray analysis is unraveling the identity of rice genes expressing in temporal and spatial manner and should help target candidate genes useful for improving traits of agronomic importance. Simultaneously, functional analysis of rice genome has been initiated by marker-based characterization of useful genes and employing functional knock-outs created by mutation or gene tagging. Integration of this enormous information is expected to catalyze tremendous activity on basic and applied aspects of rice genomics.

Chromosomes, Plant↗

Neural marker genes differently expressed in subsets of embryonic neural cells of the ascidian Halocynthia roretzi.

Ascidians are lower chordates that possess a possible prototype of the vertebrate nervous system. The central and peripheral nervous systems of ascidian larvae are composed of only a few hundred cells (Nicol and Meinertzhagen, 1991). To investigate how these ascidian nervous systems develop, dissection at the molecular level using subset-specific markers is essential. Here we describe four new genes zygotically expressed in subsets of the ascidian neural cells. The spatial expression domains of these genes overlap in some parts but not in other parts of the nervous systems. Our results suggest that there are functionally different regions in the nervous systems owing to the gene expression differences. Further analyses of these genes will enable us to determine the molecular neuro-developmental characteristics of various clusters of neural cells.

Animals↗

Definition and spatial annotation of the dynamic secretome during early kidney development.

The term "secretome" has been defined as a set of secreted proteins (Grimmond et al. [2003] Genome Res 13:1350-1359). The term "secreted protein" encompasses all proteins exported from the cell including growth factors, extracellular proteinases, morphogens, and extracellular matrix molecules. Defining the genes encoding secreted proteins that change in expression during organogenesis, the dynamic secretome, is likely to point to key drivers of morphogenesis. Such secreted proteins are involved in the reciprocal interactions between the ureteric bud (UB) and the metanephric mesenchyme (MM) that occur during organogenesis of the metanephros. Some key metanephric secreted proteins have been identified, but many remain to be determined. In this study, microarray expression profiling of E10.5, E11.5, and E13.5 kidney and consensus bioinformatic analysis were used to define a dynamic secretome of early metanephric development. In situ hybridisation was used to confirm microarray results and clarify spatial expression patterns for these genes. Forty-one secreted factors were dynamically expressed between the E10.5 and E13.5 timeframe profiled, and 25 of these factors had not previously been implicated in kidney development. A text-based anatomical ontology was used to spatially annotate the expression pattern of these genes in cultured metanephric explants.

Animals↗

Computer-generated three-dimensional reconstructions of serially sectioned mouse embryos.

We have been involved with a group of computer scientists and anatomists in the development of computer-based methodologies that not only combine the advantages of scanning electron microscopy and conventional histology, but provide the additional dimension of tissue recognition. The latter is achieved by the appropriate labelling of tissues and structures by delineation or 'painting'. Individually segmented anatomically defined tissues can be highlighted in a particular colour and viewed either in isolation or in combination with other appropriately labelled tissues and organs. Tissues can be shown in any orientation either as a transparent overlay on computer-generated histological sections or as 3-D images without the histological background. An additional feature of the system is that computer graphics technology combined with 3-D glasses now also allows the viewer to see the object under analysis in stereo. This facility has been found to be particularly helpful in drawing attention to topological relationships that had not previously been readily noted. As the mouse is now the mammalian model of choice in many areas of developmental research, it is of critical importance that a basic level of skill is available in the research community in the interpretation of serially sectioned material, for example, for the rapidly expanding field in which gene expression studies play a significant role. It is equally important that there is an understanding of the dynamic changes that occur in relation to the differentiation of the various organ systems seen in these early stages of development. What we emphasise here is the additional information that it is possible to gain from the use of this tool which, in our view, could not readily have been gained from the analysis of scanning electron micrographs or by studying conventional serial histological sections of similar stages of mouse embryonic development. The methodology has been developed as part of a large project to prepare a database of mouse developmental anatomy covering all stages from fertilisation to birth in order to allow the accurate spatial mapping of gene expression and cell lineage data onto the digital Atlas of normal mouse development. In this paper we show how this digital anatomical Atlas also represents a valuable teaching aid and research tool in anatomy.

Anatomy, Cross-Sectional↗