Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “spatial gene expression”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 685 records · Page 38Linked to original sources
PubMed1994

The spatial and temporal dynamics of Sax1 (CHox3) homeobox gene expression in the chick's spinal cord.

Sax1 (previously CHox3) is a chicken homeobox gene belonging to the same homeobox gene family as the Drosophila NK1 and the honeybee HHO genes. Sax1 transcripts are present from stage 2 H&H until at least 5 days of embryonic development. However, specific localization of Sax1 transcripts could not be detected by in situ hybridization prior to stage 8-, when Sax1 transcripts are specifically localized in the neural plate, posterior to the hindbrain. From stages 8- to 15 H&H, Sax1 continues to be expressed only in the spinal part of the neural plate. The anterior border of Sax1 expression was found to be always in the transverse plane separating the youngest somite from the yet unsegmented mesodermal plate and to regress with similar dynamics to that of the segregation of the somites from the mesodermal plate. The posterior border of Sax1 expression coincides with the posterior end of the neural plate. In order to study a possible regulation of Sax1 expression by its neighboring tissues, several embryonic manipulation experiments were performed. These manipulations included: removal of somites, mesodermal plate or notochord and transplantation of a young ectopic notochord in the vicinity of the neural plate or transplantation of neural plate sections into the extraembryonic area. The results of these experiments revealed that the induction of the neural plate by the mesoderm has already occurred in full primitive streak embryos, after which Sax1 is autonomously regulated within the spinal part of the neural plate.

Animals↗
PubMed1992

Regulation of TIMP gene expression in cell culture and during mouse embryogenesis.

We have identified elements in the 5' region of the murine tissue inhibitor of metalloproteinase (TIMP) gene which control the response to serum, phorbol esters and transforming growth factor beta (TGF-beta) in cell culture. These elements lie between -858 and -601 relative to the translation initiation start site in the gene and are distinct from those that control expression in response to virus induction. The temporal and spatial expression of the TIMP gene was also analysed during mouse embryogenesis using in situ hybridization. A transgenic mouse line was constructed which expressed a TIMP/lac Z fusion gene. Using in situ beta-galactosidase assays we were able to compare the expression of the transgene with the endogenous gene. Thus we concluded that most of the sequences controlling in vivo expression of TIMP were present in the transgene and could be localised to the 5' region of the gene.

3T3 Cells↗
PubMed1994

Spatial and temporal expression patterns of two sodium channel genes in Drosophila.

Genetic and molecular studies have identified two different sodium channel genes in Drosophila, para and DSC1. The functional contributions of the para-encoded channel have been inferred from analysis of mutant phenotypes. However, no mutations of DSC1 have been identified, so the in vivo functions of the channel it encodes are not yet known. To learn more about the possible functions of DSC1 in the Drosophila nervous system compared with those of para, we have characterized the expression patterns of these two sodium channel genes at embryonic, larval, pupal, and adult stages by tissue in situ hybridization, para encodes the predominant type of sodium channel and is ubiquitously transcribed throughout the CNS and PNS at all developmental stages. The expression pattern of DSC1 is very different from para during embryonic and larval stages during which there are very few DSC1-expressing cells in either the CNS or PNS. Double-labeling studies suggest that some of these cells are non-neuronal. However, in pupal and adult stages, para and DSC1 have completely overlapping patterns of expression in the CNS and retina. In the pupal and adult, PNS expression of these genes is still distinct because only para transcripts are detected in wing sensory neurons. The strong and widespread expression of DSC1 in the CNS of pupae and adults suggests that the DSC1 channels are likely to provide an important function in neurons during these stages. Since most, if not all, neurons in the pupal and adult CNS express both para and DSC1, these two sodium channel genes probably subserve distinct functions within these cells. Our results provide the background for elucidating the respective in vivo contributions of para and DSC1 to neuronal excitability and for dissecting the regulatory mechanisms that underlie their different patterns of expression.

Animals↗
PubMed1997

Spatial and temporal expression of the period and timeless genes in the developing nervous system of Drosophila: newly identified pacemaker candidates and novel features of clock gene product cycling.

The circadian timekeeping system of Drosophila functions from the first larval instar (L1) onward but is not known to require the expression of clock genes in larvae. We show that period (per) and timeless (tim) are rhythmically expressed in several groups of neurons in the larval CNS both in light/dark cycles and in constant dark conditions. Among the clock gene-expressing cells there is a subset of the putative pacemaker neurons, the "lateral neurons" (LNs), that have been analyzed mainly in adult flies. Like the adult LNs, the larval ones are also immunoreactive to a peptide called pigment-dispersing hormone. Their putative dendritic trees were found to be in close proximity to the terminals of the larval optic nerve Bolwig's nerve, possibly receiving photic input from the larval eyes. The LNs are the only larval cells that maintain a strong cycling in PER from L1 onward, throughout metamorphosis and into adulthood. Therefore, they are the best candidates for being pacemaker neurons responsible for the larval "time memory" (inferred from previous experiments). In addition to the LNs, a subset of the larval dorsal neurons (DNLs) expresses per and tim. Intriguingly, two neurons of this DNL group cycle in PER and TIM immunoreactivity almost in antiphase to the other DNLs and to the LNs. Thus, the temporal expression of per and tim are regulated differentially in different cells. Furthermore, the light sensitivity associated with levels of the TIM protein is different from that in the heads of adult Drosophila.

Aging↗
PubMed1988

Expression of the gene for main intrinsic polypeptide (MIP): separate spatial distributions of MIP and beta-crystallin gene transcripts in rat lens development.

The main intrinsic polypeptide (MIP) is the major protein present in the lens fiber cell membrane and is the product of a gene which, as far as is known, is expressed only in the lens. We have used in situ hybridization and immunofluorescence microscopy to characterize the expression of this gene during the course of development in the rat. At progressive stages of lens morphogenesis, we find that synthesis of the protein is closely tied to the accumulation of MIP mRNA in cells that are committed to terminal differentiation, first in the elongating presumptive primary lens fibers and later in the secondary fibers as they differentiate from the anterior epithelial cells. The transcripts accumulate in the basal cytoplasm of the primary fibers and in the cytoplasm which surrounds the cell nucleus in the secondary fibers. We have compared this pattern of expression with that of a gene for a cytoplasmic protein, beta-crystallin beta-A1/A3. In sharp contrast to the localized concentrations seen for the MIP mRNA, beta-A1/A3 transcripts are relatively uniformly distributed throughout the cytoplasm. Neither MIP nor crystallin gene appears to be transcriptionally active in the undifferentiated epithelial cell, but transcripts from the beta-A1/A3 gene appear earlier in fiber cell differentiation than do those from the gene for MIP.

Animals↗
PubMed2005

Delivery of wingless to the ventral mesoderm by the developing central nervous system ensures proper patterning of individual slouch-positive muscle progenitors.

During the development of any organism, care must be given to properly pattern gene expression in temporally and spatially regulated manners. This process becomes more complex when the signals that regulate a target tissue are produced in an adjacent tissue and must travel to the target tissue to affect gene expression. We have used the developing somatic mesoderm in Drosophila as a system in which to examine this problem. Our investigation uncovered a novel mechanism by which Wingless (Wg) can travel from its source in the ectoderm to regulate the expression of the somatic muscle founder identity gene, slouch, in the ventral mesoderm. Delivery of Wg to the mesoderm by the developing Central Nervous System (CNS) exploits the stereotypic formation of this tissue to provide high Wg levels to Slouch founder cell cluster II in a temporally specific manner. Coordinated development of these tissues provides a reliable mechanism for delivering high Wg levels to a subset of mesodermal cells. It also provides a means for one signaling pathway to be used reiteratively throughout development to impart unique positional and character information within a target field.

Animals↗
PubMed2000

Overlapping expression of amphioxus homologs of the thyroid transcription factor-1 gene and thyroid peroxidase gene in the endostyle: insight into evolution of the thyroid gland.

The endostyle is a pharyngeal organ of uro- chordates, cephalochordates, and primitive vertebrates. This organ has iodine-concentrating and iodine-metabolism activities, and therefore the endostyle is considered to be homologous to the follicle of the thyroid gland. In higher vertebrates the genes for both thyroid transcription factor-1 (TTF-1) and thyroid peroxidase (TPO) are expressed in the thyroid gland follicle. TTF-1 regulates the expression of TPO, which encodes an iodinating enzyme associated with thyroid hormone synthesis. A recent study showed that the ascidian TTF-1 and TPO genes are specifically expressed in the endostyle, but that the expression domains of these genes are not overlapping, suggesting that ascidian TPO is not regulated by TTF-1. To investigate the molecular mechanisms involved in the formation and function of the endostyle, with special reference to the evolution of the follicle of the thyroid gland, I isolated and characterized cDNA clones for the amphioxus homologs of the TTF-1 gene (BbTTF-1) and TPO gene (BbTPO) from Branchiostoma belcheri. Reverse transcriptase-polymerase chain reaction/Southern blotting revealed that both amphioxus TTF-1 and TPO genes are expressed mainly in the adult endostyle. Spatial and temporal expression patterns assessed by in situ hybridization revealed that BbTTF-1 is expressed in the endodermal cells during early embryogenesis and is maintained in all zones of the adult endostyle. On the other hand, expression of BbTPO is chiefly in zones 5 and 6 of the adult endostyle where it overlaps with that of BbTTF-1, and to a lesser extent in zones 1 and 3. This restriction of the expression of BbTTF-1 and BbTPO to the endostyle strongly suggests that the endostyle is homologous to the follicle of the thyroid gland. Moreover, the spatial and temporal expression patterns of these genes suggest that TTF-1 regulates TPO expression. The coexpression of these genes in amphioxus suggests that regulation of TPO by TTF-1 was present in the common ancestor of cephalochordates (acraniates) and craniates.

Amino Acid Sequence↗
PubMed2026

Stage-specific ROMO1 in rheumatoid arthritis: predictive immune insights into the MIF pathway and HLA-DR/IL2RA axis via integrated GWAS, transcriptomic, single-cell, and spatial profiling.

Emerging evidence links reactive oxygen species modulator 1 (ROMO1), a key mitochondrial ROS regulator, to rheumatoid arthritis (RA) pathogenesis. However, its exact mechanism remains elusive given the conflicting evidence about its specific function. We used a four-level integrative framework combining multi-omics data and literature‑supported mechanistic inference. At the genetic level, Mendelian randomization (MR) was performed to explore potential causal relationships between ROMO1, IL2RA, HLA-DR, MIF, and RA risk, followed by differential expression analysis and machine learning-based feature selection to identify key mROS genes. The temporal expression dynamics of ROMO1 were assessed in RA progression. At the cellular and tissue levels, we integrated single-cell RNA sequencing and spatial transcriptomics to map cell-type-specific expression and synovial localization of ROMO1-related immune cells and pathways. Finally, our multi-omics findings were contextualized with literature-supported mechanistic inference. (1) MR results were consistent with a potential protective effect of ROMO1 on RA (OR = 0.52) and its potential regulation of risk factors IL2RA (OR = 0.46) and HLA-DR (OR = 0.40). Conversely, IL2RA (OR = 1.42), HLA-DR (OR = 1.88), and MIF (OR = 1.17) were positively associated with RA risk. Additionally, ROMO1 was identified as a top candidate diagnostic predictor with stage-specific dynamics: downregulated in the early but upregulated in the late/remission stages. (2) Single-cell RNA sequencing showed ROMO1's cell-specific expression in CD14+ HLA-DR+ CD74+ monocytes and CD4+ IL2RA+ T cells. Cell communication analysis further suggested that these cells may participate in MIF pathway regulation. Spatial transcriptomics subsequently identified that ROMO1-related cells localized to synovial pathological regions, with MIF pathway changes correlated with RA progression. (3) Finally, literature-supported mechanistic inference suggests that ROMO1 may modulate mROS levels to promote anti-inflammatory M2 macrophage polarization, which could theoretically contribute to reduced systemic inflammation and the alleviation of multi-organ decline in RA. This integrated multi-omics investigation, supported by literature-based mechanistic inference, suggests ROMO1 as a stage-dependent biomarker candidate and potential immune regulator in RA.

Humans↗
PubMed2002

Global analysis of gene expression patterns in developing mouse neocortex using serial analysis of gene expression.

Molecular inventories of the developing mouse neocortex before and after birth were generated using the global gene expression profiling tool serial analysis of gene expression (SAGE). Libraries were generated from embryonic day 15 and postnatal day 1 mouse neocortex and more than 40,000 tags were collected (20,211 and 22,001 tags, representing 11,706 and 12,402 transcripts, respectively). Comparison of the two libraries resulted in the identification of 321 transcripts that were differentially expressed (P < 0.05). Differential expression was independently verified for selected genes by Northern blotting, and in situ hybridization revealed spatial expression patterns in the neocortex. Differentially expressed transcripts included genes known to be important in neocortical development (e.g., brain factor 1, neuroD2, and Id2), genes not previously associated with neocortical development (such as brahma-related gene 1, receptor for activated C-kinase I, hypermethylated in cancer 2, and Evi9), and genes of unknown identity or function.

Animals↗
PubMed1994

Gene ecology: a cis-acting gene-to-gene interaction due to the spatial arrangement of genes in chromosomes affects neighbouring transfected c-H-ras expression.

A cis-acting interference between gene activities, which occurs when two genes lie on the same DNA strand and have an intergenic distance less than a defined length, was previously deduced when chromosomal organizations of various higher eukaryote nuclear genes in clusters were compared. In order to investigate such an interference due to arrangement of genes along chromosomes, we have isolated a few cell lines which possessed (i) human mutated c-H-ras fused with the mouse mammary tumour virus long terminal repeat and (ii) the E. coli xanthine-guanine phosphoribosyltransferase (gpt) gene with the SV40 promoter, on the same or on different DNA strands, separated by a short intergenic distance or unlinked. Since the cancerous phenotype of a cell can be readily identified due to c-H-ras expression, we examined in these cell lines whether continuous c-H-ras expression, induced by dexamethasone, is disturbed through a cis-acting gene-to-gene interaction when the expression of the neighbouring gpt gene is enforced and as a result, the cancerous state of a cell is converted to the 'normal' state. The enforced expression of the neighbouring gpt gene was shown to alter c-H-ras expression, and thus reversible conversion of a cell between cancerous and normal states occurred only when the cell possessed an optimum number of the gene pair, in which both c-H-ras and the gpt gene were on the same DNA strand. This implies that the spatial arrangement of genes in chromosomes plays an important role in the regulation of gene expression in a cluster.

Animals↗
PubMed1996

Synthesis of a new substrate for detection of lacZ gene expression in live Drosophila embryos.

Escherichia coli lacZ, which encodes beta-galactosidase, has become a widely used reporter gene to study the developmental regulation of gene expression in a variety of organisms. To detect the presence of the beta-galactosidase, the sample must be fixed and appropriately stained. This sort of analysis yields rather crude estimates of the spatial-temporal changes in gene expression patterns. In addition, one cannot recover interesting specimens for propagation. A novel fluorogenic beta-galactosidase substrate for use in live Drosophila melanogaster embryos has been designed and synthesized. This compound provides a means to determine gene dosage in live embryos so that one can unambiguously determine the genotype of a living embryo. This will be useful for detailed analysis of cellular and morphogenetic behavior changes in live embryos that are homozygous for embryonic lethal mutations. In the course of testing this compound, a new beta-galactoside hydrolytic activity, different from the previously identified beta-galactosidase, has been discovered to reside in macrophages and the intervitelline space.

Animals↗
PubMed2003

Expression of the mouse homologue for the human GCDFP-15/PIP gene during pre- and early post-natal development.

The function of the mouse submaxillary gland/prolactin inducible protein (mSMGP/mPIP), the homologue of the human gross cystic disease fluid protein 15 (GCDFP-15)/prolactin inducible protein (hPIP) remains unknown. The human gene, normally expressed in apocrine glands of healthy individuals, is aberrantly expressed in human breast cancers where it is regulated by hormones including androgens, and in prostate cancers. We have previously reported that in the adult mouse and rat, gene expression is tissue-specific for the salivary and lacrimal glands, and is hormonally regulated. In this study, we examine the endogenous pattern of mouse SMGP/PIP (mSMGP/mPIP) gene expression in mid- and late-embryonic, and in early postnatal development. Gene expression was analyzed by RT-PCR followed by Southern blot analysis, and by in situ hybridization. Gene expression was detected in the submandibular gland as early as embryonic day 14 (E14), a period that coincides with the initiation of submandibular gland development in the embryo, suggesting that mSMGP/mPIP may have a functional role in the developing gland. Nearing the end of gestation, E18, mSMGP/mPIP transcripts were localized in the proacinar cells of the gland, and gene expression continued to be maintained following birth. In addition, during early postnatal development, mSMGP/mPIP gene expression was detected in the other two major salivary glands, the sublingual and parotid, as well as in the lacrimal gland and in reproductive tissues. In the prostate, gene expression was turned off by 10 weeks of age. The spatial and temporal pattern of the mSMGP/mPIP gene expression, in addition to our recent demonstration that mSMGP/mPIP is found in mouse saliva and can bind bacteria, suggest that this protein may have a protective role in the mouse.

Animals↗
PubMed1993

Developmental control elements in the promoter of a Drosophila vitelline membrane gene.

DNA fragments from the 5' flanking region of Drosophila melanogaster vitelline membrane gene VM26A1 were fused to hsp/lacZ reporter genes, reintroduced via P-element-mediated germ line transformation, and functionally assayed by histological staining for beta-galactosidase activity. A developmental control element capable of promoting the basic vitelline membrane (VM) expression pattern was found within a 176-bp region. Additional multiple genetic control elements were found to be involved in modifying the level and spatial pattern of reporter gene expression but these required the 176-bp element in order to function. Unexpectedly, in isolation this 176-bp core element also promotes abnormal expression of the reporter gene in border cells of stage 8 and 9 egg chambers. This abnormal border cell expression is apparently suppressed in the native gene by an adjacent negative control element.

Animals↗
PubMed1999

Time-dependent alteration of insulin-like growth factor gene expression during nerve regeneration in regions of muscle enriched with neuromuscular junctions.

Insulin-like growth factors (IGFs) increase the rate of motor axon elongation, prevent motoneuron death, and may support the reestablishment of synapses following nerve injury. In situ hybridization was used in the present study to examine the temporal and spatial distribution of IGF gene expression in soleus muscle following sciatic nerve crush in rats. In intact muscle, IGF-II gene expression was generally low, and localized to interstitial cells, possibly fibroblast and Schwann cells. These cells were found in the middle of muscle which is enriched in neuromuscular junctions. IGF-II gene expression, 4-6 days postcrush, was increased in interstitial cells. Thereafter, IGF-II gene expression was also increased in muscle cells or cells closely associated with muscle fibers, such as satellite cells. IGF-II gene expression was increased to a much greater extent in the midregion of muscle enriched in end-plates than in the two ends of muscle, but returned towards normal following the reestablishment of functional synapses. On the other hand, IGF-I gene expression was only slightly increased following nerve crush, and this increase was associated with interstitial, but not muscle cells. These results show that the IGF-I and IGF-II genes are regulated by independent signals and may play separate roles during nerve regeneration. For example, a regional increase in IGF-II gene expression may support preferential nerve terminal sprouting in the middle of muscle enriched in neuromuscular junctions, thereby increasing the probability for the reestablishment of synapses.

Animals↗
PubMed2001

Identification and expression of the mammalian homologue of Bicaudal-C.

Translational activation and repression play an important role in the spatial-temporal regulation of gene expression in embryonic development. Bicaudal-C is an RNA-binding molecule believed to function at this post-transcriptional level. Loss-of-function mutants in Drosophila affect anterior-posterior patterning because of ectopic and premature translation of the posterior determinant oskar. The Xenopus homologue of Bicaudal-C is one of the few molecules that, when microinjected ectopically, results in endoderm formation in the absence of mesoderm induction. Here we report the sequence and expression pattern of the murine and human homologues of Bicaudal-C. The human gene is located on chromosome 10q21.2. Expression analysis in mouse using in situ hybridization detects expression of Bicaudal-C not only in domains detected in Xenopus, but also in previously unreported regions. As in Xenopus, mouse Bicaudal-C mRNA is found in the growing oocyte, Hensen's node, and the developing kidney. Additionally, at later stages it is strongly expressed in the developing gut endoderm, in areas of cartilage formation, in pleuro-peritoneal membrane derivatives, in lung mesenchyme, and in the stroma of the ovary. We conclude that mouse Bicaudal-C is a maternally provided gene product that is tightly regulated during mammalian cell differentiation.

Amino Acid Sequence↗
PubMed1993

Control of segment-like patterns of gene expression in the mouse cerebellum.

A Purkinje cell-specific transgene, L7-lacZ, is expressed in a series of parasagitally oriented stripes in the mouse cerebellum. This banding pattern can be perturbed by promoter mutation, showing that a combination of positive and negative control elements contributes to the temporal and spatial map of L7 gene expression. In addition to the parasagittal stripes, certain mutations reveal Purkinje cells organized into compartments oriented in the transverse plane of the cerebellum. Transcription factors of the POU or homeobox families appear to be involved in controlling L7 expression in the transverse orientation. Strikingly, some of the domains of gene expression revealed by the mutations appear to correspond to functional compartments of Purkinje cells, thereby suggesting an underlying genetic principle used to orchestrate functional organization in the nervous system.

Animals↗
PubMed1995

A role for En-2 and other murine homologues of Drosophila segment polarity genes in regulating positional information in the developing cerebellum.

To gain insight into the molecular genetic basis of cerebellar patterning, the expression patterns of many vertebrate homologues of Drosophila segment polarity genes were examined during normal and abnormal cerebellar development, including members of the En, Wnt, Pax, Gli and Dvl gene families. Five of these genes were found to show transient, spatially restricted patterns of expression. Strikingly, expression of En-2, En-1, Wnt-7B and Pax-2 defined eleven similar sagittal domains at 17.5 dpc, reminiscent of the transient sagittal domains of expression of Purkinje cell markers which have been implicated in cerebellar afferent patterning. Postnatally, transient anterior/posterior differences in expression were observed for En-2, En-1, Gli and Wnt-7B dividing the cerebellum into anterior and posterior regions. The expression patterns of these genes were altered in cerebella of En-2 homozygous mutant mice, which show a cerebellar foliation patterning defect. Strikingly, four of the Wnt-7B expression domains that are adjacent to the En-2 domains are lost in En-2 mutant embryonic cerebella. These studies provide the first evidence of a potential network of regulatory genes that establish spatial cues in the developing cerebellum by dividing it into a grid of positional information required for patterning foliation and afferents. Taken together with previous gene expression studies, our data suggests that eleven sagittal domains and at least two anterior/posterior compartments are the basic elements of spatial information in the cerebellum.

Animals↗
PubMed1992

Expression pattern of a murine homeobox gene, Dbx, displays extreme spatial restriction in embryonic forebrain and spinal cord.

Homeobox genes specify regional identity during development. A homeobox sequence that we have named Dbx was isolated from 13.5-day embryonic mouse telencephalon cDNA. The Dbx homeodomain shows highest sequence homology to Drosophila H2.0 and chicken CHox E. We report here the expression pattern of Dbx during mouse embryogenesis. In situ hybridization analyses indicate that Dbx is expressed exclusively within the embryonic central nervous system in a highly restricted manner. Dbx transcripts are detected within a region of the prospective cerebral cortex of the midgestation telencephalon. Dbx is also expressed in the diencephalon as well as in two thin continuous columns of neuroblasts within the hindbrain and spinal cord. This expression is limited to regions of active mitosis. Dbx may act to specify subsets of neuroblasts during the development of the central nervous system.

Amino Acid Sequence↗