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Results for “spatial gene expression”

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At least 379 records · Page 21Linked to original sources
PubMed1990

Spatial expression of the Drosophila segment polarity gene armadillo is posttranscriptionally regulated by wingless.

armadillo (arm) is one of a group of Drosophila segment polarity genes that are required for normal patterning within the embryonic segment. Although arm RNA is uniformly distributed in embryos, arm protein accumulates at higher levels in regions that contain wingless, another segment polarity gene which encodes a secreted protein that regulates patterning via cell-cell communication. These local increases in arm protein require wingless activity, and mutations that alter wingless distribution produce corresponding changes in the arm protein pattern. These results suggest that wingless regulates accumulation of arm protein by a posttranscriptional mechanism. Two other segment polarity genes, porcupine and dishevelled, are required for this effect. We also show that arm protein is closely associated with the plasma membrane in virtually all cell types and often colocalizes with F-actin.

Animals↗
PubMed2006

Spatial and temporal expression of POF1B, a gene expressed in epithelia.

Mammalian epithelia possess specialized cellular components that provide an impermeable barrier between two different environments. In particular, in the skin, mitotically dividing cells undergo a programmed set of morphological and biochemical changes leading to the establishment of the epidermal permeability barrier (EPB) to prevent escape of moisture and entrance of toxic molecules. Many different skin proteins are involved in the process but not all have been identified. We report here the results of the expression studies of a novel gene, highly and specifically expressed in the granular layer of the epidermis and in the epithelia of the oro-pharyngeal and gastro-intestinal tracts. Our data show that during mouse development Pof1b expression is activated in the external layers of the epidermis just prior to formation of the EPB.

Animals↗
PubMed2002

Spatial and temporal 'knock down' of gene expression by electroporation of double-stranded RNA and morpholinos into early postimplantation mouse embryos.

Here we report the use of double-stranded RNA (dsRNA) and morpholino technologies to specifically 'knock down' gene expression in early postimplantation mouse embryos. Sequence specific interference mediated by either dsRNA or by morpholino has been a useful tool for studying gene function in several organisms. However, specifically for the dsRNA, doubts have been raised about whether it could successfully be applied on vertebrate embryos. We demonstrate that electroporation of dsRNA directed against Otx2 or Foxa2 into postimplantation mouse embryos results in specific knock down of the expression of the respective endogenous genes in a region- and germ-layer specific manner. We also show that electroporation of morpholino directed against Foxa2 into the node of mouse embryos leads to a specific down regulation of Foxa2 expression in the floor plate. Our results demonstrate for the first time that dsRNA and morpholino technologies can be successfully applied in early postimplantation mouse embryos to specifically knock down gene expression.

Animals↗
PubMed2003

Spatial and temporal expression patterns of selenoprotein genes during embryogenesis in zebrafish.

Selenium is important for embryogenesis in vertebrates but little is known about the expression patterns and biological functions of most selenoprotein genes. Taking advantage of the zebrafish model, systematic analysis of selenoprotein gene expression was performed by in situ hybridization on whole-mount embryos at different developmental stages. Twenty-one selenoprotein mRNAs were analyzed and all of them exhibited expression patterns restricted to specific tissues. Moreover, we demonstrated that highly similar selenoprotein paralogs were expressed within distinct territories. Therefore, tissue- and development-specific expression patterns provided new information for selenoproteins of unknown function.

Animals↗
PubMed2000

Detection of spatial localization of Hst-1/Fgf-4 gene expression in brain and testis from adult mice.

HST-1, a member of the fibroblast growth factor (FGF) family (FGF-4), has been shown to be a signaling molecule whose expression is essential for embryonic development. However, HST-1/FGF-4 expression has not been detected or reported in adult tissues so far analysed. To investigate whether there is a possible role of HST-1/FGF-4 in adult stage, we have carried out a highly sensitive RT-PCR analysis of Hst-1/Fgf-4 gene expression in adult mice tissues. Results show Hst-1/Fgf-4 gene expression in the nervous system, intestines, and testis of normal adult mice. In situ hybridization technique was used to localize Hst-1/Fgf-4 gene expression in the cerebellum and testis from 10-week-old mice. Cell type-specific gene expression was detected: Purkinje cells in the cerebellum and Sertoli cells in testis. These findings suggest that the Hst-1/Fgf-4 gene also plays an important role in adult tissues, and may offer insights into the biological significance of HST-1/FGF-4 in cerebellar and testicular functions.

3T3 Cells↗
PubMed1994

A cotyledon regulatory region is responsible for the different spatial expression patterns of Arabidopsis 2S albumin genes.

The 2S albumin genes of Arabidopsis thaliana are a model system to study gene expression during late embryogenesis. The at2S1 gene has previously been shown to be expressed essentially in the embryo axis, unlike at2S2, which is expressed throughout the embryo. Hybrid promoter constructs between at2S1 and at2S2 were introduced into Arabidopsis and used to identify a cotyledon regulatory region necessary for 2S albumin expression in palisade parenchyma and specific epidermal cells. Other promoter sequences flanking this tissue-specific promoter element were shown to control mRNA expression levels independently of the mRNA distribution throughout the embryos. Certain hybrid promoters resulted in the alteration of the time course of expression in cotyledons. Differential expression of 2S albumin genes is discussed in terms of layered cellular organization and mitotic activity throughout the embryo.

Albumins↗
PubMed2003

Temporal-spatial characterization of chicken clock genes: circadian expression in retina, pineal gland, and peripheral tissues.

The molecular core of the vertebrate circadian clock is a set of clock genes, whose products interact to control circadian changes in physiology. These clock genes are expressed in all tissues known to possess an endogenous self-sustaining clock, and many are also found in peripheral tissues. In the present study, the expression patterns of two clock genes, cBmal1 and cMOP4, were examined in the chicken, a useful model for analysis of the avian circadian system. In two tissues which contain endogenous clocks--the pineal gland and retina--circadian fluctuations of both cBmal1 and cMOP4 mRNAs were observed to be synchronous; highest levels occurred at Zeitgeber time 12. Expression of these genes is also rhythmic in several peripheral tissues; however, the phases of these rhythms differ from those in the pineal gland and retina: in the liver the peaks of cMOP4 and cBmal1 mRNAs are delayed 4-8 h and in the heart they are advanced by 4 h, relative to those in the pineal gland and retina. These results provide the first temporal characterization of cBmal1 and cMOP4 mRNAs in avian tissues: their presence in avian peripheral tissues indicates they may influence temporal features of daily rhythms in biochemical, physiological, and behavioral functions at these sites.

ARNTL Transcription Factors↗
PubMed2004

Unique and overlapping expression patterns among the Arabidopsis 1-amino-cyclopropane-1-carboxylate synthase gene family members.

1-Aminocyclopropane-1-carboxylate synthase (ACS) catalyzes the rate-limiting step in the ethylene biosynthetic pathway in plants. The Arabidopsis genome encodes nine ACS polypeptides that form eight functional (ACS2, ACS4-9, and ACS11) homodimers and one nonfunctional (ACS1) homodimer. Transgenic Arabidopsis lines were constructed expressing the beta-glucuronidase (GUS) and green fluorescence protein (GFP) reporter genes from the promoter of each of the gene family members to determine their patterns of expression during plant development. All genes, except ACS9, are expressed in 5-d-old etiolated or light-grown seedlings yielding distinct patterns of GUS staining. ACS9 expression is detected later in development. Unique and overlapping expression patterns were detected for all the family members in various organs of adult plants. ACS11 is uniquely expressed in the trichomes of sepals and ACS1 in the replum. Overlapping expression was observed in hypocotyl, roots, various parts of the flower (sepals, pedicle, style, etc.) and in the stigmatic and abscission zones of the silique. Exogenous indole-3-acetic acid (IAA) enhances the constitutive expression of ACS2, 4, 5, 6, 7, 8, and 11 in the root. Wounding of hypocotyl tissue inhibits the constitutive expression of ACS1 and ACS5 and induces the expression of ACS2, 4, 6, 7, 8, and 11. Inducers of ethylene production such as cold, heat, anaerobiosis, and Li(+) ions enhance or suppress the expression of various members of the gene family in the root of light-grown seedlings. Examination of GUS expression in transverse sections of cotyledons reveals that all ACS genes, except ACS9, are expressed in the epidermis cell layer, guard cells, and vascular tissue. Similar analysis with root tip tissue treated with IAA reveals unique and overlapping expression patterns in the various cell types of the lateral root cap, cell division, and cell expansion zones. IAA inducibility is gene-specific and cell type-dependent across the root tip zone. This limited comparative exploration of ACS gene family expression reveals constitutive spatial and temporal expression patterns of all gene family members throughout the growth period examined. The unique and overlapping gene activity pattern detected reveals a combinatorial code of spatio-temporal coexpression among the various gene family members during plant development. This raises the prospect that functional ACS heterodimers may be formed in planta.

Arabidopsis↗
PubMed1997

Light-Dependent Spatial and Temporal Expression of Pigment Regulatory Genes in Developing Maize Seeds.

Both light and developmental stimuli are directly involved in the regulation of plant gene expression. In maize, activation of the anthocyanin pathway represents an excellent model system for studying the interactions between an external factor, such as light, and internal factors that regulate plant and seed development. By analyzing in detail the aleurone and pericarp seed layers, different developmental windows for light have been found in the two tissues[mdash]the former in the advanced stages of development and the latter in the early stages of seed development. Transcriptional control of the structural genes involved in anthocyanin deposition within the pericarp is known to be exerted by the Sn and pl genes, whereas the aleurone is controlled by the R and C1 regulatory genes. By using in situ hybridization analysis, we detected tissue-specific expression of Sn and R in the seed layers, revealing a correlation between structural gene activation and anthocyanin accumulation. In addition, RNA gel blot analysis revealed that Sn expression is enhanced by light, whereas the R gene expression is not. However, the light-induced expression of the myb-type genes C1 and pl, detected by reverse transcriptase-polymerase chain reaction, was found to be the limiting factor for conferring the developmental competence of the pericarp and the aleurone layers to light responsiveness.

Journal Article↗
PubMed1991

Spatial control of gut-specific gene expression during Caenorhabditis elegans development.

The nematode Caenorhabditis elegans was transformed with constructs containing upstream deletions of the gut-specific ges-1 carboxylesterase gene. With particular deletions, ges-1 was expressed, not as normally in the gut, but rather in muscle cells of the pharynx (which belong to a sister lineage of the gut) or in body wall muscle and hypodermal cells (which belong to a cousin lineage of the gut). These observations suggest that gut-specific gene expression in C. elegans involves not only gut-specific activators but also multiple repressors that are present in particular nongut lineages.

Animals↗
PubMed2006

Spatial and temporal expression of Lactobacillus plantarum genes in the gastrointestinal tracts of mice.

Lactobacillus plantarum is a common inhabitant of mammalian gastrointestinal tracts, and L. plantarum strain WCFS1 is a human isolate with a known genome sequence. L. plantarum WCFS1 survives intestinal passage in an active form, and its transit time and transcriptional activities were monitored in 15 BALB/c mice at 2, 4, 6, 8, and 24 h after being fed a single intragastric dose of this organism. Enumeration of viable cells isolated from fecal material revealed that the majority of the L. plantarum inoculum transited the mouse intestine within 4 h after ingestion. Three mice were sacrificed at each time point, and total RNA was isolated from the mouse intestinal compartments (stomach through colon). Quantification of L. plantarum 16S rRNA by quantitative real-time reverse-transcription-PCR revealed that L. plantarum was present at elevated levels in the stomach and small intestine for at least 4 h following ingestion and for over 8 h in the cecum and colon. We also examined the expression of 9 L. plantarum housekeeping genes and 15 L. plantarum in vivo-inducible (ivi) genes previously identified by recombination-based in vivo expression technology to be induced in the mouse gastrointestinal tract. The relative expression levels of the ivi genes increased up to 350-fold in the mouse intestine compared to levels observed for L. plantarum WCFS1 cells grown in a rich laboratory medium. Moreover, several genes displayed intestinal compartment-specific (small intestine versus colon) activities. These results confirm that L. plantarum displays specific and differential responses at various sites along the mammalian intestine.

Animals↗
PubMed2000

Spatial and temporal variations in chitinolytic gene expression and bacterial biomass production during chitin degradation.

Growth of the chitin-degrading marine bacterium S91 on solid surfaces under oligotrophic conditions was accompanied by the displacement of a large fraction of the surface-derived bacterial production into the flowing bulk aqueous phase, irrespective of the value of the surface as a nutrient source. Over a 200-h period of surface colonization, 97 and 75% of the bacterial biomass generated on biodegradable chitin and a nonnutritional silicon surface, respectively, detached to become part of the free-living population in the bulk aqueous phase. Specific surface-associated growth rates that included the cells that subsequently detached from the substrata varied depending on the nutritional value of the substratum and during the period of surface colonization. Specific growth rates of 3.79 and 2.83 day(-1) were obtained when cells first began to proliferate on a pure chitin film and a silicon surface, respectively. Later, when cell densities on the surface and detached cells as CFU in the bulk aqueous phase achieved a quasi-steady state, specific growth rates decreased to 1.08 and 0.79 day(-1) on the chitin and silicon surfaces, respectively. Virtually all of the cells that detached from either the chitin or the silicon surfaces and the majority of cells associated with the chitin surface over the 200-h period of surface colonization displayed no detectable expression of the chitin-degrading genes chiA and chiB. Cells displaying high levels of chiA-chiB expression were detected only on the chitin surface and then only clustered in discrete areas of the surface. Surface-associated, differential gene expression and displacement of bacterial production from surfaces represent adaptations at the population level that promote efficient utilization of limited resources and dispersal of progeny to maximize access to new sources of energy and maintenance of the population.

Alteromonas↗
PubMed1992

Molecular mechanisms of pattern formation in the vertebrate hindbrain.

During early stages of neural development a series of repeated bulges, termed rhombomeres, form in the vertebrate hindbrain. Studies in the chick have shown that rhombomeres are segments that underlie the patterning of nerves in the hindbrain, and this raises the question of the molecular basis of segment development. Several genes have been found with expression patterns consistent with roles in the formation or differentiation of rhombomeres. The zinc finger gene Krox-20 is expressed in two alternating rhombomeres, r3 and r5, in the mouse hindbrain; these stripes of gene expression are established prior to the morphological appearance of segments. Krox-20 is also expressed in this pattern in the chick and Xenopus, suggesting that it has a conserved role, possibly in the formation of rhombomeres. Four members of the Hox-2 homeobox gene cluster have limits of expression at rhombomere boundaries. Three genes, Hox-2.6, -2.7 and -2.8 have progressively more anterior limits of expression at two-segment intervals, whereas expression of Hox-2.9 is restricted to one rhombomere, r4. The Hox-2 genes are expressed in spatially restricted patterns in early neural crest cells. These findings suggest that the Hox genes have roles in specifying the identity of rhombomeres and of neural crest.

Animals↗
PubMed2003

Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts.

BACKGROUND: Transcriptional regulation in eukaryotes often involves multiple transcription factors binding to the same transcription control region, and to understand the regulatory content of eukaryotic genomes it is necessary to consider the co-occurrence and spatial relationships of individual binding sites. The determination of conserved sequences (often known as phylogenetic footprinting) has identified individual transcription factor binding sites. We extend this concept of functional conservation to higher-order features of transcription control regions. RESULTS: We used the genome sequences of four yeast species of the genus Saccharomyces to identify sequences potentially involved in multifactorial control of gene expression. We found 989 potential regulatory 'templates': pairs of hexameric sequences that are jointly conserved in transcription regulatory regions and also exhibit non-random relative spacing. Many of the individual sequences in these templates correspond to known transcription factor binding sites, and the sets of genes containing a particular template in their transcription control regions tend to be differentially expressed in conditions where the corresponding transcription factors are known to be active. The incorporation of word pairs to define sequence features yields more specific predictions of average expression profiles and more informative regression models for genome-wide expression data than considering sequence conservation alone. CONCLUSIONS: The incorporation of both joint conservation and spacing constraints of sequence pairs predicts groups of target genes that are specific for common patterns of gene expression. Our work suggests that positional information, especially the relative spacing between transcription factor binding sites, may represent a common organizing principle of transcription control regions.

Base Sequence↗
PubMed2026

Ten quick tips for spatial transcriptomics analysis.

Spatial transcriptomics (ST) enables genome-wide gene expression profiling while retaining spatial context within tissue sections. Since the foundational work by Ståhl et al. in 2016, the field has expanded rapidly, with diverse platforms now spanning sequencing-based (e.g., Visium, Visium HD, Slide-seq, Stereo-seq, and Seq-Scope) and imaging-based (e.g., MERFISH, Xenium, and CosMx SMI) approaches. The breadth of platforms, data structures, and computational tools, however, can be daunting for newcomers. Here, we present ten quick tips spanning the entire ST research workflow: whether ST suits a given biological question, how to select a platform aligned with study objectives, how to understand and process ST data, and which software tools to employ for analysis and visualization. We further discuss interpreting spatial patterns in biological context, integrating complementary modalities such as single-cell RNA sequencing and spatial proteomics, and leveraging public datasets and sharing results. Finally, we highlight current limitations of ST, particularly the challenge of reconstructing three-dimensional tissue architecture from serial tissue sections. This review provides biologists, bioinformaticians, and clinician-scientists with a concise, platform-neutral roadmap for incorporating ST into research, from experimental design to biological discovery.

Spatial Transcriptomics↗
PubMed1998

Discrete spatial and temporal cis-acting elements regulate transcription of the Arabidopsis floral homeotic gene APETALA3.

The APETALA3 floral homeotic gene is required for petal and stamen development in Arabidopsis. APETALA3 transcripts are first detected in a meristematic region that will give rise to the petal and stamen primordia, and expression is maintained in this region during subsequent development of these organs. To dissect how the APETALA3 gene is expressed in this spatially and temporally restricted domain, various APETALA3 promoter fragments were fused to the uidA reporter gene encoding beta-glucuronidase and assayed for the resulting patterns of expression in transgenic Arabidopsis plants. Based on these promoter analyses, we defined cis-acting elements required for distinct phases of APETALA3 expression, as well as for petal-specific and stamen-specific expression. By crossing the petal-specific construct into different mutant backgrounds, we have shown that several floral genes, including APETALA3, PISTILLATA, UNUSUAL FLORAL ORGANS, and APETALA1, encode trans-acting factors required for second-whorl-specific APETALA3 expression. We have also shown that the products of the APETALA1, APETALA3, PISTILLATA and AGAMOUS genes bind to several conserved sequence motifs within the APETALA3 promoter. We present a model whereby spatially and temporally restricted APETALA3 transcription is controlled via interactions between proteins binding to different domains of the APETALA3 promoter.

Arabidopsis↗
PubMed1998

Anterior specification of embryonic ectoderm: the role of the Xenopus cement gland-specific gene XAG-2.

In a search for novel developmental genes expressed in a spatially restricted pattern in dorsal ectoderm of Xenopus we have identified XAG-2, a cement gland-specific gene with a putative role in ectodermal patterning. XAG-2 encodes a secreted protein, which is expressed in the anterior region of dorsal ectoderm from late gastrula stages onwards. Activation of XAG-2 transcription is observed in response to organizer-secreted molecules including the noggin, chordin, follistatin and cerberus gene products. Overexpression of XAG-2 but not of the related cement gland marker XAG-1 induces both cement gland differentiation and expression of anterior neural marker genes in the absence of mesoderm formation. Further, we show that XAG-2 signaling depends on an intact fibroblast growth factor (FGF) signal transduction pathway and that XAG-2-induced anterior neural fate of ectodermal cells can be transformed to a more posterior character by retinoic acid. Based on these findings we propose a role for XAG-2 in the specification of dorsoanterior ectodermal fate, i.e. in the formation of cement gland and induction of forebrain fate of Xenopus.

Amino Acid Sequence↗