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At least 217 records · Page 12Linked to original sources
PubMed1997

Spatial features of calcium-regulated gene expression.

A key characteristic of an animal's nervous system is that it can respond to brief environmental stimuli with lasting changes in its structure and function. These changes are triggered by specific patterns of neuronal electrical activity and are manifested as changes in the strength and patterns of synaptic connectivity between activated neurons. The biochemical mechanisms that control these changes are unclear, but cytoplasmic rises in Ca2+ levels may play a critical role, especially in regulating neuronal gene expression for making activity-induced synaptic changes permanent. Recently, two reports have explored the spatial features by which activity-induced rises in Ca2+ levels activate transcription factors and gene expression. The reports suggest that Ca2+ influx acts both locally at the synapse and distantly within the nucleus to regulate transcription factors and gene expression. The results also show that regulatory elements within genes can respond differentially, depending on spatial differences in intracellular Ca2+ rises. These reports suggest new spatial mechanisms by which Ca(2+)-dependent gene expression could contribute to activity-dependent synaptic changes.

Animals↗
PubMed2003

Gene expression in spider appendages reveals reversal of exd/hth spatial specificity, altered leg gap gene dynamics, and suggests divergent distal morphogen signaling.

Leg development in Drosophila has been studied in much detail. However, Drosophila limbs form in the larva as imaginal discs and not during embryogenesis as in most other arthropods. Here, we analyze appendage genes in the spider Cupiennius salei and the beetle Tribolium castaneum. Differences in decapentaplegic (dpp) expression suggest a different mode of distal morphogen signaling suitable for the specific geometry of growing limb buds. Also, expression of the proximal genes homothorax (hth) and extradenticle (exd) is significantly altered: in the spider, exd is restricted to the proximal leg and hth expression extends distally, while in insects, exd is expressed in the entire leg and hth is restricted to proximal parts. This reversal of spatial specificity demonstrates an evolutionary shift, which is nevertheless compatible with a conserved role of this gene pair as instructor of proximal fate. Different expression dynamics of dachshund and Distal-less point to modifications in the regulation of the leg gap gene system. We comment on the significance of this finding for attempts to homologize leg segments in different arthropod classes. Comparison of the expression profiles of H15 and optomotor-blind to the Drosophila patterns suggests modifications also in the dorsal-ventral patterning system of the legs. Together, our results suggest alterations in many components of the leg developmental system, namely proximal-distal and dorsal-ventral patterning, and leg segmentation. Thus, the leg developmental system exhibits a propensity to evolutionary change, which probably forms the basis for the impressive diversity of arthropod leg morphologies.

Amino Acid Sequence↗
PubMed1988

Interaction of spatially separated protein-DNA complexes for control of gene expression: operator conversions.

Two operators, spatially separated from each other and from the promoters, repress the gal operon when bound to Gal repressor. Conversion of either gal operator to a lac operator results in derepression, although both Gal and Lac repressors are present, suggesting that mere occupation of operator sites is not sufficient to cause repression. Conversion of both operators to lac operators restores normal repression in the presence of Lac repressor protein. We propose that normal repression requires interaction between operator-bound like repressor molecules; this generates a DNA loop, which is part of a higher order structure. RNA polymerase and cyclic AMP receptor protein are present in this complex but unable to initiate transcription because of the higher order structure. Such higher order DNA-multiprotein complexes could occur in a variety of genetic regulatory systems that are controlled from distal sites by regulatory proteins.

Base Sequence↗
PubMed2004

Temporal and spatial expression patterns of canonical clock genes and clock-controlled genes in the suprachiasmatic nucleus.

In mammals, the suprachiasmatic nuclei (SCN) of the hypothalamus control endogenous circadian rhythms and entrainment to the environment. A core SCN region of calbindin (CalB)-containing cells is retinorecipient and the cells therein lack rhythmic expression of clock genes and electrical activity. The core is surrounded by a 'shell' of rhythmic oscillator cells. In the present experiments, we studied the spatial arrangement of oscillator cells by examining the spatial and temporal patterns of expression of the canonical clock genes Per1, Per2 and vasopressin mRNA, a clock-controlled gene. Surprisingly, in the SCN shell, the dorsomedial cells were the first to rhythmically express both Per1 and VP mRNA, with gene expression then spreading very slowly through much of the nucleus for the next 12 h then receding to baseline levels. Following a light pulse, Per expression increased after 1 h in the core SCN and after 1.5 h in the shell. Although expression in the shell occurred earlier in light-pulsed animals than in those housed in constant darkness, it still followed the same spatial and temporal expression pattern as was observed in constant darkness. The results suggest that not only is the SCN organized into light-responsive and rhythmic regions but also that the rhythmic region of the SCN itself has an ordered arrangement of SCN oscillator cells.

Animals↗
PubMed2003

Identification of spatial and temporal cues that regulate postembryonic expression of axon maintenance factors in the C. elegans ventral nerve cord.

Patterns of gene expression are under precise spatial and temporal control. A particularly striking example is represented by several members of the zig gene family, which code for secreted immunoglobulin domain proteins required for maintaining ventral nerve cord organization in Caenorhabditis elegans. These genes are coordinately expressed in a single interneuron in the ventral nerve cord, known as PVT. Their expression is initiated at a precise postembryonic stage, long after PVT has been generated in mid-embryogenesis. We define spatial and temporal cues that are required for the precise regulation of zig gene expression. We find that two LIM homeobox genes, the Lhx3-class gene ceh-14 and the Lmx-class gene lim-6 are coordinately required for zig gene expression in PVT. Temporal control of zig gene expression is conferred by the heterochronic gene lin-14, a nuclear factor previously implicated in developmental timing in various contexts. Loss of the lim-6 and ceh-14 transcription factors and the developmental timer lin-14 cause not only a loss of zig gene expression but also lead to defects in the maintenance of ventral nerve cord architecture. Overriding the normal spatiotemporal control of zig gene expression through expression of one of the zig genes under control of heterologous promoters also causes axon patterning defects in the ventral nerve cord. Our findings illustrate the importance of spatial and temporal control of gene expression in the nervous system and, furthermore, implicate heterochronic genes in postmitotic neural patterning events.

Animals↗
PubMed2004

Regionalisation of early head ectoderm is regulated by endoderm and prepatterns the orofacial epithelium.

The oral epithelium becomes regionalised proximodistally early in development, and this is reflected by the spatial expression of signalling molecules such as Fgf8 and Bmp4. This regionalisation is responsible for regulating the spatial expression of genes in the underlying mesenchyme. These genes are required for the spatial patterning of bone, cartilage orofacial development and, in mammals, teeth. The mechanism and timing of this important regionalisation during head epithelium development are not known. Using lipophilic dyes to fate map the oral epithelium in chick embryos, we show that the cells that will occupy the epithelium of the distal and the proximal mandible primordium already occupy different spatial locations in the developing head ectoderm prior to the formation of the first pharyngeal arch and neural crest migration. Moreover, the ectoderm cells fated to become proximal oral epithelium express Fgf8 and this expression requires the presence of endoderm. Thus, the first fundamental patterning process in jaw morphogenesis is controlled by the early separation of specific areas of ectoderm that are regulated by ectoderm-endoderm interactions, and does not involve neural crest cells.

Animals↗
PubMed1998

A transcription activation system for regulated gene expression in transgenic plants.

A widely applicable promoter system is described that allows a gene of interest to be activated in specific plant tissues after a cross between defined transgenic lines. The promoter, pOp, consists of lac operators cloned upstream of a minimal promoter. No expression was detected from this promoter when placed upstream of a beta-glucuronidase (GUS) reporter gene in transgenic plants. Transcription from the promoter was activated by crossing reporter plants with activator lines that expressed a chimeric transcription factor, LhG4. This factor comprised transcription-activation domain-II from Gal4 of Saccharomyces cerevisiae fused to a mutant lac-repressor that binds its operator with increased affinity. When LhG4 was expressed from the CaMV 35S promoter, the spatial and quantitative expression characteristics of the 35S promoter were exhibited by the GUS reporter. The LhG4/pOp system may be used to study toxic or deleterious gene products, to coordinate the expression of multiple gene products, to restrict transgene phenotypes to the F1 generation, and to generate hybrid seed. The LhG4 system offers spatially regulated gene expression in the tissues of whole plants growing under normal conditions without the need for external intervention. It complements inducible expression systems that offer temporal control of gene expression in tissues that can be treated with inducing chemicals.

Bacterial Proteins↗
PubMed2025

Spatial Genomic Approaches to Investigate HOX Genes in Mouse Brain Tissues.

Spatial transcriptomic tools are an upcoming and powerful way to investigate targeted gene expression patterns within tissues. These tools offer the unique advantage of visualizing and understanding gene expression while preserving tissue integrity, thereby maintaining the spatial context of genes. Curio is a robust spatial transcriptomic tool that facilitates high throughput comprehensive spatial gene expression analysis across the entir e transcriptome with high efficiency. Here, we present a bioinformatics protocol for performing whole transcriptome gene expression analysis of mouse brain tissue using Curio. Specifically, we demonstrate using computational techniques to visualize expression patterns of various HOX genes in the mouse brain.

Animals↗
PubMed2026

jsPCA: fast, scalable, and interpretable identification of spatial domains and variable genes across multi-slice and multi-sample spatial transcriptomics data.

MOTIVATION: Spatial transcriptomics technologies record genome-wide measurements of gene expression with high spatial resolution. These technologies generate large and high-dimensional datasets requiring efficient automated methods for their analysis. We introduce joint spatial PCA (jsPCA), a novel, fast, scalable and interpretable method for the automatic identification of spatial domains and variable genes in multi-slice and multi-sample spatial transcriptomics data. RESULTS: jsPCA relies on a simple mathematical formulation of a spatial covariance defined as the product of the gene expression covariance with the spatial autocorrelation. The principal components of this spatial covariance yield a biologically meaningful low-dimensional representation. From this representation, spatial domains are derived by simple clustering and spatially variable genes are identified directly from the principal component coefficients. A joint representation of multiple slices and samples without spatial alignment is obtained by computing common principal components via joint diagonalization. By leveraging data sparsity and non-convex manifold optimization, jsPCA leads to computing time in the order of seconds to minutes, substantially outperforming state-of-the-art approaches. We benchmarked jsPCA against 10 state-of-the-art methods on two reference databases. Our approach demonstrated excellent performance, comparable or better than state-of-the-art methods, while being much faster, interpretable, and scalable to very large datasets.

Journal Article↗
PubMed2001

Hemodynamics and the focal origin of atherosclerosis: a spatial approach to endothelial structure, gene expression, and function.

Atherosclerosis originates at predictable focal and regional sites that are associated with complex flow disturbances and flow separations in large arteries. The spatial relationships associated with hemodynamic shear stress forces acting on the endothelial monolayer are considered in experiments that model regions susceptible to atherosclerosis (flow disturbance) and resistant to atherosclerosis (undisturbed flow). Flow disturbance in vitro induced differential expression at the single gene level as illustrated for the intercellular communication gene and protein, connexin 43. Transcription profiles of individual endothelial cells isolated from both disturbed and undisturbed flow regions exhibited more expression heterogeneity in disturbed than in undisturbed flow. We propose that within highly heterogeneous populations of endothelial cells located in disturbed flow regions, proatherosclerotic gene expression may occur within the range of expression profiles induced by the local hemodynamics. These may be sites of initiation of focal atherosclerosis. Mechanisms are proposed to account for heterogeneous endothelial responses to shear stress by reference to the decentralized model of endothelial mechanotransduction. Length scales ranging from centimeters to nanometers are useful in describing regional, single cell, and intracellular mechanotransduction mechanisms.

Arteriosclerosis↗
PubMedDate not supplied

Spatial expression of a DNA repair gene, N-methylpurine-DNA glycosylase (MPG) during development in mice.

BACKGROUND: DNA repair is a crucial phenomenon that maintains the chromosome integrity of genome which are continuously damaged by endogenous and exogenous alkylating agents. If the damaged DNA is not repaired, it may lead to mutation, chromosomal aberration, aging and cancer. N-methylpurine-DNA glycosylase (MPG), a ubiquitous DNA repair enzyme, removes N-methylpurine and other damaged purines in DNA. MATERIALS AND METHODS: MPG mRNA expression was revealed at various stages of mouse development from day 7.5 p.c. (post coitum) embryo to day 400 mature adult by Northern blot hybridization or RT-PCR. RESULTS: MPG transcripts were abundant in the mouse embryo during pregnancy and in adult testis and ovary. The MPG mRNA level in the testis was low in 1-week-old mice, but the level showed its maximum among the organs tested in 4-week-old young adults. In placenta, the level of MPG mRNA continuously decreased from day 7.5 p.c. to day 17.5 p.c. CONCLUSIONS: The spatial expression of MPG gene is highly regulated. Transcription of MPG is maximum in rapidly dividing and growing tissues during development. These data suggest that an elevated rate of MPG transcription is required for DNA replication.

Animals↗
PubMed1995

Spatial regulation of SpMTA metallothionein gene expression in sea urchin embryos by a regulatory cassette in intron 1.

The SpMTA metallothionein (MT) gene of the sea urchin Strongylocentrotus purpuratus is restricted in its expression to the aboral ectoderm in gastrulae and pluteus larvae. The proximal 1.6 kb of the 5'-flanking region together with the 1.12-kb first intron of the SpMTA gene are sufficient for its correct cell-type specific expression in transgenic embryos. This restricted spatial expression is largely eliminated by deletion of an interior 405-bp region in the intron. Within this region is a 295-bp, genomically repetitive, transposon-like segment (Nemer et al., 1993), containing several sequence motifs highly homologous to posited regulatory elements in the promoters of other genes (Thiebaud et al., 1990). The P3A and P5 sites in this apparent regulatory cassette were shown through competition to bind with relatively high affinities the same nuclear factors, bound by their counterpart sites in the CyIIIa actin promoter.

Actins↗
PubMed1990

Positional cues and differential gene expression in somatic embryos of higher plants.

Much of the organization of higher vascular plants is determined during the formation of the embryo. In addition to the zygotic embryo which results from sexual fertilization in the ovule, many plants are capable of producing embryos from somatic cells. Of particular interest to plant developmental biologists is the phenomenon of somatic embryogenesis in cultures of the domesticated carrot which, because of its tractable nature in experimental manipulations, is presently regarded as a suitable model for studying pattern formation in plants. This short review considers the state of our knowledge concerning the origin and perception of positional information in plant embryos, and the temporal and spatial expression of genes. The available data provide a number of promising leads for cell-cell interactions in embryos, and there are some clear indications that the spatial distribution of certain gene products is correlated with changes in morphology. However, there is, as yet, insufficient evidence with which to forge a link between positional cues and the expression of genes which influence developmental transitions in embryos.

Cell Differentiation↗
PubMedDate not supplied

Spatial and temporal patterns of Krüppel gene expression in early Drosophila embryos.

The Krüppel (Kr) locus is a member of the 'gap' class of segmentation genes of Drosophila melanogaster. Mutations at the Kr locus cause the deletion of contiguous segments from the embryonic body pattern. We have elucidated the spatial and temporal characteristics of Kr gene expression during early embryo development, the localization of cytoplasmic Kr+ activity and its spatial requirement for normal segmentation.

Animals↗
PubMed1994

Temporal and spatial expression of lipospermine-compacted genes transferred into chick embryos in vivo.

We have optimized a lipospermine-based transfection method for introducing genes into intact vertebrate embryos in vivo. The method employs small amounts of the cationic lipid Transfectam (DOGS), in a concentrated (40 mM) ethanolic solution, to compact and to transfer exogenous genes into chick embryos during the early stages of development (< 36 h of incubation). Plasmid vectors containing the reporter gene luciferase were used to follow the time course of expression. Luciferase activity was detected as early as 12 h post-transfection and was highest at this time. Enzyme activity then decreased over the next two days and was usually undetectable by 72-h post-transfection. To follow the spatial expression of the exogenous genes, a Rous sarcoma virus (RSV)-beta-galactosidase vector was used. When the transfection complex was applied externally around the developing embryo, the main site of expression was the cardiac tissue. Expression could be targeted to the nervous system by micro-injecting the DNA/DOGS (DNA/dioctadecylamidoglycylspermine) complex into the developing brain. The results show that reporter genes can be efficiently expressed in both the developing central nervous system and heart. This raises the possibility that lipospermines can be used to transfer functional genes into embryos during defined periods of development and also to deliver genes in other species and in other in vivo contexts.

Animals↗
PubMed2004

Genomic organization and regulation of the LeIMP-1 and LeIMP-2 genes encoding myo-inositol monophosphatase in tomato.

Myo-inositol (inositol) monophosphatase (IMP), an enzyme which catalyzes the synthesis of free inositol from various inositol monophosphates, is encoded by a small multigene family in many organisms. The tomato IMP gene family encodes three IMP isoforms with identical in vitro biochemical properties. To determine the role of each tomato LeIMP gene in plant growth, we isolated the genomic DNA copies of the LeIMP-1 and LeIMP-2 genes. The LeIMP-1 gene spans approximately 5.8 kb and consists of 12 exons, whereas the LeIMP-2 gene consists of an uninterrupted, single open reading frame (ORF). We have previously shown that steady-state levels of LeIMP-2 mRNA were very low in comparison to LeIMP-1 and LeIMP-3 mRNA levels. To determine whether LeIMP-2 gene expression was spatially restricted to a discreet domain within the plant we constructed transgenic plants containing an LeIMP-2 promoter::uidA gene fusion. Analysis of transgenic seedlings revealed that the LeIMP-2 promoter directed gene expression within epidermal and cortex cells of specific stem/leaf junctions in an abaxial-specific pattern and in the shoot apical meristem. Further, inositol, the product of IMP catalysis, and Li+, an inhibitor of IMP catalysis, decreased expression of the LeIMP-2 promoter as measured by a decrease in beta-glucuronidase activity after treatment.

Animals↗
PubMed1990

Spatial harmonics and pattern specification in early Drosophila development. Part I. Bifurcation sequences and gene expression.

Molecular probes have now provided an unprecedented wealth of detail revealing the changing spatial patterns of gene products in early Drosophila development. This is examined for dynamic properties which might provide insights into the underlying behaviour of the patterning process. What emerges is that transcripts and protein products of members of the major categories of zygotically active genes involved in segmentation pass through transient spatial patterns that are suggestive of harmonic sequences arising from spatial frequency-doubling bifurcations. That is to say, these patterns are typically periodic in space and show a doubling in the number of domains of spatial expression as development proceeds. One of these patterns reflects the primary functional role of the gene in the establishment of the spatial pattern. The different categories of segmentation gene pass through these transients at different rates, those with the longest functional wavelength progressing most slowly. Each gene in a category has its own unique phase relationship to other members, as well as particular variations on the harmonic sequence theme. The result is that the developing embryo experiences a spatial hierarchy of phase-shifted patterning influences that span the range from the whole embryo to single segments, providing progressively more spatial resolution in the patterning process. The characteristic transients and the dynamic relationships between genes of the different categories suggest that gene products expressed in longer-wavelength patterns act as bifurcation parameters on the dynamic system generating the next shorter wavelength category. Such parametric influences are known to result in frequency-doubling bifurcations in Turing reaction-diffusion systems. A general model is proposed of a hierarchically-nested set of quasi-autonomous dynamic systems involving gene activities that can generate the progressively finer spatial order that emerges during embryogenesis. This model has implications for the general stability properties of evolving epigenetic systems.

Animals↗
PubMed2003

Diploid-dependent regulation of gene expression: a genetic cause of abnormal development in fish haploid embryos.

A diploid-dependent regulatory mechanism of gene expression for spatial patterning of the eye in vertebrates has been determined by analyzing the phenotypes of haploid goldfish embryos. There are two gene loci in charge of eye spatial patterning during embryonic morphogenesis. The expressional probability for each copy of the two genes in a set of chromosomes is 50%. A pair of genes in two sets of homologous or heterologous chromosomes is 100% and essential for normal gene expression. The haploid condition itself would result in the obstruction of gene expression and abnormal development because the diploid-dependent regulatory apparatus will regulate gene expression in a haploid embryo according to the same rule as in the diploid embryo.

Animals↗