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Results for “spatial gene expression”

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At least 307 records · Page 17Linked to original sources
PubMed2002

Insulin-like growth factor-I improves cellular and molecular aspects of healing in a collagenase-induced model of flexor tendinitis.

Flexor tendinitis is a common and debilitating injury of elite and recreational athletes. Healing may be improved through intratendinous injection of insulin-like growth factor-I (IGF-I), which has been shown in vitro to stimulate mitogenesis and enhance tendon matrix production. This study investigated the effects of intratendinous injection of IGF-I on tendon healing in an equine model of flexor tendinitis. Collagenase-induced lesions were created in the tensile region of theflexor digitorum superficialis tendon of both forelimbs of eight horses. Treated tendons were injected with 2 microg rhlGF-I intralesionally every other day for 10 injections, while controls received 0.9% NaCl. Tendon fiber deposition and organization were evaluated serially using ultrasonography throughout the 8 week trial period. Following euthanasia, the tendons were harvested and DNA, hydroxyproline, and glycosaminoglycan content determined, mechanical strength and stiffness evaluated, gene expression and spatial arrangement of collagen types I and III assessed by northern blot and in situ hybridization, and tendon fiber architecture assessed by polarized light microscopy. Local soft tissue swelling was reduced in the IGF-I treated limbs. Similarly, lesion size in IGF-I treated tendons was smaller 3 and 4 weeks after initiation of treatment. Cell proliferation and collagen content of the IGF-I treated tendons were increased compared to controls. Mechanically, IGF-I treated tendons showed a trend toward increased stiffness compared to saline treated controls. Considered together with the decreased soft tissue swelling and improved sonographic healing, these data support the potential use of intralesional IGF-I for treatment of debilitating tendon injuries.

Animals↗
PubMed1994

Complex spatial and temporal expression of lipoxygenase genes during Phaseolus vulgaris (L.) development.

A new member (Lox1) of the lipoxygenase (LOX) gene family in French bean was isolated and its specific expression compared to the general expression pattern of related LOX genes. LOX transcripts detected by a French bean cDNA LOX probe were generally abundant in young, developing tissues, and LOX protein, detected on immunoblots showed a similar distribution. Tissue prints showed that cell-specific, locally high amounts of LOX protein were observed in some tissues, for example in parts of the starch sheath in the hypocotyl and a cell layer in the pericarp. The Lox1 gene from Phaseolus vulgaris was shown in genomic Southerns to be present as a single copy per haploid genome. RNase protection studies showed that the gene is active and the transcription start site was mapped by cDNA primer extension. RNase protection studies showed that Lox1 mRNA was present only in flowers and embryonic primary leaves, in stems and most strongly, in young secondary leaves but not in any of the other organs tested (i.e. not in roots, nodules, hypocotyls, cotyledons, older secondary leaves, pericarp or seeds). Lox1 gene transcripts did not accumulate in leaves in response to methyl jasmonate or pathogen inoculation, even though these treatments caused the accumulation of other LOX transcripts. Thus, the various lipoxygenase genes are regulated differentially during French bean development and in response to different stress stimuli, and possible functions are discussed in view of the specific expression patterns observed.

Amino Acid Sequence↗
PubMed2001

P[Switch], a system for spatial and temporal control of gene expression in Drosophila melanogaster.

We have developed a method for turning on and off the expression of transgenes within Drosophila in both time and space. Two different enhancer detector elements carrying an RU486-inducible form of the yeast transcription factor GAL4 were constructed and used to generate enhancer detector lines. These lines were screened for RU486-inducible reporter gene expression in the adult head. We identified lines that exhibit inducible expression in many cell and tissue types, verifying that the elements respond to nearby enhancers. No expression was detected in the absence of the ligand. The P[Switch1] element responded to genomic enhancers less efficiently than P[Switch2] but produced more specific patterns of expression. Two P[Switch] lines were used to ablate fat body tissue in adult females through the induced expression of diphtheria toxin. These females were sterile, which correlates with fat body loss, and they died prematurely.

Animals↗
PubMed1992

Displacement of BrdUrd-induced YY1 by serum response factor activates skeletal alpha-actin transcription in embryonic myoblasts.

Muscle-restricted transcription of the skeletal alpha-actin gene is controlled in part by a positive regulator, serum response factor (SRF), and a negative regulator, F-ACT1, which bind competitively to the most proximal serum response element (SRE1). We show here that F-ACT1 is identical to a transcription factor recently cloned and described as YY1, NF-E1, delta, or UCRBP. We found that although the DNA-binding activity of SRF accumulates during myogenesis, that of YY1 diminishes simultaneously. Myoblasts rendered incapable of differentiation by BrdUrd treatment exhibited the highest level of YY1 and the lowest level of SRF activities. Transfected SRF could directly transactivate the skeletal alpha-actin promoter by overcoming the inhibitory effect of BrdUrd-induced YY1. The transactivation depends on intact SRE DNA elements and requires the DNA-binding/dimerization domain of SRF as well as its C-terminal half rich in serines and threonines. Since the functions of YY1 and SRF appear to be developmentally regulated, the convergence of their binding sites upon the SRE constitutes an integrated mechanism whereby temporal and spatial muscle gene expression may be accomplished.

Actins↗
PubMed1999

RNA sorting in Xenopus oocytes and embryos.

Cytoplasmic localization of mRNA molecules has emerged as a powerful mechanism for generating spatially restricted gene expression. This process is an important contributor to cell polarity in both somatic cells and oocytes, and can provide the basis for patterning during embryonic development. In vertebrates, this phenomenon is perhaps best documented in the frog, Xenopus laevis, where polarity along the animal-vegetal axis coincides with the localization of numerous mRNA molecules. Research over the last several years has made exciting progress toward understanding the molecular mechanisms underlying cytoplasmic mRNA localization.

Animals↗
PubMed1992

Identification of Embryoid-Abundant Genes That Are Temporally Expressed during Pollen Embryogenesis in Wheat Anther Cultures.

Uninucleate microspores in anther cultures of bread wheat (Triticum aestivum cv Pavon) are capable of producing haploid pollen embryoids and plants. To gain an understanding of this alternate pathway of pollen development, we constructed a cDNA library to young pollen embryoids, isolated embryoid-specific genes, and analyzed their expression patterns during morphogenesis. Two embryoid-abundant clones, pEMB4 and 94, were expressed very early during culture, suggesting that these genes are associated with development and are not simply expressed as a consequence of differentiation. The accumulation patterns of five cloned mRNAs may indicate the activation of specific genes associated with the major morphological and physiological activities connected with the differentiation of embryoids in vitro. These results suggest that embryoid-abundant gene expression is causally related to this pathway because gene expression is spatially and temporally specific and is not observed when microspores are cultured under noninductive conditions.

Journal Article↗
PubMed2025

The auxin gatekeepers: Evolution and diversification of the YUCCA family.

The critically important YUCCA (YUC) gene family is highly conserved and specific to the plant kingdom, primarily responsible for the final and rate-limiting step for indole-3-acetic acid (IAA) biosynthesis. IAA is an essential phytohormone, involved in virtually all aspects of plant growth and development. In addition, IAA is involved in fine-tuning plant responses to biotic and abiotic interactions and stresses. While the YUC gene family has significantly expanded throughout the plant kingdom, a detailed analysis of the evolutionary patterns driving this diversification has not been performed. Here, we present a comprehensive phylogenetic analysis of the YUC family, combining YUCs from species representing key evolutionary plant lineages. The evolutionary history of YUCs is complex and suggests multiple recruitment events via horizontal gene transfer from bacteria. We identify and hierarchically classify the YUC family into an early diverging grade, five distinct classes and 41 subclasses. Angiosperm YUC diversity and expansion are explained in the context of protein sequence conservation, as well as spatial and gene expression patterns. The presented YUC gene landscape offers new perspectives on the distribution and evolutionary trends of this crucial family, which facilitates further YUC characterization within plant development and response to environmental change.

Indoleacetic Acids↗
PubMed1997

Temporal and spatial expression pattern of the angiotensinogen gene in mice and rats.

In situ hybridization for mouse angiotensinogen (Ao) mRNA was performed using a Stu I-Pst I 0.43-kb fragment of exon 2 as a template to synthesize RNA probes. The mouse Ao mRNA expression patterns were different from those reported for rats. Ao mRNA was expressed in the fetal liver as early as 12.5 days postcoitus, and the liver remained the predominant organ of its expression in utero. Within the developing kidney, Ao mRNA was demonstrated at 17.5 days postcoitus in the proximal straight tubules undergoing loop formation in the medulla. In the matured mouse kidney, the expression site is within the outer stripe of outer medulla, hence identified as the pars recta, not proximal convoluted tubules. Additional studies revealed that, in rats also, Ao mRNA was localized in the pars recta. This was in contrast to previously published results that showed that Ao mRNA was localized primarily in the proximal convoluted tubules in rats. Thus the pars recta appears to be an important intrarenal source of Ao for both rats and mice throughout pre- and postnatal periods, whereas the liver can be the major extrarenal source in utero in mice, but not in rats.

Aging↗
PubMed1999

Sex steroids mediate HOXA11 expression in the human peri-implantation endometrium.

Under the influence of sex steroids, human endometrium undergoes sequential development in preparation for implantation. Hoxa11 is essential for implantation in the mouse. Here we describe a potential role for HOXA11 in human endometrial development and implantation. Northern analysis demonstrates that HOXA11 is expressed in a menstrual cycle phase-dependent fashion in adult human endometrium. HOXA11 messenger RNA levels dramatically increase at the time of implantation and remain increased in pregnancy. In vitro, HOXA11 expression is increased in response to estrogen or progesterone. There is a dose-responsive increase over the physiologic range of progesterone concentration. Pretreatment with Cyclohexamide does not decrease the response to estrogen. Steroids are novel regulators HOX gene expression. The spatial and temporal pattern of HOXA11 expression in the human endometrium suggests a role in endometrial development, implantation, and maintenance of pregnancy.

Embryo Implantation↗
PubMed1996

Evidence from normal expression and targeted misexpression that bone morphogenetic protein (Bmp-4) plays a role in mouse embryonic lung morphogenesis.

Epithelial-mesenchymal interactions are critical for the branching and differentiation of the lung, but the mechanisms involved are still unclear. To investigate this problem in mouse embryonic lung, we have studied the temporal and spatial expression of genes implicated in the morphogenesis of other organs. At 11.5 days p.c., hepatocyte nuclear factor-3beta (Hnf-3beta) is expressed uniformly throughout the epithelium, while Wnt-2 expression is confined to the distal mesenchyme. Sonic hedgehog (Shh) transcripts are found throughout the epithelium, with high levels in the distal tips of the terminal buds, while bone morphogenetic protein-4 (Bmp-4) transcripts are localized at high levels in the distal tips of the epithelium, with lower levels in the adjacent mesenchyme. Epithelial expression is also seen for Bmp-7, but transcripts are less dramatically upregulated at the distal tips. The Type I Bone morphogenetic protein receptor gene (Bmpr/Tfr-11/Brk-1) is expressed at low levels in the epithelium and in the distal mesenchyme. To investigate the role of Bmp-4 in lung development, we have misexpressed the gene throughout the distal epithelium of transgenic lungs using a surfactant protein C enhancer/promoter. From 15.5 days p.c., transgenic lungs are smaller than normal, with grossly distended terminal buds and, at birth, contain large air-filled sacs which do not support normal lung function. Labeling with BrdU reveals an inhibition of epithelia] proliferation in 15.5 days p.c. transgenic lungs. A small but significant stimulation of proliferation of mesenchymal cells is also observed, but this is accompanied by an increase in cell death. In situ hybridization with riboprobes for the proximal airway marker, CC10, and the distal airway marker, SP-C, shows normal differentiation of bronchiolar Clara cells but a reduction in the number of differentiated Type II cells in transgenic lungs. A model is proposed for the role of BMP4 and other signalling molecules in embryonic lung morphogenesis.

Animals↗
PubMed1997

Temporal and spatial expression of distinct troponin T genes in embryonic/larval tail striated muscle and adult body wall smooth muscle of ascidian.

During development of the ascidian Halocynthia roretzi, the tadpole larva hatched from the tailbud embryo metamorphoses to the adult with a body wall muscle. Although the adult body wall muscle is morphologically nonsarcomeric smooth muscle, it contains a troponin complex consisting of three subunits (T, I, and C) as do vertebrate striated muscles. Different from vertebrate troponins, however, the smooth muscle troponin promotes actin-myosin interaction in the presence of high concentration of Ca2+, and this promoting property is attributable to troponin T. To address whether the embryonic/larval tail striated muscle and the adult smooth muscle utilize identical or different regulatory machinery, we cloned troponin T cDNAs from each cDNA library. The embryonic and the adult troponin Ts were encoded by distinct genes and shared only < 60% identity with each other. These isoforms were specifically expressed in the embryonic/larval tail striated muscle and the adult smooth muscle, respectively. These results may imply that these isoforms regulate actin-myosin interaction in different manners. The adult troponin T under forced expression in mouse fibroblasts was unexpectedly located in the nuclei. However, a truncated protein with a deletion including a cluster of basic amino acids colocalized with tropomyosin on actin filaments. Thus, complex formation with troponin I and C immediately after the synthesis is likely to be essential for the protein to properly localize on the thin filaments.

Amino Acid Sequence↗
PubMed2006

RNA trafficking and local protein synthesis in dendrites: an overview.

It is now widely accepted that mRNAs localize to dendrites and that translation of these mRNAs is regulated in response to neuronal activity. Recent studies have begun to reveal the underpinnings of these processes and to underscore the importance of local protein synthesis to synaptic remodeling and plasticity. When Steward and Levy (1982) first reported their observation of polyribosomes at the base of spines, the prevailing view was that all proteins were synthesized in the cell body and then transported to distal compartments of neurons. Steward and Levy's discovery, however, raised the intriguing possibility that mRNAs could be transported to synapses and locally translated in response to synaptic stimulation. This provided an elegant mechanism for spatially restricting gene expression within the neuron, such that individual synapses could independently regulate their morphology and efficacy, in a persistent, protein synthesis-dependent manner, in response to specific stimuli. It is now widely accepted that mRNAs do localize to dendrites and that translation of these mRNAs contributes to synaptic plasticity. As is evident from the collection of Mini-Reviews on dendritic protein synthesis in this issue of The Journal of Neuroscience, the field has evolved to focus on a series of key questions, including the following: (1) what mRNAs are present in dendrites? (2) How are these mRNAs transported from the nucleus into the dendrite? (3) How is translation of these mRNAs regulated by neuronal activity? and (4) What is the function of local translation of specific transcripts? In this brief introductory overview, we will consider each of these questions in turn.

Animals↗
PubMed2006

Identification of process-localized mRNAs from cultured rodent hippocampal neurons.

The regulated translation of localized mRNAs in neurons provides a mechanism for spatially restricting gene expression in a synapse-specific manner. To identify the population of mRNAs present in distal neuronal processes of rodent hippocampal neurons, we grew neurons on polycarbonate filters etched with 3 microm pores. Although the neuronal cell bodies remained on the top surface of the filters, dendrites, axons, and glial processes penetrated through the pores to grow along the bottom surface of the membrane where they could be mechanically separated from cell bodies. Quantitative PCR and immunochemical analyses of the process preparation revealed that it was remarkably free of somatic contamination. Microarray analysis of RNA isolated from the processes identified over 100 potentially localized mRNAs. In situ hybridization studies of 19 of these transcripts confirmed that all 19 were present in dendrites, validating the utility of this approach for identifying dendritically localized transcripts. Many of the identified mRNAs encoded components of the translational machinery and several were associated with the RNA-binding protein Staufen. These findings indicate that there is a rich repertoire of mRNAs whose translation can be locally regulated and support the emerging idea that local protein synthesis serves to boost the translational capacity of synapses.

Animals↗
PubMedDate not supplied

[Spatial registration of data on gene expression in situ].

For registering data on the in situ expression of segmentation genes, a method of image registration was developed basing on the spline approximation. The reference points for the registration were the coordinates of extrema in one-dimensional patterns of gene expression. This registration method is characterized by a very high accuracy. A method of creating a generalized pattern of gene expression in single cells is proposed. Such patterns were constructed for nine segmentation genes belonging to the gap and pair-rule classes of genes.

Gene Expression Profiling↗
PubMed1987

Spatial regulation of homeo box gene expression in Drosophila.

1. Each of the 17 known homeo box genes shows a unique pattern of expression during early embryonic development. Thus, virtually every embryonic cell contains a unique combination of active and inactive homeo box genes. 2. These different permutations of homeo box gene expression are thought to specify unique positional values, and appear to play key roles in selecting diverse pathways of morphogenesis. 3. It has been proposed that selective patterns of homeo box gene expression involve cross-regulatory interactions. For example, it appears that homeotic genes expressed in posterior regions of the embryo (such as abd-A and Abd-B) repress the expression of those homeotic genes expressed in more anterior regions (such as Antp and Ubx). Such interactions might involve sequence-specific DNA binding and occur at the level of transcription. 4. The establishment of selective patterns of pair-rule gene expression along the anterior-posterior embryonic body axis might involve the differential regulation of these genes by a common set of transcription factors. In particular, it appears that eve and ftz show opposite responses to regulatory products that are either directly or indirectly specified by several gap genes.

Amino Acid Sequence↗
PubMed1985

Contrabithorax and the control of spatial expression of the bithorax complex genes of Drosophila.

Cbx1 is a dominant mutation of the bithorax complex (BX-C) of Drosophila partially transforming the second thoracic (T2) segment towards the third one (T3). Molecular analysis has shown that Cbx1 arose from a transposition within the BX-C of a DNA fragment of 17 kb containing pbx+ inserted into the Ubx area. In addition to the dominant phenotype, the Cbx1 mutation produces a set of recessive homeotic transformations that we show are characteristic of the Ubx mutations. We present evidence that the dominant and the recessive transformations arise from different mechanisms and suggest the dominant transformation is caused by an alteration of the normal regulatory role of pbx+ resulting in an adventitious expression of some Ubx+ products in T2, while the Ubx phenotype is caused by the breakpoint of the insertion.

Animals↗
PubMed2025

Spatial transcriptomics-aided localization for single-cell transcriptomics with STALocator.

Single-cell RNA-sequencing (scRNA-seq) techniques can measure gene expression at single-cell resolution but lack spatial information. Spatial transcriptomics (ST) techniques simultaneously provide gene expression data and spatial information. However, the data quality of the spatial resolution or gene coverage is still much lower than the quality of the single-cell transcriptomics data. To this end, we develop a ST-Aided Locator for single-cell transcriptomics (STALocator) to localize single cells to corresponding ST data. Applications on simulated data showed that STALocator performed better than other localization methods. When applied to the human brain and squamous cell carcinoma data, STALocator could robustly reconstruct the relative spatial organization of critical cell populations. Moreover, STALocator could enhance gene expression patterns for Slide-seqV2 data and predict genome-wide gene expression data for fluorescence in situ hybridization (FISH) and Xenium data, leading to the identification of more spatially variable genes and more biologically relevant Gene Ontology (GO) terms compared with the raw data. A record of this paper's transparent peer review process is included in the supplemental information.

Single-Cell Analysis↗
PubMed1993

Ethanol-induced changes in astrocyte gene expression during rat central nervous system development.

Disruption of spatial and temporal patterns of gene expression in cells of the developing brain could result in abnormal development. We report that briefly exposing neonatal rats to a moderate dose of ethanol on postnatal days 5 through 7 caused a large, specific increase in glial fibrillary acidic protein (GFAP) mRNA and GFAP. Astrocytes of the cerebral cortex were apparently more sensitive to this effect of ethanol than astrocytes in several other brain regions. As a first step in the characterization of an vitro model of ethanol's effect on GFAP gene expression, ethanol was added to the media of primary cultures of cortical astrocytes in a pattern of exposure and at concentrations equal to pups' peak blood levels. This resulted in an increase in GFAP mRNA whose magnitude and specificity mirrored that observed in the animal model. Together, these results suggest that even brief exposure to ethanol can alter gene expression in astrocytes, and forms the foundation for further characterization of an in vitro model that may be used to determine the mechanism of this effect.

Animals↗