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Results for “spatial gene expression”

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PubMed1993

Murine FGF-4 gene expression is spatially restricted within embryonic skeletal muscle and other tissues.

Fibroblast growth factors are believed to play many distinct roles in vertebrate development, owing to their ability to stimulate cell growth, prevent cell death, determine cell fate, and inhibit terminal differentiation in a variety of in vitro culture systems. We have used in situ hybridization to localize fibroblast growth factor-4 (FGF-4, also termed HST and K-FGF) gene expression in 7.5 to 16.5 day gestation mouse embryos. Seven discrete sites of gene expression were detected: (1) primitive streak (E7.5-8.5); (2) paraxial presomitic mesoderm in the trunk (E7.5-11.5); (3) primitive neuroectoderm (E8.0-8.5); (4) pharyngeal pouch endoderm (E8.5-9.5); (5) branchial arch ectoderm (E8.5-9.5); (6) limb apical ectoderm (E10.5-12.5), and (7) skeletal myoblast groups (E9.5-13.5). FGF-4 gene expression is spatially restricted within many of these sites. The profile of FGF-4 gene expression among skeletal muscle groups is overlapping, but distinct, from that of FGF-5, thereby revealing myoblast heterogeneity at the molecular level and suggesting distinct roles for multiple FGFs in muscle development.

Animals↗
PubMed1993

Differential, temporal and spatial expression of genes involved in storage oil and oleosin accumulation in developing rapeseed embryos: implications for the role of oleosins and the mechanisms of oil-body formation.

The temporal and spatial expression of oleosin and delta 9-stearoyl-ACP desaturase genes and their products has been examined in developing embryos of rapeseed, Brassica napus L. var. Topas. Expression of oleosin and stearate desaturase genes was measured by in situ hybridisation at five different stages of development ranging from the torpedo stage to a mature-desiccating embryo. The temporal pattern of gene expression varied dramatically between the two classes of gene. Stearate desaturase gene expression was relatively high, even at the torpedo stage, whereas oleosin gene expression was barely detectable at this stage. By the stage of maximum embryo fresh weight, stearate desaturase gene expression had declined considerably while oleosin gene expression was at its height. In contrast to their differential temporal expression, the in situ labelling of both classes of embryo-specific gene showed similar, relatively uniform patterns of spatial expression throughout the embryo sections. Immunogold labelling of ultra-thin sections from radicle tissue with anti-oleosin antibodies showed similar patterns to sections from cotyledon tissue. However, whereas at least three oleosin isoforms were detectable on western blots of homogenates from cotyledons, only one isoform was found in radicles. This suggests that some of the oleosin isoforms may be expressed differentially in the various types of embryo tissue. The differential timing of stearate desaturase and oleosin gene expression was mirrored by similar differences in the timing of the accumulation of their ultimate products, i.e. storage oil and oleosin proteins.(ABSTRACT TRUNCATED AT 250 WORDS)

Brassica↗
PubMed2006

Memantine protects against LPS-induced neuroinflammation, restores behaviorally-induced gene expression and spatial learning in the rat.

Neuroinflammation is reliably associated with the pathogenesis of a number of neurodegenerative diseases, and can be detected by the presence of activated microglia. Neuroinflammation can be induced by chronic lipopolysaccharide (LPS) infusion into the 4th ventricle of the rat resulting in region-selective microglia activation and impaired hippocampal-dependent memory. Furthermore, this treatment results in altered behaviorally-induced expression of the immediate early gene Arc, indicating altered network activity. LPS is known to activate microglia directly, leading to increased glutamate release, and in enhanced N-methyl-d-aspartate (NMDA) -dependent signaling. Taken together, the foregoing suggests that decreasing NMDA receptor activation during early stages of chronic neuroinflammation should reduce a) microglia activation, b) overexpression of Arc, and c) spatial memory deficits. Memantine, a low to moderate affinity open channel uncompetitive NMDA receptor antagonist, at low doses was used here to test these hypotheses. Rats were chronically infused into the 4th ventricle for 28 days with LPS alone, vehicle alone (via osmotic minipump) or LPS and memantine (10 mg/kg/day memantine s.c.). The results reported here demonstrate that memantine reduces OX6-immunolabeling for activated microglia, spares resident microglia, returns Arc (activity-regulated cytoskeletal associated protein, protein) -expressing neuronal populations to control levels (as revealed by Arc immunolabeling and fluorescence in situ hybridization), and ameliorates the spatial memory impairments produced by LPS alone. These data indicate that memantine therapy at low doses, recreating plasma levels similar to those of therapeutic doses in human, acts in part through its ability to reduce the effects of neuroinflammation, resulting in normal gene expression patterns and spatial learning. Combined, these findings suggest that low, therapeutically relevant doses of memantine delivered early in the development of neuroinflammation-influenced diseases may confer neural and cognitive protection.

Animals↗
PubMed2026

GenOT: generative optimal transport enables spatiotemporal interpolation and generation in cross-platform spatial transcriptomics.

Spatial transcriptomics technologies have revolutionized the analysis of spatial gene expression, yet integrating spatial information and generating data across heterogeneous samples remain challenging. We present GenOT, a generative framework combining multi-scale graph self-supervised contrastive learning with optimal transport barycenter theory for efficient cross-slice and cross-platform spatiotemporal interpolation. The core innovation of GenOT lies in introducing an optimal transport barycenter-based interpolation algorithm, which mathematically models spatial distribution differences across heterogeneous samples to reconstruct spatiotemporal gene expression dynamics. Extensive evaluations demonstrate that GenOT consistently outperforms existing approaches in spatial domain identification, cross-platform interpolation, and developmental trajectory reconstruction.

Spatial Transcriptomics↗
PubMed2006

Experience-dependent regulation of zif268 gene expression and spatial learning.

Environmental enrichment (EE) is known to enhance the cognitive ability of rodents. To translate EE to the human condition, it is important to understand the parameters of its efficacy. In this study, we examine if the cognitive enhancement associated with EE is permanent and whether a developmental window exists for its efficacy. Rats were housed in continuous isolation (ISO), continuous enrichment (EE), enrichment from postnatal day (PN) 21-50, and then isolation from PN50-79 (PM), or isolation from PN21-50 and then enriched from PN50-79 (CW). Spatial learning ability and basal expression of the immediate-early genes zif268 and Arc as well as the NR1 subunit of the NMDA receptor were assessed. Rats housed in an enriched environment at the time of testing (EE and CW) performed significantly better in the spatial learning task than rats housed in an isolated environment at the time of testing (ISO and PM). Enhanced performance in the spatial learning task was associated with a higher expression of zif268 only in the CA3/CA4 region of the hippocampus. Our study further defines parameters that make environmental enrichment effective in enhancing learning performance and the findings may be helpful in the translation of this intervention to the human condition.

Animals↗
PubMed2003

From flour to flower: how Polycomb group proteins influence multiple aspects of plant development.

Cell identity and differentiation are determined by patterns of regulatory gene expression. Spatially and temporally regulated homeotic gene expression defines segment identities along the anterior-posterior axis of animal embryos. Polycomb group (PcG) proteins form a cellular memory system that maintains the repressed state of homeotic gene expression. Conserved PcG proteins control multiple aspects of Arabidopsis development and maintain homeotic gene repression. In animals, PcG proteins repress their target genes by modifying histone tails through deacetylation and methylation, generating a PcG-specific histone code that recruits other chromatin remodeling proteins to establish a stable, heritable mechanism of epigenetic expression control. Plant PcG proteins might function through a similar biochemical mechanism owing to their conserved structural and functional relationship to animal PcG proteins.

Arabidopsis↗
PubMed2005

Complex networks approach to gene expression driven phenotype imaging.

MOTIVATION: The need is to visualize and quantify gene expression spatial patterns. Because of their generality for representation of interaction among several elements, complex networks are used to measure the spatial interactions and adjacencies defined by gene expression patterns. RESULTS: Enhanced visualization of spatial interactions between elements where genes are expressed is possible, allowing the identification of structures which would go unnoticed by using conventional imaging. The quantification of the expression intensity in terms of the node degree and clustering coefficient allows the identification of different types of interactions, yielding insights about cell signaling and differentiation, and providing the basis for comparison and discrimination of the patterns along the developmental stages. AVAILABILITY: Supplementary Material, including visualizations as well as the basic routines for translating gene expression images into complex networks and obtaining node degree and clustering coefficient measurements, are provided. CONTACT: luciano@if.sc.usp.br; diambra@univap.br.

Algorithms↗
PubMed1993

The human sucrase-isomaltase gene directs complex patterns of gene expression in transgenic mice.

Sucrase-isomaltase (SI) is an enterocyte-specific gene that is expressed in complex developmental and spatial patterns. In this study, we examine the ability of regulatory elements within the human SI (hSI) gene to direct appropriate cell lineage and spatial patterns of expression in transgenic mice. Transgenic mouse lines were established using a construct containing bases -3424 to +54 of the hSI gene linked to the human growth hormone (hGH) structural gene. In each transgenic line, hGH mRNA and protein were expressed only in the small intestine and colon. In contrast to the endogenous mouse SI (mSI) gene, which was expressed along the entire length of the small intestine, hGH mRNA expression was predominantly found in the distal jejunum and ileum, with very low levels in more proximal portions of the small intestine. However, the pattern of transgene expression along the small intestinal crypt-villus axis was identical to the pattern of the endogenous mSI gene. These results suggest that regulatory elements necessary for intestine-specific transcription and differential expression along the intestinal crypt-villus axis are included in the 5'-flanking region of the hSI gene. Furthermore, these data suggest that different DNA regulatory regions regulate transcription along the horizontal intestinal axis. In the colon, there was aberrant expression of hGH in a subpopulation of enteroendocrine cells that contained peptide tyrosine tyrosine (PYY). This suggests that there are DNA regulatory elements, missing in the transgene construct, which normally suppress expression of the endogenous mSI gene in these cells. Taken together, these findings define the SI gene as a useful model for studies of differentiation, cell lineage determination, and mechanisms of complex spatial gene expression in the intestine.

Animals↗
PubMed2000

MAP kinase signaling induces nuclear reorganization in budding yeast.

BACKGROUND: During the mating pheromone response in budding yeast, activation of a mitogen-activated protein kinase (MAP kinase) cascade results in well-characterized changes in cytoskeletal organization and gene expression. Spatial reorganization of genes within the nucleus has been documented during cell-type differentiation in mammalian cells, but no information was previously available on the morphology of the yeast nucleus during the major transcriptional reprogramming that accompanies zygote formation. RESULTS: We find that in response to mating pheromone, budding yeast nuclei assume an unusual dumbbell shape, reflecting a spatial separation of chromosomal and nucleolar domains. Within the chromosomal domain, telomeric foci persist and maintain their associated complement of Sir proteins. The nucleolus, on the other hand, assumes a novel cup-shaped morphology and a position distal to the mating projection tip. Although microtubules are required for this orientation with respect to the projection tip, neither microtubules nor actin polymerization are necessary for the observed changes in nuclear shape. We find that activation of the pheromone-response MAP kinase pathway by ectopic expression of STE4 or STE11 leads to identical nuclear and nucleolar reorganization in the absence of pheromone. Mutation of downstream effector MAP kinases Fus3p and Kss1p, or of the transcriptional regulator Ste12p, blocks nuclear shape changes, whereas overexpression of Ste12p promotes dumbbell-shaped nuclei in the absence of pheromone. CONCLUSIONS: Nuclear remodeling occurs when the MAP kinase cascade is activated by yeast pheromone, but it is independent of the cytoskeletal reorganization regulated by the same signaling pathway. Activation of the Ste12p transcription factor is necessary, and may be sufficient, for the changes in nuclear structure that coincide with developmentally significant changes in gene expression.

Actins↗
PubMed1990

Distribution of type I and type II collagen gene expression during the development of human long bones.

The temporal and spatial gene expression of collagen type I and type II during the development of the human long bones was studied by the technique of in situ hybridization covering the period from the cartilagenous bone anlage to the formation of a regular growth plate in the newborn. Analysis of the early stages around the seventh week of gestation revealed for type II collagen a strong hybridization signal limited to the chondrogenic tissue. The surrounding connective tissue and the perichondrium showed weak type I collagen expression, while the zones of desmal ossification like the clavicle gave a strong signal. Beginning with the eighth week of gestation, type I collagen mRNA was detectable in newly formed osteoblasts at the diaphysis and appeared along with the formation bone marrow, in the areas of enchondral ossification. Parallel to the development of the different zones of cartilage differentiation, a specific pattern of type II expression could be observed: type II was mainly found in the chondrocytes of the hypertrophic zone and to a lesser degree in the zone of proliferation, while the resting zone and the zone of provisional calcification showed little activity. This segregation of type II expression was most pronounced in the early stages of cartilage calcification and in the growth plate of the newborn.

Bone Development↗
PubMed2006

cis-regulatory processing of Notch signaling input to the sea urchin glial cells missing gene during mesoderm specification.

The glial cells missing regulatory gene of Strongylocentrotus purpuratus (spgcm) was proposed earlier to be the genomic target of Delta/Notch (D/N) signaling required for specification of the mesodermal precursors of pigment cells. Here, we show that microinjection of a spgcm antisense morpholino oligonucleotide results in larvae without pigment cells. Microinjection of an mRNA encoding a dominant negative form of Suppressor of Hairless (dn-Su(H)) results in reduced levels of spgcm mRNA, disruption of mesodermal founder cell specification and failure to produce pigment cells. These results confirm that this gene is required for pigment cell specification. Three cis-regulatory modules of the spgcm gene were identified, which when incorporated in a GFP expression construct recapitulate the early expression pattern of this gene. Spatial expression of this GFP expression construct is severely disrupted by co-expression of dn-Su(H) mRNA, confirming that spgcm is a direct target of canonical N signaling mediated through Su(H) inputs. cis-perturbation analysis by mutation of consensus Su(H) sites identified a conserved motif paired-site and a lone site in the middle module that function both to drive expression in SMC precursors which receive the Delta signal and to repress expression in ectopic locations which lack this signal. While these Su(H) target sites provide the cis-regulatory architecture with the core of an N signaling transcriptional response switch, both the on and off outputs from this module require additional inputs.

Animals↗
PubMed1992

Spatial expression of genes encoding c-kit receptors and their ligands in mouse cerebellum as revealed by in situ hybridization.

Expression of mRNA for c-kit receptors and their ligands was examined in the cerebellum of mice by in situ hybridization technique. The c-kit receptors were expressed in the molecular layer of the cerebellum and the ligands for the c-kit receptors were detected at the boundary of molecular and granular layers. The expression of the c-kit ligands was not detectable in the cerebellum of lurcher (Lc/+) mutant mice that lack Purkinje cells, indicating the cells expressing the c-kit ligands were Purkinje cells. The cells expressing c-kit receptors decreased but were present in the cerebellum of Lc/+ mice. The c-kit mRNA-positive cells appeared to represent basket cells and stellate cells from their appearance and location. Since neurons in the molecular layer construct suppressive neurojunctions with Purkinje cells, the present result suggests that c-kit receptors and their ligands may play an important role for the construction of their junctions.

Animals↗
PubMed1991

Temporal and spatial expression of genes for cartilage extracellular matrix proteins during avian mandibular arch development.

We have examined the temporal expression of genes for extracellular matrix proteins (type I collagen, type II collagen, and the cartilage specific proteoglycan core protein) during the development of the avian mandibular arch. We detected low levels of type II collagen mRNA in the mandibular arch as early as stage 15. Type II collagen mRNA remained low but increased slightly as development progressed from stage 15 to stage 25. More dramatic increases occurred after stage 25 coincident with overt chondrogenesis. In contrast, mRNA for the core protein of cartilage specific proteoglycan was not detected prior to the onset of chondrogenesis, appeared at stage 25, and increased thereafter. Type I collagen mRNA was also present as early as stage 15 and dramatically increased after stage 28/29, coincident with initiation of osteogenesis. Using in situ hybridization, we found that type II collagen mRNA became detectable in the center of the mandible around stage 24/25 coincident with the initiation of chondrogenesis. At later stages (26-32) type II collagen mRNA was localized in the cartilaginous rudiment. The pattern of hybridization observed with the proteoglycan core protein probe at later stages of development was essentially identical to that observed with the type II collagen probe. In contrast, the probe for the alpha 1 (I) collagen mRNA was localized over the perichondrium, over differentiated bone, and in areas within the mandibular arch where bone formation had been initiated.

Animals↗
PubMed2005

Changes in the spatial expression of genes with aging in the mouse RPE/choroid.

PURPOSE: We recently used microarray and reverse transcriptase PCR (RT-PCR) analysis to show an upregulation of cathepsin S (CatS) and glutathione peroxidase 3 (GPX3) in the aging mouse RPE/choroid. To evaluate the mRNA distribution and levels in the RPE and choroid, in situ hybridizations were performed. METHODS: Eye sections from 2-month-old and 24-month-old C57BL/6 mice were probed for CatS or GPX3 mRNA by in situ hybridization. The ratio of mRNA labeled cells to total cells counted per section was compared between the two age groups for the RPE and choroid separately. RESULTS: The CatS labeled RPE cell ratio increased significantly with age. The GPX3 labeled RPE cell ratio did not increase with age. CONCLUSIONS: The increases in mRNA levels for CatS and GPX3 found in the aging C57BL/6 RPE/choroid appear to represent an increase in both the numbers of cells expressing these messages and an increase in the level of expression in individual cells.

Aging↗
PubMed1990

Detection of spatially regulated gene expression by hybridization histochemistry.

Steady state measurements of kidney androgen-regulated protein (KAP) mRNA suggested that KAP gene expression was unusually sensitive to low hormone-receptor levels. Two of the criteria used to reach this conclusion involved relative insensitivity to treatment with a competitive antiandrogen and a partial androgen response of the gene in Tfm/Y androgen receptor (AR) deficient mice. These data may indicate the ability of the KAP gene to respond to an extremely low level of androgen-AR complex or that the effect of androgens is, at least in part, indirect. Hybridization in situ revealed that KAP mRNA expression was restricted to proximal tubule epithelial cells in the juxtamedullary region of castrated animals rather than throughout the cortex as in intact males. Examination of sections of kidneys from Tfm/Y mice before and after testosterone (T) treatment revealed that only the juxtamedullary tubules expressed KAP mRNA and that T increased the level of KAP mRNA in these cells. Treatment of Tfm/Y animals with other steroids showed that beta-estradiol treatment mimicked the effect of T while dihydrotestosterone (DHT) had no effect. The facts that DHT and T both stimulate cortical expression of KAP mRNA in normal animals but DHT has no effect on the juxtamedullary cells in the Tfm/Y variant may indicate that the action of T is due to an estrogenic metabolite. Castrated, hypophysectomized males exhibited no KAP gene expression, while in the presence of T, expression was observed throughout the cortex as in intact males. These results clearly indicate the involvement of pituitary hormones in KAP gene expression in the juxtamedullary tubules. These studies have shown that the regulation of KAP gene expression in the mouse kidney is much more complex than originally believed. Future studies will further investigate the roles of estrogen and specific pituitary hormones in KAP gene expression.

Androgen-Insensitivity Syndrome↗
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↗
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↗