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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↗
PubMed2006

The expression patterns of SAG12/Cab genes reveal the spatial and temporal progression of leaf senescence in Brassica napus L. with sensitivity to the environment.

Despite a high nitrate uptake capacity, the nitrogen use efficiency (NUE) of oilseed rape is weak due to a relatively low N remobilization from vegetative (mostly leaves) to growing parts of the plant. Thus, this crop requires a high rate of N fertilization and leaves fall with a high N content. In order to reduce the rate of N fertilization and to improve the environmental impact of oilseed rape, new genotypes could be selected on their capacity to mobilize the foliar N. Various indicators of leaf senescence in oilseed rape were analysed during plant growth, as well as during senescence induced by N deprivation. Metabolic changes in leaves of increasing age were followed in N-supplied and N-deprived rosettes by measuring chlorophyll, total N, and soluble protein contents. Similarly, the expression of genes known to be up-regulated (SAG12) or down-regulated (Cab) during leaf senescence was monitored. The amount of soluble proteins per leaf was a better indicator of leaf senescence than chlorophyll or total N content, but was not evaluated as an accurate indicator under conditions of N deprivation. On the other hand, up-regulation of SAG12 concomitantly with down-regulation of Cab in the leaf revealed the spatial and temporal progression of leaf senescence in oilseed rape. This study shows, for the first time at the whole plant level, that the SAG12/Cab gene expressions match the sink/source transition for N during both developmental and nutrient stress-induced leaf senescence.

Aging↗
PubMed1999

Spatial pattern of constitutive and heat shock-induced expression of the small heat shock protein gene family, Hsp30, in Xenopus laevis tailbud embryos.

We employed whole-mount in situ hybridization and immunohistochemistry to study the spatial pattern of hsp30 gene expression in normal and heatshocked embryos during Xenopus laevis development. Our findings revealed that hsp30 mRNA accumulation was present constitutively only in the cement gland of early and midtailbud embryos, while hsp30 protein was detected until at least the early tadpole stage. Heat shock-induced accumulation of hsp30 mRNA and protein was first observed in early and midtailbud embryos with preferential enrichment in the cement gland, somitic region, lens placode, and proctodeum. In contrast, cytoskeletal actin mRNA displayed a more generalized pattern of accumulation which did not change following heat shock. In heat shocked midtailbud embryos the enrichment of hsp30 mRNA in lens placode and somitic region was first detectable after 15 min of a 33 degrees C heatshock. The lowest temperature capable of inducing this pattern was 30 degrees C. Placement of embryos at 22 degrees C following a 1-h 33 degrees C heat shock resulted in decreased hsp30 mRNA in all regions with time, although enhanced hsp30 mRNA accumulation still persisted in the cement gland after 11 h compared to control. In late tailbud embryos the basic midtailbud pattern of hsp30 mRNA accumulation was enhanced with additional localization to the spinal cord as well as enrichment across the embryo surface. These studies demonstrate that hsp30 gene expression can be detected constitutively in the cement gland of tailbud embryos and that heat shock results in a preferential accumulation of hsp30 mRNA and protein in certain tissues.

Animals↗
PubMed2001

Stanniocalcin gene expression during mouse urogenital development: a possible role in mesenchymal-epithelial signalling.

Stanniocalcin (STC) is a polypeptide hormone first discovered in fish and more recently in mammals. In mammals, the STC gene is widely expressed and the hormone is involved in a variety of functions, but STC does not normally circulate in the blood. In both kidney and gut, STC regulates phosphate fluxes across the transporting epithelia, whereas in brain it protects neurons against cerebral ischemia and promotes neuronal cell differentiation. However, the gene is most highly expressed in ovary and expression is dramatically up-regulated by both pregnancy and nursing. STC mRNA levels are also high in the developing mouse embryo, but literally nothing is known of the tissue pattern of gene expression. Therefore, the aim of this study was to map the temporal and spatial patterns of gene expression during mouse embryologic development, starting with the urogenital system where the gene is so highly expressed in adults. STC mRNA was evident as early as E10.5 in both the mesonephros and genital ridge. Between E10.5 and 14.5 in developing kidney, STC was produced in undifferentiated mesenchyme cells and sequestered by ureteric bud epithelial cells that did not express the gene but nonetheless contained high levels of STC protein. Thereafter, the distribution pattern resembled that in adults such that gene expression predominated in collecting duct cells, whereas protein was present in most nephron segments. The pattern of gene expression during gonadal development was sexually dimorphic. In males, expression was first evident on E12.5 in interstitial mesenchyme cells surrounding the developing sex cords, whereas the protein accumulated in developing gonocytes within the sex cords that did not express the gene. This pattern became more pronounced over the course of gestation. In contrast, ovarian gene expression was only weakly evident during development. Collectively, the evidence suggests that in addition to its regulatory effects in adults, STC has novel and distinctive roles in the mesenchymal-epithelial interactions that are vital to normal organogenesis.

Animals↗
PubMed1999

Initiation, establishment and maintenance of Hox gene expression patterns in the mouse.

Spatially and temporally restricted expression of the Hox genes along the main and appendicular axes is essential for correct patterning of vertebrate embryos. In this overview we discuss the latest data that shed light on the mechanisms underlying the generation of the expression domains of the Hox genes. The molecular genetic interactions governing initial transcription of the Hox genes in the posterior part of the primitive streak during mouse and chick gastrulation remain enigmatic. But the recent discovery by Kondo and Duboule (Cell, 97, 1999, 407-417) of a "cluster repressive regulation", will undoubtedly lead to a better understanding of the molecular genetic mechanism underlying colinear and sequential initiation of Hox gene transcription. Recently progress has been booked in characterizing the basal processes driving progression of the Hox expression domains during their establishment. Hox expression is still labile while being established. The transcriptional state of Hox genes in anterior tissues can be reprogrammed under the influence of more posterior locations. Posteriorizing activity may involve RA and FGF signaling. It is only when these interactions and, in some cases at least, regulatory interactions with Hox and cdx gene products occur appropriately, that the Hox expression domains would be correctly established. After the Hox expression domains have been established, regulatory processes involving the products of Polycomb and trithorax- Group genes start operating, perpetuating the transcriptional state of the Hox genes within and outside the expression domains. Whether control at the level of chromatin structure, believed to operate during the late maintenance phase of Hox gene expression, is also involved in regulating concerted initial expression of these genes, is a possibility that has been suggested.

Animals↗
PubMed1999

Different temporal and spatial expression of two hydrophobin-encoding genes of the edible mushroom Agaricus bisporus.

In a search for genes that are only expressed in fruit bodies of the basidiomycete Agaricus bisporus, two cDNAs, hypA and hypB that encode hydrophobins have been isolated previously. In this study, the structure of hypB is resolved and it is shown that the two genes are differentially expressed, indicating that the encoded hydrophobins serve different functions in A. bisporus mushrooms. hypB encodes a polypeptide (HYPB) of 119 aa that shows little sequence identity with HYPA apart from the characteristic arrangement of eight cysteines found exclusively in hydrophobins. The temporal and spatial expression of the two hydrophobin-encoding genes during fruit body development was compared using Northern analysis and in situ hybridization. Accumulation of hypA mRNA was found in tissue fractions consisting of undifferentiated white hyphae. In situ hybridization showed that the highest hypA mRNA levels are not found in the outermost cell layers of the pileipellis but in the cell layers adjacent to that. The highest level of expression of hypB occurs early in development when the primordium differentiates into densely packed, randomly oriented cap hyphae and loosely packed, vertically oriented stipe hyphae. In mature mushrooms, a strong accumulation of hypB transcripts was found only in the transitional zone between cap and stipe tissue, demonstrating that transcription regulation of hypB is clearly distinct from hypA.

Agaricus↗
PubMed1991

The homeotic gene Sex combs reduced of Drosophila melanogaster is differentially regulated in the embryonic and imaginal stages of development.

The Sex combs reduced (Scr) locus is unique among the genes contained within the Antennapedia complex (ANT-C) of Drosophila melanogaster in that it directs functions that are required for both cephalic and thoracic development in the embryo and the adult. Antibodies raised against protein encoded by Scr were used to follow the distribution of this gene product in embryos and imaginal discs of third instar larvae. Analysis of Scr protein accumulation in embryos hemizygous for breakpoint lesions mapping throughout the locus has allowed us to determine that sequences required for establishment of the Scr embryonic pattern are contained within a region of DNA that overlaps with the identified upstream regulatory region of the segmentation gene fushi tarazu (ftz). Gain-of-function mutations in Scr result in the presence of ectopic sex comb teeth on the first tarsal segment of mesothoracic and metathoracic legs of adult males. Heterozygous combinations of gain-of-function alleles with a wild-type Scr gene exhibit no evidence of ectopic protein localization in the second and third thoracic segments of embryos. However, mesothoracic and metathoracic leg imaginal discs can be shown to accumulate ectopically expressed Scr protein, implying a differential regulation of the Scr gene during these two periods of development. Additionally, we have found that the spatial pattern of Scr gene expression in imaginal tissues involved in the development of the adult thorax is governed in part by synapsis of homologous chromosomes in this region of the ANT-C. However, those imaginal discs that arise anteriorly to the prothorax do not appear to be sensitive to this form of gene regulation. Finally, we have demonstrated that the extent of Scr expression is influenced by mutations at the Polycomb (Pc) locus but not by mutant alleles of the zeste (z) gene. Taken together, our data suggests that Scr gene expression is differentially regulated both temporally and spatially in a manner that is sensitive to the structure of the locus.

Animals↗
PubMed2006

Expression analysis of IGFBP-rP10, IGFBP-like and Mig30 in early Xenopus development.

To date, five members of the insulin-like growth factor-binding protein (IGFBP) superfamily have been described in Xenopus laevis. Here, we report the isolation of two new IGFBPs: xIGFBP-rP10, and xIGFBP-like. The proteins share the same domain architecture, and together with Mig30, form a subgroup within the IGFBP superfamily. Temporal expression analysis shows that they are expressed differentially during early development. xIGFBP-rP10 is continuously expressed, whereas Mig30 expression peaks during gastrulation. IGFBP-like is expressed from neurulation onward. The three genes have characteristic spatial expression domains, which overlap in some regions. Both xIGFBP-rP10 and Mig30 are expressed on the dorsal side of the embryo during gastrulation. Later, xIGFBP-rP10 is expressed in the notochord, the floor plate, the somites, and the fin. xIGFBP-like expression is seen primarily in the developing central nervous system and overlaps with Mig30 expression at the end of neurulation in the developing somites and in tail bud stages in the eyes.

Amino Acid Sequence↗
PubMed2002

Evolutionary divergence of vertebrate Hoxb2 expression patterns and transcriptional regulatory loci.

Hox gene expression is regulated by a complex array of cis-acting elements that control spatial and temporal gene expression in developing embryos. Here, we report the isolation of the striped bass Hoxb2a gene, comparison of its expression to the orthologous gene from zebrafish, and comparative genomic analysis of the upstream regulatory region to that of other vertebrates. Comparison of the Hoxb2a gene expression patterns from striped bass to zebrafish revealed similar expression patterns within rhombomeres 3, 4, and 5 of the hindbrain but a notable absence of expression in neural crest tissues of striped bass while neural crest expression is observed in zebrafish and common to other vertebrates. Comparative genomic analysis of the striped bass Hoxb2a-b3a intergenic region to those from zebrafish, pufferfish, human, and mouse demonstrated the presence of common Meis, Hox/Pbx, Krox-20, and Box 1 elements, which are necessary for rhombomere 3, 4, and 5 expression. Despite their common occurrence, the location and orientation of these transcription elements differed among the five species analyzed, such that Krox-20 and Box 1 elements are located 3' to the Meis, Hox/Pbx elements in striped bass, pufferfish, and human while they are located 5' of this r4 enhancer in zebrafish and mouse. Our results suggest that the plasticity exhibited in the organization of key regulatory elements responsible for rhombomere-specific Hoxb2a expression may reflect the effects of stabilizing selection in the evolution cis-acting elements.

Animals↗
PubMed1985

Temporal and spatial control of flagellar and chemotaxis gene expression during Caulobacter cell differentiation.

Each Caulobacter cell division yields daughter cells that differ from one another both structurally and functionally. By focusing on the biogenesis of the polar flagellum and the proteins of the chemosensory system, several laboratories have now defined an extensive network of genes whose temporal expression is controlled in the predivisional cell. The differential turn-on of these genes contributes to the generation of asymmetry in the predivisional cell in that the products of these genes are targeted to specific cellular locations. To define the mechanisms that mediate this temporal and spatial control, fla genes whose products are not known were accessed by the insertion of transposon-carried drug resistance markers. The transposons were altered so that upon insertion into the chromosome, transcription fusions are formed in which the promoter regions of fla genes drive the expression of the downstream promoter-less drug resistance genes. Assays of the differential placement of the promoter-less drug resistance proteins (encoded within the interrupted fla genes) allow us to determine whether the positioning of the fla gene products is controlled by signal sequences in their proteins, by specific mRNA-targeting sequences in the 5'-regulatory regions of these genes, or by specific transcription from only one of the two newly replicated chromosomes in the predivisional cell.

Cell Cycle↗
PubMed1996

Spatial and temporal relationships between Shh, Fgf4, and Fgf8 gene expression at diverse signalling centers during mouse development.

During limb outgrowth, Shh, Fgf4, and Fgf8 act as signals controlling limb growth and patterning. Because these genes are expressed in the limb bud and other known signalling centers, we have explored the relationships between the expression of these during mouse development using double in situ hybridization. Within the node and limb bud the expression domains of these genes contact each other, whereas in the floor plate the Fgf8 expression domain does not contact that of Shh. The relative temporal order of gene expression varies in different centers. The spatial and temporal expression of Fgf4, Fgf8, and Shh suggests that conservation of molecular mechanisms in different organizing centers as well as differences between them.

Animals↗
PubMed2005

Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey.

The myotome in gnathostome vertebrates, which gives rise to the trunk skeletal muscles, consists of epaxial (dorsal) and hypaxial (ventral) portions, separated by the horizontal myoseptum. The hypaxial portion contains some highly derived musculature that is functionally as well as morphologically well differentiated in all the gnathostome species. In contrast, the trunk muscles of agnathan lampreys lack these distinctions and any semblance of limb muscles. Therefore, the lamprey myotomes probably represent a primitive condition compared with gnathostomes. In this review, we compare the patterns of expression of some muscle-specific genes between the lamprey and gnathostomes. Although the cellular and tissue morphology of lamprey myotomes seems uniform and undifferentiated, some of the muscle-specific genes are expressed in a spatially restricted manner. The lamprey Pax3/7 gene, a cognate of gnathostome Pax3, is expressed only at the lateral edge of the myotomes and in the hypobranchial muscle, which we presume is homologous to the gnathostome hypobranchial muscle. Thus, the emergence of some part of a hypaxial-specific gene regulatory cascade might have evolved before the agnathan/gnathostome divergence, or before the evolutionary separation of epaxial and hypaxial muscles.

Animals↗
PubMed2004

A combined in situ hybridization and RT-PCR method to detect spatial and temporal patterns of Noggin gene expression in embryonic and postnatal rat hippocampus.

Recent studies indicate that Noggin not only plays an important role in the early development of the nervous system, but may also plays a role in postnatal central nervous system (CNS) development. In this study, we examined the relative levels and localization of Noggin mRNA in the hippocampus of rats of different developmental stages with reverse transcriptase-polymerase chain reaction (RT-PCR) and in situ hybridization. RT-PCR showed that the peak level of expression of Noggin mRNA was observed at embryonic day 13 (E13), subsequently gradually declined at 1-3 months (P1-3M) postnatal, and was detected only at a low level at P18M. In situ hybridization revealed that at embryonic stages, Noggin mRNA was localized throughout all hippocampal regions, whereas at early postnatal ages, Noggin mRNA was primarily localized in the anterior subiculum. At later postnatal ages, Noggin mRNA expression was obviously observed in the dentate gyrus and in the CA1-CA3 pyramidal cell layers. Taken together, our results demonstrate that Noggin is expressed in embryonic and postnatal hippocampus, and that the temporal and spatial patterns of its expression is developmentally regulated.

Aging↗
PubMed1990

Expression of GHF-1 protein in mouse pituitaries correlates both temporally and spatially with the onset of growth hormone gene activity.

The relationship between expression of the pituitary-specific transcription factor, GHF-1, and activation of the growth hormone and prolactin genes during mouse anterior pituitary development was investigated. While GHF-1 transcripts were detected within 24 hr of the first observable events in anterior pituitary differentiation, no GHF-1 protein could be detected until about 3 days later. The appearance of GHF-1 protein showed good temporal and spatial correlation with activation of the growth hormone gene. Prolactin gene expression, on the other hand, was observed transiently during embryonic day 16 in two different populations of cells, of which the major one does not contain GHF-1 or growth hormone. These results suggest that expression of GHF-1 is controlled both transcriptionally and posttranscriptionally. The spatial and temporal correlation between the appearance of GHF-1 protein and growth hormone gene activation suggests that GHF-1 is responsible for this very last step in the specialization of somatotrophic cells.

Animals↗
PubMed2001

Possible roles for stanniocalcin during early skeletal patterning and joint formation in the mouse.

Stanniocalcin (STC) is a polypeptide hormone discovered first in fish and more recently in mammals. In mammals, the gene is widely expressed and the hormone is, so far, known to be involved in regulating the transport of calcium or phosphate across renal and gut epithelia, and into neuronal cells. Gene expression is also high during development, and in an earlier study we mapped the temporal and spatial pattern of gene expression in the mouse urogenital system. Our data suggested that STC probably acted as a signaling molecule that was produced in mesenchyme cells and targeted to epithelial cell layers in both kidney and testes. Here we have examined STC mRNA and protein distributions between developmental stages E10.5 and E18.5 in the axial and appendicular skeleton. In the axial skeleton, STC was transiently expressed in a rostral-caudal fashion during vertebral development; protein appeared to be made in intervertebral disc mesenchyme cells and targeted to vertebral hypertrophic and prehypertrophic chondrocytes. By stage E18.5, the STC gene was active only in vertebral perichondrocytes. The pattern of expression in the appendicular skeleton was equally striking. Early in development, STC gene expression defined the initial lengths of bone primordia. The gene was expressed in mesenchyme cells at either ends of precartilaginous condensations defining future long bones and the secreted protein was targeted to the chondroblasts. Later on during joint formation, STC was highly expressed in interzone cells that defined all future joints. After cavitation, STC gene expression was greatest in perichondrocytes lining the joints. Underlying resting, proliferative and prehypertrophic chondrocytes appeared to be the targets of STC both during and after cavitation. Therefore, its pattern of expression was indicative of a role in early skeletal patterning and joint formation. Moreover, as occurs during urogenital development, it appeared that STC is made in undifferentiated mesenchyme cells and sequestered by those destined to differentiate.

Animals↗
PubMed2006

MicroRNAs in mammalian development.

Development in mammals is a complex process requiring gene expression to be spatially and temporally well-regulated. Factors modulate gene functioning by controlling transcription, translation, or mRNA degradation. microRNAs (miRNAs) are a group of small RNA molecules (approximately 22 nucleotides) that attenuate gene activity posttranscriptionally by suppressing translation or destabilizing mRNAs. miRNAs have been recently validated to regulate many animal developmental events including proliferation, differentiation, and apoptosis. Many miRNAs display intriguing expression and functioning patterns throughout these pathways. Here we will review achievements to date about studies of how miRNAs affect a variety of animal developmental transitions, from the formation of early embryos to the generation of highly specialized tissues.

Animals↗
PubMed2025

BISON: bi-clustering of spatial omics data with feature selection.

MOTIVATION: The advent of next-generation sequencing-based spatially resolved transcriptomics (SRT) techniques has reshaped genomic studies by enabling high-throughput gene expression profiling while preserving spatial and morphological context. Understanding gene functions and interactions in different spatial domains is crucial, as it can enhance our comprehension of biological mechanisms, such as cancer-immune interactions and cell differentiation in various regions. It is necessary to cluster tissue regions into distinct spatial domains and identify discriminating genes (DGs) that elucidate the clustering result, referred to as spatial domain-specific DGs. Existing methods for identifying these genes typically rely on a two-stage approach, which can lead to the phenomenon known as double-dipping. RESULTS: To address the challenge, we propose a unified Bayesian latent block model that simultaneously detects a list of DGs contributing to spatial domain identification while clustering these DGs and spatial locations. The efficacy of our proposed method is validated through a series of simulation experiments, and its capability to identify DGs is demonstrated through applications to benchmark SRT datasets. AVAILABILITY AND IMPLEMENTATION: The R/C++ implementation of BISON is available at https://github.com/new-zbc/BISON.

Software↗