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PubMed2004

Temporally and spatially controlled induction of gene expression in Arabidopsis thaliana.

Temporally and spatially regulated induction of gene expression is an important tool of genetic analysis. In plants, several systems are available for spatially unregulated induction of gene expression, or for spatially regulated expression. Here, we describe a new system that provides both temporal and spatial control for transgene expression. It combines the advantages of its two constituent components: temporally regulated activity of the ethanol-dependent AlcR transcription factor, and tissue specificity of a plant promoter. As a proof of principle, transgenic lines were developed in which the promoter of the meristem identity gene LEAFY (LFY) provided flower-specific expression of the AlcR activator. Tissue-specific activity of AlcR was confirmed with a responder in which the beta-glucuronidase (GUS) reporter was under the control of the alcA response element. As expected, reporter activity in a pattern typical for the LFY promoter was ethanol dependent. Next, we placed the LFY coding sequenced under control of the AlcA response element. In a strong lfy-12 background, this construct in combination with the LFY:AlcR driver provided complete, ethanol-dependent rescue of the lfy phenotype, including restoration of fertility. Apart from facilitating the investigation of temporal and spatial requirements of gene activity, this technology will permit new types of genetic modifier screens starting with mutations that otherwise confer lethality or sterility.

Arabidopsis↗
PubMed2003

Divergence in the spatial pattern of gene expression between human duplicate genes.

Microarray gene expression data provide a wealth of information for elucidating the mode and tempo of molecular evolution. In the present study,we analyze the spatial expression pattern of human duplicate gene pairs by using oligonucleotide microarray data,and study the relationship between coding sequence divergence and expression divergence. First,we find a strong positive correlation between the proportion of duplicate gene pairs with divergent expression (as presence or absence of expression in a tissue) and both synonymous (K(S)) and nonsynonymous divergence (K(A)). The divergence of gene expression between human duplicate genes is rapid, probably faster than that between yeast duplicates in terms of generations. Second,we compute the correlation coefficient (R) between the expression levels of duplicate genes in different tissues and find a significant negative correlation between R and K(S). There is also a negative correlation between R and K(A), when K(A) <or= 0.2. These results indicate that protein sequence divergence and divergence of spatial expression pattern are initially coupled. Finally,we compare the functions of those duplicate genes that show rapid divergence in spatial expression pattern with the functions of those duplicate genes that show no or little divergence in spatial expression.

Computational Biology↗
PubMed2005

Temporal and spatial manipulation of gene expression in Xenopus embryos by injection of heat shock promoter-containing plasmids.

The temporal and spatial manipulation of gene expression is useful in analyzing the mechanisms of early embryogenesis. This report describes a modified strategy to achieve controlled gene expression by directed plasmid injection using the hsp70 promoter and heat treatment. Two control genes, enhanced green fluorescent protein (EGFP) and beta-catenin, were also expressed by this method. When embryos were injected with HsS1/EGFP and subsequently heat-treated, ectopic EGFP was expressed only in the injected area. No severe defects were attributable to the heat treatment alone. Western blotting confirmed that no EGFP induction occurred in the absence of heat treatment and that, in the presence of heat induction, EGFP expression was detected within 1 hr after treatment. These results suggest that heat-mediated gene expression in the restricted area was regulated temporally. In addition, HsS1/beta-catenin injection into the animal pole of 8-cell embryos, followed by heat treatment, caused loss of head formation that was similar to that seen with CS2/beta-catenin injection. Although a hormone-inducible gene induction system already exists in Xenopus, our modified technique provides an alternative method for controlling temporal and spatial gene expression.

Animals↗
PubMed1998

Evaluation of metanephric maturation in a human fetal kidney explant model.

We have developed a unique human fetal kidney explant model to study the role of the insulin-like growth factor (IGF) system in metanephric development. Kidneys from 10-18 wk gestation human abortuses were maintained in serum-free conditions and defined medium, which was shown to support the induction and differentiation of the viable metanephric blastema. Histologically the tissue remained viable to 192 h of serum-free culture, while metanephric differentiation, reflected by a shrinking nephrogenic zone and the formation of maturing S-shape and glomerular forms, was accelerated and occurred between 48 and 96 h. In the nephrogenic zone, a significant decrease in IGF-II gene expression occurred, which reflected the differentiation of the metanephric blastema cell mass, IGF-II expression persisted, however, in the expanded interstitial mesenchyme. With differentiation over 48 h an increase in IGFBP-2 and WT1 gene expression by Northern blot analysis occurred, and was localized by in situ hybridization to the differentiating glomerular epithelial cell mass. Analysis of the explant-conditioned media by Western ligand blot demonstrated an increase in the rate of IGF binding protein (IGFBP)-2 peptide production by the differentiating explant, consistent with an increase in IGFBP-2 gene expression and with metanephric differentiation. This pattern of temporal and spatial gene expression closely approximates that of normal in vivo fetal renal development and of glomerular epithelial cell differentiation.

Cell Differentiation↗
PubMed2004

Spatial and temporal gene expression profiling of the contused rat spinal cord.

Microarray technology was used to examine gene expression changes following contusive injury of the adult rat spinal cord. To obtain a global understanding of the changes triggered by the injury, differential gene expression was examined spatially, using tissue samples from the epicenter of injury as well as 1 cm rostral and 1 cm caudal to the epicenter, and temporally, at 3 h, 24 h, 7 days, and 35 days post-injury. To filter out gene expression changes that were due to the laminectomy, samples of contused tissue were compared to laminectomy-only controls. We took advantage of four different, complementary methods of data analysis to detect differentially expressed genes. We have identified functional groups of genes that are differentially regulated in our model, including those associated with apoptosis, cell cycle, inflammation, and cholesterol metabolism. Our analysis has led to the identification of novel potential therapeutic targets within each group of genes that is discussed.

Animals↗
PubMedDate not supplied

Low-light image analysis of transgenic organisms using bacterial luciferase as a marker.

Methods for measurement of a novel light-emitting reporter gene system in bacteria, yeast, plant cells, plant tissues and intact plant organs are described. The principle underlying the assay procedures is the bacterial luciferase catalysed oxidation of reduced flavin mononucleotide (FMNH2) in the presence of the ten carbon aldehyde decanal, to yield FMN, decanoic acid, water and a photon of light at 490 nm which can be captured by X-ray film, a photomultiplier tube or, for in vivo measurements, an image-intensifier coupled to a video camera. This light measuring assay system is sensitive, easy to use, inexpensive, does not require radioactivity, and has been used successfully for rapid detection of bacterial transformants, the quantitative measurement of transient and stable gene expression in bacteria and yeast, and in vivo measurement of temporal and spatial gene expression throughout plant and animal development.

Animals↗
PubMed1997

Switching of gene expression: analysis of the factors that spatially and temporally regulate plant gene expression.

In this chapter, we have reviewed the present research and understanding of several families of transcription factors in plants. From this information, it appears there is good conservation between the types of transcription factors in plants and animals. However, there are several types of factors which have been isolated in plants that remain to be documented in animals (e.g., HD-Zip and GT). These as well as the presence of two types of TATA-binding proteins (TBPs) in plants suggest that although transcription in eukaryotes is highly conserved, fundamental differences may exist. Despite the differences, the modes of regulating transcription are well conserved. Figure 3 summarizes these modes of regulation. In recent years, the role of chromatin structure as well as subcellular localization have been the focus of a vast amount of research in mammals, Drosophila and yeast. However, very little research in these areas has been done in plants. Isolation of genes such as Curly leaf suggest a conservation of genes that influence the formation of heterochromatin-like structures. Whether or not this gene influences chromatin/heterochromatin structure in plants, however, remains to be tested. The study of nuclear localization of factors such as COP1 and KN1 is now leading to models for regulating nuclear transport as well as intercellular transport of transcription factors. Further study of the inter- and intracellular movement of these and other transcription factors may provide information on new modes of regulating transcription. In addition to understanding the role chromatin structure and subcellular localization of transcription factors may have on transcription initiation, the biological role of many plant transcription factors remains to be identified. Several approaches may be taken to understand the mechanisms by which transcription factors influence biochemical and physiological processes in the plant. These steps include 1) identification of the DNA-binding sites of the factors as well as the promoter regions which contain these sites. Presently, this approach is limiting in that not many non-coding regions have been sequenced and characterized in detail. Furthermore, the presence of a putative binding site within a promoter does not necessarily indicate that the factor will bind to the site in vivo. 2) Analysis of the binding affinity for a particular factor to a binding site in comparison to other related factors, via in vitro competition assays and quantitative titrations. This will provide information on how strongly these factors are binding to the sites, but without knowledge of all the factors present in a single cell it is difficult to recreate the in vivo conditions. 3) Generation of transgenic plants or microinjection of DNA/RNA to express a particular factor ectopically, reduce expression of the factor via antisense expression, and creation of dominant negative mutants by overexpression of key dimerization domains may provide information concerning what biological pathways these factors influence. 4) Isolation of mutations in particular transcription factors has been extremely informative in floral development. However, this approach usually entails isolation of a mutant due to a phenotype and eventual mutated locus. The cloning of the locus may or may not involve a transcription factor. 5) Many plant transcription factors have been isolated via sequence similarity to other previously identified and/or characterized transcription factors. However, the biological role of may of these factors is not known. In addition to ectopic expression of these factors by creating transgenic plants, isolation of a loss-of-function mutation may provide valuable information concerning the role of this factor in vivo. Many loss-of-function mutations in MADS box genes have led to a better understanding of how the MADS domain proteins interact with one another as well as how they influence floral development. (ABSTRACT TRUNCATED)

Cell Compartmentation↗
PubMed2004

Spatial patterns of gene expression in the olfactory bulb.

How olfactory sensory neurons converge on spatially invariant glomeruli in the olfactory bulb is largely unknown. In one model, olfactory sensory neurons interact with spatially restricted guidance cues in the bulb that orient and guide them to their target. Identifying differentially expressed molecules in the olfactory bulb has been extremely difficult, however, hindering a molecular analysis of convergence. Here, we describe several such genes that have been identified in a screen that compiled microarray data to create a three-dimensional model of gene expression within the mouse olfactory bulb. The expression patterns of these identified genes form the basis of a nascent spatial map of differential gene expression in the bulb.

Animals↗
PubMed2005

Real-time quantitative PCR analysis of temporal-spatial alterations in gene expression after spinal cord contusion.

Rat spinal cord contusion injury models the histopathology associated with much clinical spinal cord injury (SCI). Studies on altered gene expression after SCI in these models may identify therapeutic targets for reducing secondary injury after the initial trauma and/or enhancing recovery processes. However, complex spatial and temporal alterations after injury could complicate interpretation of changes in gene expression. To test this hypothesis, we selected six genes and studied their temporal and spatial patterns of expression at 1 h, 1, 3 and 7 days after a standardized spinal cord contusion produced by a weight drop device (10 g x 25 mm at T8). Real-time RT-PCR using TaqMan probes was employed to quantify mRNA for proteolipid protein, glyceraldehyde-3-phosphate dehydrogenase, glial fibrillary acidic protein, nestin, and the GluR2 and NR1 subunits of glutamate receptors. We found widely different temporal and spatial patterns of altered gene expression after SCI, including instances of opposing up- and down-regulation at different locations in tissue immediately adjacent to the injury site. We conclude that greater use of the reliable and extremely sensitive technique of quantitative real-time PCR for regional tissue analysis is important for understanding the altered gene expression that occurs after CNS trauma.

Animals↗
PubMed1999

The -700/-310 fragment of the apolipoprotein A-IV gene combined with the -890/-500 apolipoprotein C-III enhancer is sufficient to direct a pattern of gene expression similar to that for the endogenous apolipoprotein A-IV gene.

Spatial gene expression in the intestine is mediated by specific regulatory sequences. The three genes of the apoA-I/C-III/A-IV cluster are expressed in the intestine following cephalocaudal and crypt-to-villus axes. Previous studies have shown that the -780/-520 enhancer region of the apoC-III gene directs the expression of the apoA-I gene in both small intestinal villi and crypts, implying that other unidentified elements are necessary for a normal intestinal pattern of apoA-I gene expression. In this study, we have characterized transgenic mice expressing the chloramphenicol acetyltransferase gene under the control of different regions of the apoC-III and apoA-IV promoters. We found that the -890/+24 apoC-III promoter directed the expression of the reporter gene in crypts and villi and did not follow a cephalocaudal gradient of expression. In contrast, the -700/+10 apoA-IV promoter linked to the -500/-890 apoC-III enhancer directed the expression of the reporter gene in enterocytes with a pattern of expression similar to that of the endogenous apoA-IV gene. Furthermore, linkage of the -700/-310 apoA-IV distal promoter region to the -890/+24 apoC-III promoter was sufficient to restore the appropriate pattern of intestinal expression of the reporter gene. These findings demonstrate that the -700/-310 distal region of the apoA-IV promoter contains regulatory elements that, in combination with proximal promoter elements and the -500/-890 enhancer, are necessary and sufficient to restrict apoC-III and apoA-IV gene expression to villus enterocytes of the small intestine along the cephalocaudal axis.

Animals↗
PubMed1986

Transposable elements generate novel spatial patterns of gene expression in Antirrhinum majus.

The pallida gene of A. majus encodes a product required for the synthesis of red flower pigment. We have shown that the unstable pallida(recurrens) mutation is due to the insertion of the Tam3 transposable element near the promoter of the gene. Imprecise excision of Tam3 alters pallida gene expression and generates new spatial patterns or different intensities of flower pigmentation. Distinct spatial patterns may also result from rearrangements induced by Tam3 that alter the relative position of the pallida gene. Changes in Tam3 structure or position result in new unstable phenotypes. These findings suggest that genes may be rendered genetically hypervariable as a consequence of transposable element insertion and excision.

Alleles↗
PubMed2005

High-throughput screen for genes predominantly expressed in the ICM of mouse blastocysts by whole mount in situ hybridization.

Mammalian preimplantation embryos provide an excellent opportunity to study temporal and spatial gene expression in whole mount in situ hybridization (WISH). However, large-scale studies are made difficult by the size of the embryos ( approximately 60mum diameter) and their fragility. We have developed a chamber system that allows parallel processing of embryos without the aid of a microscope. We first selected 91 candidate genes that were transcription factors highly expressed in blastocysts, and more highly expressed in embryonic (ES) than in trophoblast (TS) stem cells. We then used the WISH to identify 48 genes expressed predominantly in the inner cell mass (ICM) and to follow several of these genes in all seven preimplantation stages. The ICM-predominant expressions of these genes suggest their involvement in the pluripotency of embryonic cells. This system provides a useful tool to a systematic genome-scale analysis of preimplantation embryos.

Animals↗
PubMed2001

Spatial and temporal gene expression in chondrogenesis during fracture healing and the effects of basic fibroblast growth factor.

Chondrogenesis is an essential component of endochondral fracture healing, though the molecular and cellular events by which it is regulated have not been fully elucidated. In this study, we used a rat model of closed fracture healing to determine the spatial and temporal expression of genes for cartilage-specific collagens. Furthermore, to determine the effects of basic fibroblast growth factor (bFGF) on chondrogenesis in fracture healing, we injected 100 microg recombinant human bFGF into the fracture site immediately after fracture. In normal calluses, pro-alpha1(II) collagen mRNA (COL2A1) was detected in proliferative chondrocytes beginning on day 4 after the fracture, and pro-alpha1(X) collagen mRNA (COL10A1) in hypertrophic chondrocytes beginning on day 7. In FGF-injected calluses, the cartilage enlarged in size significantly. On day 14, both COL2A1- and COL10A1-expressing cells were more widely distributed, and the amounts of COL2A1 and COL10A1 mRNAs were both approximately 2-fold increased when compared with uninjected fractures. Temporal patterns of expression for these genes were, however, identical to those found in normal calluses. The number of proliferating cell nuclear antigen-positive cells was increased in the non-cartilaginous area in the bFGF-injected calluses by day 4. The present molecular analyses demonstrate that a single injection of bFGF enhances the proliferation of chondroprogenitor cells in fracture callus, and thus contributes to the formation of a larger cartilage. However, maturation of chondrocytes and replacement of the cartilage by osseous tissue are not enhanced by exogenous bFGF, and this results in the prolonged cartilaginous callus phase. We conclude that, in the healing of closed fractures of long bones, exogenous bFGF has a capacity to enlarge the cartilaginous calluses, but not to induce more rapid healing.

Animals↗
PubMed2003

Multi-stage analysis of differential gene expression in BALB/C mouse liver development by high-density microarrays.

The development of a complex organ such as the liver relies on precise temporal and spatial gene expression patterns during ontogenesis. The unique adult phenotype is a result of a cascade of transcriptional events that finally trigger gene expression in a liver-specific fashion. Development in mice starts at embryonic stage E8.5-9.5 with the expression of several genes typically associated with liver tissue. While the role of some genes and their expression is well studied, little is known about the complex expression pattern changes during embryonic and fetal liver development. High-density oligonucleotide microarrays, which allow simultaneous expression analysis of 12,488 mouse mRNA transcripts and EST sequences, were used to study the gene expression profiles in day 7.5 embryonic tissue, in micro-dissected fetal liver tissue from day 11.5 and day 13.5 embryos, and in adult liver. In pairwise comparisons of all stages, a total of 4242 distinct genes or ESTs were found to be differentially regulated. Cross-comparisons of data from all stages detected the highest number of differentially regulated genes in E11.5 fetal liver tissue versus adult liver (3063 genes) and the lowest number in E11.5 versus E13.5 fetal liver tissue (517 genes). Using adult liver as reference tissue, 212 genes were regulated exclusively in E7.5 embryonic tissue, 303 genes in E11.5 and 198 in E13.5 fetal liver tissue. Expression profiles of the 31 genes with significant regulation at all stages as well as of a number of known developmentally regulated genes were compared with published results and interpreted. The gene expression profiles detected by microarray hybridization were independently confirmed for selected genes by quantitative RT-PCR. Our data presented here suggest that a relatively small number of stage-specific genes exist, which may be of particular importance for liver development, growth and differentiation. Furthermore, the microarray approach led to the identification of a number of genes, which have not yet been associated with liver organogenesis and maturation.

Animals↗
PubMed2003

Hippocampal gene expression profiling in spatial discrimination learning.

Learning and long-term memory are thought to involve temporally defined changes in gene expression that lead to the strengthening of synaptic connections in selected brain regions. We used cDNA microarrays to study hippocampal gene expression in animals trained in a spatial discrimination-learning paradigm. Our analysis identified 19 genes that showed statistically significant changes in expression when comparing Nai;ve versus Trained animals. We confirmed the changes in expression for the genes encoding the nuclear protein prothymosin(alpha) and the delta-1 opioid receptor (DOR1) by Northern blotting or in situ hybridization. In additional studies, laser-capture microdissection (LCM) allowed us to obtain enriched neuronal populations from the dentate gyrus, CA1, and CA3 subregions of the hippocampus from Nai;ve, Pseudotrained, and spatially Trained animals. Real-time PCR examined the spatial learning specificity of hippocampal modulation of the genes encoding protein kinase B (PKB, also known as Akt), protein kinase C(delta) (PKC(delta)), cell adhesion kinase(beta) (CAK(beta), also known as Pyk2), and receptor protein tyrosine phosphatase(zeta/beta) (RPTP(zeta/beta)). These studies showed subregion specificity of spatial learning-induced changes in gene expression within the hippocampus, a feature that was particular to each gene studied. We suggest that statistically valid gene expression profiles generated with cDNA microarrays may provide important insights as to the cellular and molecular events subserving learning and memory processes in the brain.

Animals↗
PubMed2002

Isolation and developmental expression analysis of Tbx22, the mouse homolog of the human X-linked cleft palate gene.

Mutations in the TBX22 gene have been identified recently in patients with the X-linked cleft palate and ankyloglossia syndrome, suggesting that the TBX22 transcription factor plays an important role in palate development. However, because ankyloglossia has been reported in the majority of patients with TBX22 mutations, it has been speculated that the cleft palate phenotype is secondary to defective fetal tongue movement. To understand the role of TBX22 in disease pathogenesis and in normal development, it is necessary to carry out a detailed temporal and spatial gene expression analysis. We report here the isolation and developmental expression analysis of the mouse homolog Tbx22. The mouse Tbx22 gene encodes a putative protein of 517 amino acid residues, which shares 72% overall amino acid sequence identity with the human TBX22 protein. By using interspecific backcross analysis, we have localized the Tbx22 gene to mouse chromosome X, in a region syntenic to human chromosome Xq21, where the TBX22 gene resides, indicating that Tbx22 is the ortholog of human TBX22. Our in situ hybridization analysis shows that Tbx22 is expressed in a temporally and spatially highly restricted pattern during mouse palate and tongue development. Together with the mutant phenotypes in human patients, our data indicate a primary role for Tbx22 in both palate and tongue development.

Amino Acid Sequence↗
PubMed2025

Single-cell-scale spatial transcriptome of the developing and adult mouse ovary.

Mammalian ovary development is essential for female fertility, involving the complex spatial patterning of diverse cell types to establish the finite reserve of ovarian follicles. While single-cell transcriptome analyses have provided important insights into the mechanisms driving specification and developmental trajectories of ovarian cells, they disrupt this crucial spatial context. To overcome this limitation, we used 10X Genomics Visium HD spatial transcriptomics to analyze the developing mouse ovary while maintaining its native cellular architecture. We captured all ovarian cell types at eight key fetal and postnatal timepoints, generating a near single cell resolution library of spatial gene expression across ovarian development. This comprehensive dataset allows analysis of dynamic transcriptional signatures associated with unique spatial patterning throughout development, including the establishment of cortex and medulla and assembly of ovarian follicles in each region. This dataset represents a fundamental resource for the investigation of regulatory mechanisms driving spatial patterning of the ovary and opens new avenues to explore the spatial determinants of female fertility and reproductive longevity.

Journal Article↗
PubMed1996

Binary expression of olfactory bulb-protein tyrosine phosphatase in rat central nervous system: developmental gene regulation in neonate cerebral cortex and constitutive expression in olfactory-rhinencephalon.

Olfactory bulb-protein tyrosine phosphatase (OB-PTP) is a receptor type PTPase dominantly expressed in olfactory bulb. Previously, we isolated and molecularly cloned a rat OB-PTP cDNA from an embryonal brain cDNA library. In the present study, we investigated its temporal and spatial gene expression by Northern blot and in situ hybridization analysis. The expression of OB-PTP gene was firstly detected in day 16 post coitum embryo and significantly increased during the late-gestational stage, attaining the highest level in the first week of neonate. The OB-PTP transcript was then down-regulated postnatally and was detected barely in an adult brain. In situ hybridization analysis showed that the transcript was characteristically localized in the postmitotic neurons of cerebral cortex and subcortical structures, and was down-regulated by day 28 when the cortical and subcortical structures have been organized. In the olfactory-rhinencephalon system including olfactory bulb and piriform cortex, the OB-PTP was preferentially expressed in the postmitotic neurons, and in contrast continuously expressed in the matured brain. Based on the evidence that DPTP10D, the Drosophila homolog of OB-PTP, is localized in the axons of specific pioneer neurons in Drosophila embryo, the OB-PTP is presumably involved in the axonogenesis of cortical and subcortical neurons as well as olfactory neurons in mammalian central nervous system. The biological significance of transcriptional regulation in olfactory system is discussed in terms of continuous axonal connections by regenerating olfactory neurons.

Animals↗