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PubMed1995

Expression of mef2 genes in the mouse central nervous system suggests a role in neuronal maturation.

Members of the myocyte enhancer factor 2 (MEF2) gene family are expressed in a dynamic pattern during development of the CNS of pre- and postnatal mice. The four MEF2 genes, Mef2A, -B, -C, -D, encode transcription factors belonging to the MADS (MCM1-agamous-deficiens-serum response factor) superfamily of DNA binding proteins. MEF2 factors have previously been shown to be positive regulators of gene expression in terminally differentiated muscle cells. To begin to determine the role of MEF2 factors in CNS development, we used in situ hybridization with gene-specific cRNA probes to define the expression patterns of each of the four Mef2 mRNAs in the developing and mature mouse CNS. Mef2C mRNA was first detected in a ventral portion of the telencephalon at 11.5 d postcoitum (p.c.). By 13.5 d p.c., each of the four Mef2 genes were expressed in overlapping yet distinct patterns in regions of the frontal cortex, midbrain, thalamus, hippocampus, and hindbrain. Temporal and spatial patterns of embryonic Mef2 gene expression appeared to follow gradients of neuron maturation and suggested that the onset of Mef2 gene expression coincides with withdrawal from the cell cycle and initiation of neuronal differentiation. This correlation is particularly striking for Purkinje cells in the cerebellum. Since the molecular mechanisms that regulate neuron differentiation are unknown, we propose that the MEF2 factors are likely to play an important role in this process.

Animals↗
PubMedDate not supplied

Pit-1-dependent expression of the receptor for growth hormone releasing factor mediates pituitary cell growth.

In Snell (dw) and Jackson (dwJ) dwarf mice, mutations in the gene encoding Pit-1, a tissue-specific POU-domain transcription factor, lead to the absence of somatotroph, lactotroph and thyrotroph cells. Pre-somatotroph proliferation is stimulated by increased intracellular levels of cyclic AMP, normally induced by growth hormone releasing factor (GRF; refs 7-17). Here we report the cloning of mouse and rat complementary DNAs encoding a new member of the seven-transmembrane-helix, G-protein-coupled receptor family restricted to the pituitary gland, which mediates increases in intracellular cAMP and cAMP-dependent gene transcription in response to GRF. The receptor is expressed in a spatial and temporal pattern corresponding precisely to growth hormone gene expression, and neither is expressed in dw/dw mice. The pituitary hypoplasia in these mice thus appears to be due, at least in part, to the absence of GRF receptor, which is in turn due to the absence of functional Pit-1.

Amino Acid Sequence↗
PubMed1992

Early mRNAs, spatially restricted along the animal-vegetal axis of sea urchin embryos, include one encoding a protein related to tolloid and BMP-1.

The cloning and characterization of cDNAs representing four genes or small gene families that are coordinately expressed in a spatially restricted pattern during the very early blastula (VEB) stage of sea urchin development are presented. The VEB genes encode multiple transcripts that are expressed transiently in embryos of Strongylocentrotus purpuratus between 16-cell stage and hatching, with peak abundance 12 to 15 hours post-fertilization (approximately 150-250 cells). The VEB transcripts share the same spatial pattern in the early blastula embryo: they are asymmetrically distributed along the animal-vegetal axis but their distribution around this axis is uniform. Thus, the VEB transcripts are the earliest messages to reveal asymmetry along the primary axis in the sea urchin embryo. The temporal and spatial patterns of VEB transcript accumulation are not consistent with involvement of these gene products in cell division or in tissue-specific functions. Furthermore, VEB messages cannot be detected in either ovary or adult tissues, suggesting that these genes function exclusively during embryogenesis. We suggest that the VEB genes function in constructing the early blastula. Two VEB genes encode metalloendoproteases: one (SpHE) is hatching enzyme and the other (SpAN) is similar to bone morphogenetic protein-1 (BMP-1; Wozney et al., Science 242: 1528-1534, 1988) and the Tolloid gene product (tld) (Shimell et al., Cell 67: 459-482, 1991). Several lines of evidence suggest that the VEB genes are regulated directly by factors or regulatory activities localized along the maternally specificed animal-vegetal axis.

Animals↗
PubMed2005

Dual regulation and redundant function of two eye-specific enhancers of the Drosophila retinal determination gene dachshund.

Drosophila eye development is controlled by a conserved network of retinal determination (RD) genes. The RD genes encode nuclear proteins that form complexes and function in concert with extracellular signal-regulated transcription factors. Identification of the genomic regulatory elements that govern the eye-specific expression of the RD genes will allow us to better understand how spatial and temporal control of gene expression occurs during early eye development. We compared conserved non-coding sequences (CNCSs) between five Drosophilids along the approximately 40 kb genomic locus of the RD gene dachshund (dac). Our analysis uncovers two separate eye enhancers in intron eight and the 3' non-coding regions of the dac locus defined by clusters of highly conserved sequences. Loss- and gain-of-function analyses suggest that the 3' eye enhancer is synergistically activated by a combination of eya, so and dpp signaling, and only indirectly activated by ey, whereas the 5' eye enhancer is primarily regulated by ey, acting in concert with eya and so. Disrupting conserved So-binding sites in the 3' eye enhancer prevents reporter expression in vivo. Our results suggest that the two eye enhancers act redundantly and in concert with each other to integrate distinct upstream inputs and direct the eye-specific expression of dac.

3' Untranslated Regions↗
PubMed2001

Neuron-specific expression of Cre recombinase during the late phase of brain development.

Gene targeting to disrupt gene expression in a temporal and spatial manner in a specific tissue using Cre recombinase-mediated gene inactivation has been proven to be useful to study in vivo gene function. To delete genes specifically in neurons during the late phase of brain development, we have generated transgenic mouse lines that express Cre recombinase under the control of the murine neurofilament-H (mNF-H) gene promoter. In this study, we report that one of these mouse lines expresses Cre recombinase specifically in the neurons of the brain and spinal cord during the late stage of their development. The transgenic line displays specific excision of the loxP-flanked gene in the neurons just after embryonic day 18.5 (E.18.5), which coincides with the later phase of brain maturation including spinal cord and olfactory bulb area. This mNF-H-cre transgenic mouse line will be valuable for studying in vivo functions of neuron-specific genes, particularly, defining their precise roles in the mature nervous system using conditional gene targeting strategies.

Age Factors↗
PubMed2004

Does looping and clustering in the nucleus regulate gene expression?

There has been considerable interest in the way that chromatin is spatially organised within the cell nucleus and how that may relate to gene expression and its control. New molecular techniques have identified looped chromatin domains at the mammalian beta-globin and the Drosophila hsp70 loci. Looped domains may insulate chromatin from the influence of neighbouring domains, and the bases of loops may also act to concentrate proteins locally within the nucleus. The spatial clustering of sequences from the Drosophila bithorax complex, located in trans, has also been demonstrated. An emerging theme is that bringing DNA and proteins together within a defined sub-region of the nuclear volume facilitates both the activation and the repression of gene expression. Nuclear compartments may also be involved in the post-translational modification of proteins by sumoylation and ubiquitylation.

Animals↗
PubMed2002

A common translational control mechanism functions in axial patterning and neuroendocrine signaling in Drosophila.

Translational repression of maternal nanos (nos) mRNA by a cis-acting Translational Control Element (TCE) in the nos 3'UTR is critical for anterior-posterior patterning of the Drosophila embryo. We show, through ectopic expression experiments, that the nos TCE is capable of repressing gene expression at later stages of development in neuronal cells that regulate the molting cycle. Our results predict additional targets of TCE-mediated repression within the nervous system. They also suggest that mechanisms that regulate maternal mRNAs, like TCE-mediated repression, may function more widely during development to spatially or temporally control gene expression.

Animals↗
PubMed1996

Spatial and temporal information processing in the sea urchin embryo: modular and intramodular organization of the CyIIIa gene cis-regulatory system.

The CyIIIa cytoskeletal actin gene of Strongylocentrotus purpuratus is expressed specifically in the aboral ectoderm. In earlier work we identified a 2.3 kb cis-regulatory region that is necessary and sufficient for correct spatial and temporal expression of a CyIIIa.CAT gene. This region includes about 20 sites of specific protein-DNA interaction, at which at least nine different transcription factors may be bound. All except two of these factors have been cloned. In this work we have analyzed by deletion or mutagenesis each specific interaction. A specific function was identified for every binding site examined. These individual functions include control of amplitude and timing of expression at different phases of embryogenesis, and control of spatial expression. We show that particular negative regulatory interactions are required to repress expression of the CyIIIa.CAT construct in oral ectoderm and in skeletogenic mesenchyme at different stages. In further experiments we determined the overall functional organization of the CyIIIa cis-regulatory system, and we show that this system is modular in its regulatory structure. The 'proximal module' (with respect to the transcription start site) extends upstream for about 800 base pairs, and includes nine target sites serviced by six different transcription factors. Its major role is to establish CyIIIa expression in the aboral ectoderm territory as the blastomere founder cells are specified and the oral-aboral axis is determined, and to activate the CyIIIa gene late in cleavage. The 'middle module,' which lies upstream of the proximal module, acquires major control of CyIIIa function after the blastula stage. It includes six target sites, serviced by four different factors. The middle module is responsible for a sharp increase in expression occurring during gastrulation, mediated by the positively acting factors that bind within it. The middle module also includes sites at which two different negatively acting spatial control factors bind, the functions of which are required for correct spatial expression late in embryogenesis. The 'distal module' contains a number of sites at which a positively acting factor binds, but this module exercises no spatial regulatory function. Interactions within the distal module are required for the normal levels of function of both the proximal and middle modules.

Actins↗
PubMed2026

stDyer-image improves clustering analysis of spatially resolved transcriptomics and proteomics with morphological images.

MOTIVATION: Spatially resolved transcriptomics (SRT) and spatially resolved proteomics (SRP) data enable the study of gene expression and protein abundances within their precise spatial and cellular contexts in tissues. Certain SRT and SRP technologies also capture corresponding morphology images, adding another layer of valuable information. However, few existing methods developed for SRT data effectively leverage these supplementary images to enhance clustering performance. RESULTS: Here, we introduce stDyer-image, an end-to-end deep learning framework designed for clustering for SRT and SRP datasets with images. Unlike existing methods that utilize images to complement gene expression data, stDyer-image directly links image features to cluster labels. This approach draws inspiration from pathologists, who can visually identify specific cell types or tumor regions from morphological images without relying on gene expression or protein abundances. Benchmarks against state-of-the-art tools demonstrate that stDyer-image achieves superior performance in clustering. Moreover, it is capable of handling large-scale datasets across diverse technologies, making it a versatile and powerful tool for spatial omics analysis. AVAILABILITY AND IMPLEMENTATION: The source code of stDyer-image and detailed tutorials are available at https://github.com/ericcombiolab/stDyer-image.

Proteomics↗
PubMed2004

Expression of photosynthesis-related genes and their regulation by light during somatic embryogenesis in Daucus carota.

To clarify the spatial and temporal pattern of gene expression for photosynthesis-associated proteins during somatic embryogenesis in Daucus carota L., the localization of mRNAs for three genes, rbcL, Lhcb and por, was examined in dark-grown and light-irradiated somatic embryos by in situ hybridization. The three mRNAs were expressed in common in the mesophyll precursor cells of light-irradiated embryos at the late torpedo and plantlet stages, but characteristic expression patterns of each photosynthesis-related gene were also observed. Expression of rbcL mRNA first occurred throughout the embryo but gradually became localized in the mesophyll precursor cells and cortex during early embryogenesis. Localization of Lhcb mRNA in the mesophyll precursor cells and shoot apical meristem became clear in the early torpedo stage. Expression of Lhcb mRNA was not affected by light during early embryogenesis, but could be induced by light in the torpedo stage, suggesting that light-inducible expression of Lhcb mRNA arises within the torpedo stage. At the late torpedo stage, clear localization of por mRNA started in mesophyll precursor cells of the cotyledon in light-irradiated embryos. Greening potency of the embryo also appeared first at this stage. Therefore, greening and initial differentiation of photosynthetic tissues during somatic embryogenesis seem to be associated with coordinated expression of mRNA for rbcL, Lhcb and por in late torpedo-shaped embryos.

Darkness↗
PubMed2003

Structure and expression of spermidine synthase genes in apple: two cDNAs are spatially and developmentally regulated through alternative splicing.

Three cDNAs (MdSPDS1, 2a and 2b) encoding spermidine synthase (SPDS), a key enzyme in the polyamine biosynthesis, have been cloned from apple [Malus sylvestris (L.) Mill. var. domestica (Borkh.) Mansf.]. The deduced amino acid sequences of their protein products share 76-83% identity with SPDSs of other higher plants. A comparison of the sequences of the three cDNAs and of the two corresponding genomic DNA fragments (SPDS1 and SPDS2) indicated that MdSPDS1 was transcribed from the SPDS1 sequence, whereas MdSPDS2a and MdSPDS2b were both derived from SPDS2 by alternative splicing. To learn more about the physiological roles of MdSPDS1, MdSPDS2a and MdSPDS2b, Northern analyses were carried out, together with measurements of polyamine content. Levels of both MdSPDS1 and MdSPD2a were higher in young leaves than in mature leaves and shoots. In fruits, mRNA levels were nearly as high as in young leaves and remained high during fruit development. By RT-PCR, MdSPDS2b transcripts were detected in mature leaves and shoots, but not in young leaves and fruits. These results indicate that MdSPDS2a and MdSPDS2b are differentially regulated in a tissue- and developmentally specific manner. The content of free polyamines in mesocarp tissues was measured at five stages of fruit development. At all stages, spermidine (Spd) was the predominant form of polyamine. The level of Spd was high at the early growth stage and declined to about 90% during later developmental stages. The possible regulation of SPDS expression during apple fruit development is discussed.

Alternative Splicing↗
PubMed2003

Gene expression in the mouse preimplantation embryo.

Mouse preimplantation development represents a tightly controlled programme of gene expression and cell division, which starts with the fertilized egg and ends with implantation of the blastocyst approximately 4.5 days later. Spatial and temporal differences in gene expression underpin establishment of axes at the two-cell stage and development of the trophectoderm and inner cell mass after embryo compaction at the eight-cell stage. Approximately 15 700 mouse genes expressed during preimplantation development have been identified from cDNA sequences deposited in the UniGene database of the National Institutes of Health. This inventory of preimplantation genes is the starting point for identifying signalling modules that function in preimplantation development.

Animals↗
PubMed2004

Wound healing and inflammation genes revealed by array analysis of 'macrophageless' PU.1 null mice.

BACKGROUND: Wound healing is a complex process requiring the collaborative efforts of different tissues and cell lineages, and involving the coordinated interplay of several phases of proliferation, migration, matrix synthesis and contraction. Tissue damage also triggers a robust influx of inflammatory leukocytes to the wound site that play key roles in clearing the wound of invading microbes but also release signals that may be detrimental to repair and lead to fibrosis. RESULTS: To better define key cellular events pivotal for tissue repair yet independent of inflammation we have used a microarray approach to determine a portfolio of over 1,000 genes expressed across the repair response in a wild-type neonatal mouse versus its PU.1 null sib. The PU.1 null mouse is genetically incapable of raising the standard inflammatory response, because it lacks macrophages and functioning neutrophils, yet repairs skin wounds rapidly and with reduced fibrosis. Conversely, by subtraction, we have determined genes that are either expressed by leukocytes, or upregulated by fibroblasts, endothelial cells, muscle cells and others at the wound site, as a consequence of inflammation. To determine the spatial expression pattern for several genes in each cluster we have also performed in situ hybridization studies. CONCLUSIONS: Cluster analysis of genes expressed after wounding wild-type mice versus PU.1 null sibs distinguishes between tissue repair genes and genes associated with inflammation and its consequences. Our data reveal and classify several pools of genes, giving insight into their likely functions during repair and hinting at potential therapeutic targets.

Animals↗
PubMed1988

Expression of lipid body protein gene during maize seed development. Spatial, temporal, and hormonal regulation.

The storage lipids of seeds are packaged into lipid bodies, simple organelles containing a triacylglycerol core surrounded by a layer of phospholipids and proteins. A cDNA encoding the major protein from lipid bodies of maize (L3) was used as a hybridization probe to analyze the regulation of lipid body biosynthesis during seed development and germination. Immunofluorescent microscopy demonstrates that L3 protein accumulation is tissue-specific, confined to the embryo (scutellum and embryonic axis) and the aleurone layer of developing seed. Northern analyses show that L3 mRNA also accumulates to high levels in the embryo and is not found in any nonseed tissue. The steady-state level of L3 mRNA is developmentally regulated, increasing during early seed development and peaking at about the midpoint of seed development. It then decreases slowly, to 20% of the peak level, in the embryo of the mature seed and declines rapidly to undetectable levels as the seed germinates. The high level of L3 gene expression during seed development is not due to amplification of the L3 gene, since Southern analyses of maize genomic DNA indicate that the L3 gene has the same relatively low copy number throughout development (1-4 copies/haploid) genome). Rather, the increase in the steady-state level of L3 mRNA during seed development is transcriptionally regulated. The developmental changes in L3 mRNA levels are paralleled by changes in the transcription of the L3 gene, as measured by run-off transcription in isolated nuclei. The role of the plant growth regulator abscisic acid in regulating L3 gene expression was investigated. When the mature seed is allowed to imbibe in the presence of exogenous abscisic acid, germination is retarded, and the period of L3 gene expression is extended. The extended period of L3 gene expression in the presence of exogenous abscisic acid is due, at least in part, to a dramatic and specific increase in L3 gene transcription.

Abscisic Acid↗
PubMed1988

In situ hybridization patterns of zebrafish homeobox genes homologous to Hox-2.1 and En-2 of mouse.

Vertebrate homeobox genes have been identified on the basis of sequence homology to Drosophila segmentation and homeotic genes. We have analyzed the spatial distribution patterns in hatching larvae of transcripts from two different types of zebrafish (Brachydanio rerio) homeobox genes. Tritiated DNA fragments from one zebrafish gene (ZF-21) of the Antennapedia-class and one (ZF-EN) of the engrailed-type were used as probes to detect transcripts in larval tissue sections. Both zebrafish genes are expressed mainly in spatially restricted regions of the central nervous system. The transcripts from ZF-21 was detected in the posterior part of the hindbrain, and ZF-EN was found to be most intensively expressed in a restricted domain located in the region of the junction between the mid- and hindbrain. These neural expression patterns are very similar to those of the homologous murine genes Hox-2.1 and En-2 and clearly suggest a strong functional conservation.

Animals↗
PubMed2005

Identification of genes differentially expressed in extraradical mycelium and ectomycorrhizal roots during Paxillus involutus-Betula pendula ectomycorrhizal symbiosis.

The development of ectomycorrhizal symbiosis leads to drastic changes in gene expression in both partners. However, little is known about the spatial regulation of symbiosis-regulated genes. Using cDNA array profiling, we compared the levels of expression of fungal genes corresponding to approximately 1,200 expressed sequenced tags in the ectomycorrhizal root tips (ECM) and the connected extraradical mycelium (EM) for the Paxillus involutus-Betula pendula ectomycorrhizal association grown on peat in a microcosm system. Sixty-five unique genes were found to be differentially expressed in these two fungal compartments. In ECM, a gene coding for a putative phosphatidylserine decarboxylase (Psd) was up-regulated by 24-fold, while genes coding for urea (Dur3) and spermine (Tpo3) transporters were up-regulated 4.1- and 6.2-fold in EM. Moreover, urea was the major nitrogen compound found in EM by gas chromatography-mass spectrometry analysis. These results suggest that (i) there is a spatial difference in the patterns of fungal gene expression between ECM and EM, (ii) urea and polyamine transporters could facilitate the translocation of nitrogen compounds within the EM network, and (iii) fungal Psd may contribute to membrane remodeling during ectomycorrhiza formation.

Basidiomycota↗
PubMed2005

Somatic transgenesis in the avian model system.

The chick embryo is a versatile model system, in which classical embryology can be combined with modern molecular approaches. In the last two decades, several efficient methods have been developed to introduce exogenous genes into the chick embryo. These techniques allow alteration of gene expression levels in a spatially and temporally restricted manner, thereby circumventing embryonic lethality and/or eliminating secondary effects in other tissues. Here, we present the current status of avian somatic transgenic techniques, focusing on electroporation and retrovirus-mediated gene transfer. Electroporation allows quick and efficient gain-of-function studies based on transient misexpression of genes. Retroviral vectors, which are capable of integrating exogenous genes into the host chromosome, permit analysis of long-term effects of gene misexpression. The variety of methods available for somatic transgenesis, along with the recent completion of the chicken genome, are transforming the chick embryo into one of the most attractive model systems to examine function of genes that are important for embryonic development.

Animals↗
PubMed2002

Subchromosomal positioning of the epidermal differentiation complex (EDC) in keratinocyte and lymphoblast interphase nuclei.

The epidermal differentiation complex (EDC) at 1q21 is host to many structurally and functionally related genes coding for proteins involved in the differentiation process of keratinocytes. The grouping together of these genes which share spatial and temporal expression and interrelated functions is a remarkable genomic feature which has led to suggestions that the region may have a coordinated transcription control mechanism. With the growing awareness that the organization of the genome within the interphase nucleus is relevant to transcriptional activity, we have investigated the spatial organization of the EDC in the nuclei of keratinocytes, where the EDC genes are highly expressed, and lymphoblasts, where they are silent. Using 2D and 3D FISH we find that in keratinocyte nuclei the EDC is frequently positioned external to the chromosome 1 territory compared to lymphoblasts where the EDC more often adopts a peripheral or internal location. It has been previously shown that the MHC region can extend from the chromosome 6 territory in relation to transcriptional activity. This study of the EDC thus provides a further example of a gene-dense complex capable of assuming extraterritorial positioning in relation to cell type/transcription status.

B-Lymphocytes↗