Gene expression in the human placental trophoblast: a model for developmental gene regulation.
Explore the source record for details and available documents.
Alkaline Phosphatase↗
SEARCH · PubMed Health
Results for “Gene Expression Regulation, Developmental”
Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Comprehensive circRNA expression profile and hub genes screening during human liver development.
BACKGROUND: Understanding the expression of non-coding RNA in the liver during embryonic development provides important insights into liver diseases. Therefore, we investigated circular RNA (circRNA) roles in human liver development, an unexplored research domain. METHODS: Using high-throughput sequencing and bioinformatics, we analysed foetal liver samples across developmental stages (7-20 weeks post-conception). Differentially expressed (DE) genes were identified and subjected to enrichment analysis using Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG), and Disease Ontology (DO). Modular analysis was performed using the Search Tool for Retrieval of Interacting Genes (STRING), followed by construction of a protein-protein interaction (PPI) network using Cytoscape software. The key genes were screened using Molecular Complex Detection (MCODE). The mRNA levels of hub genes were validated using quantitative reverse transcription polymerase chain reaction (qRT-PCR). RESULTS: There were 645 DE circRNAs and 5,145 DE mRNAs between human livers at the three growth stages (HB, EH, and LH). It was found that the activity of circRNAs was boosted remarkably in the hepatoblastic stage. Enrichment analysis found they mainly involved in nervous system regulation of liver function, embryonic organ development and digestive system development. In addition, DE circRNAs were primarily involved in the PI3K-AKT, MAPK and calcium pathways, potentially contributing to adult liver diseases. Notably, only hsa_circ_001471 and novel_circ_017382 were simultaneously identified at all stages and were persistently downregulated. A co-expression regulatory network involving these circRNAs was established. Three hub genes (LGR5, FOXL1 and RSPO3) were identified from the PPI network of 167 genes and may play key roles in human liver development. The RT-qPCR validation results were in agreement with the sequencing data. CONCLUSIONS: Our findings provide the first insights into the roles and regulatory networks of circRNAs in human liver development, laying the groundwork for further investigations of molecular and signalling networks.
Humans↗
Developmental regulation of sarcomeric gene expression.
Explore the source record for details and available documents.
Animals↗
Developmental regulation of nuclear gene expression in Trypanosoma brucei.
Explore the source record for details and available documents.
Animals↗
Developmental regulation of CUP gene expression through DNA methylation in Mucor spp.
Inserts which carried the CUP gene from Saccharomyces cerevisiae or Mucor racemosus were used as hybridization probes to measure the methylation state and expression of the CUP gene from Mucor rouxii at different stages of growth. It was observed that the fungus contains a CUP multigene family. All the CUP genes were present in a hypermethylated DNA region in nongrowing and isodiametrically growing spores and were not transcribed at these stages. After germ tube emergence, CUP genes became demethylated and transcriptionally active. Development, demethylation, and transcription of CUP genes were blocked by the ornithine decarboxylase inhibitor 1,4-diaminobutanone. These results suggest that genes that are activated during development became demethylated in this fungus.
Carrier Proteins↗
Developmental regulation of villin gene expression in the epithelial cell lineages of mouse digestive and urogenital tracts.
The expression of villin, an actin-binding protein and major structural component of the brush border of specialized absorptive cells, was studied during mouse embryogenesis. We show that the ontogeny of villin expression is limited to the epithelial cell lineages of the digestive and uro-genital tracts and accounts for the tissue-specific expression observed in adult mice. This spatiotemporal pattern of villin expression is distinctive in sequence, intensity, regional distribution and polarization. During the development of the primitive gut, villin is faintly and discontinuously expressed in the invaginating foregut but it is expressed in every cell bordering the hindgut pocket. Later, villin expression increases along the developing intestine and concentrates in the brush border of the epithelium bordering the villi. In gut derivatives, villin is present in liver and pancreas primordia but only biliary and pancreatic cells maintain a faint villin expression as observed in adults. In the urogenital tract, mesonephric tubules are the first mesodermal derived structures to express villin. This expression is maintained in the ductuli efferents, paradidymis and epoöphoron. Villin then appears in the proximal metanephric tubules and later increases and concentrates in the brush border of the renal proximal tubular epithelial cells. Thus villin expression can be considered as an early marker of the endodermal cell lineage during the development of the digestive system. Conversely, during the development of the excretory and genital system, villin is only expressed after the mesenchyme/epithelium conversion following the appearance of tubular structures. These observations emphasize the multiple levels of regulation of villin gene activity that occur during mouse embryogenesis and account for the strict pattern of tissue-specific expression observed in adults. In the future, regulatory elements of the villin gene may be used to target the early expression of oncogenes to the digestive and urogenital tracts of transgenic mice.
Animals↗
Metabolic effects of developmental, tissue-, and cell-specific expression of a chimeric phosphoenolpyruvate carboxykinase (GTP)/bovine growth hormone gene in transgenic mice.
Transgenic mice were used to investigate sequences within the promoter of the gene for the cytosolic form of phosphoenolpyruvate carboxykinase (GTP) from the rat (EC 4.1.1.32) (PEPCK) which are involved in tissue-specific and developmental regulation of gene expression. Segments of the PEPCK promoter between -2000 and -109 were linked to the structural gene for bovine growth hormone (bGH) and introduced into the germ line of mice by microinjection. Bovine growth hormone mRNA was found in tissues that express the endogenous PEPCK gene, mainly in the liver but to a lesser extent in the kidney, adipose tissue, small intestine, and mammary gland. In the liver the chimeric PEPCK/bGH(460) gene was expressed in periportal cells, which is consistent with the zonation of endogenous PEPCK. The PEPCK/bGH gene was not transcribed in the livers of fetal mice until immediately before birth; at birth the concentration of bGH mRNA increased 200-fold. Our results indicate that the region of the PEPCK promoter from -460 to +73 base pairs contains regulatory sequences required for tissue-specific and developmental regulation of PEPCK gene expression. Mice transgenic for PEPCK/bGH(460) were not hyperglycemic or hyperinsulinemic in response to elevated bGH, as were transgenic mice with the MT/bGH gene. The number of insulin receptors in skeletal muscle was no different in mice transgenic for MT/bGH when compared with mice transgenic for PEPCK/bGH(460) and control animals. However, mRNA abundance for the insulin-sensitive glucose transporter in skeletal muscle was decreased in mice transgenic for the MT/bGH gene. The differences in glucose homeostasis noted with the two types of transgenic mice may be the result of the relative site of expression, the different developmental pattern, or hormonal regulation of expression of the bGH gene.
Animals↗
Gene expression in the Caenorhabditis elegans dauer larva: developmental regulation of Hsp90 and other genes.
Under conditions unfavorable to growth, the nematode Caenorhabditis elegans enters a developmentally arrested stage, the dauer larva. We have examined gene expression in the dauer larva and during recovery from the dauer stage. Run-on transcription assays with isolated nuclei reveal a depression of general RNA polymerase II transcription to 11-17% of that in other stages. Transcription of individual gene families (including actin, collagen, hsp70, and histone) is similarly depressed relative to actively growing stages. Dauer larvae are, however, capable of being induced for heat shock messages, indicating that they are competent to initiate and elongate transcripts. For most genes surveyed, reduced transcription in dauer larvae correlates with a decrease in message abundance. Hsp70 mRNA, however, is transcribed at lower rates but accumulates at levels comparable to those in other stages. Interestingly, dauer larvae are 15-fold enriched in a mRNA for a C. elegans hsp90 gene. Hsp90 mRNA accumulation is regulated at least in part by differential stability. Dauer larvae thus appear to have a unique pattern of gene expression. Upon placement in food, dauer larvae reenter the developmental pathway as late-stage larvae. Dauer recovery is accompanied by a temporally regulated sequence of gene expression. At least four distinct patterns of gene expression can be distinguished during exit from the dauer stage. Steady-state levels of hsp70 and polyubiquitin mRNA rise sharply within 75 min of recovery before declining by the fourth hour. Actin and histone mRNAs increase steadily following 2-4 hr of recovery, whereas myosin mRNA increases after 10 hr. In contrast, hsp90 mRNA declines sharply within the first 75 min of recovery. Changes in mRNA populations during dauer formation and exit may be physiologically relevant.
Animals↗
Mapping Shroom3 expression across the adult mouse.
Shroom3 is an actin binding protein integral to apical constriction and apical-basal elongation during mammalian morphogenesis. Shroom3 function has been demonstrated in the development of the heart, neural tube, gut tube, eye, thyroid bud, and kidneys, with mutations linked to human congenital defects including anencephaly, spina bifida, cleft lip and palate, and ventricular septal defects. Genome-wide association studies implicate Shroom3 in human conditions such as chronic kidney disease and heterotaxy. While this suggests that Shroom3 expression continues postnatally, the extent of adult expression patterns remain unexplored. To address this, we first harvested organs from adult mice heterozygous for a LacZ reporter inserted into the Shroom3 allele (Shroom3+/Gt). Organs were stained in wholemount with X-gal and cleared in glycerol to identify which tissues expressed Shroom3 and to localize the expression within the tissue. Wildtype organs were then harvested and fluorescently stained to localize Shroom3 protein in tissue sub-structures. From this, we have characterized previously unknown Shroom3 expression in many adult organs including the bladder and reproductive systems, as well as established postnatal Shroom3 expression in organs thought to only have developmental expression including the eye and whisker pad. Our results also demonstrate organs which did not show Shroom3 expression, including the liver and pancreas. This data suggests that Shroom3 has roles in a wider number of tissues than previously thought and provides a foundation for future hypotheses regarding the biological and pathological significance of Shroom3.
Animals↗
Positive and negative gene regulation in muscle.
By the analysis of cis and trans-acting element involved in transcriptional regulation of chicken myosin alkali light chain genes, we have identified the MLC box, muscle specific enhancer element and negative regulatory element. The MLC box is an essential element for the expression of MLC genes located at approximately 100 bp upstream from mRNA start sites. The core sequence of MLC box is similar to the consensus of actin gene CArG box and SRE of c-fos oncogene. In vitro DNA-protein binding assay has revealed that the MLC box, CArG box and SRE might bind to a common or a similar protein complex. CMD1, cMyogenin, and cMRF4 transactivate the promorter with an intact MLC box, but not the promoter lacking MLC box, indicating that the MLC box itself is transactivated by the myogenic regulatory factors. This transactivation must have been due to the indirect effect of the myogenic regulatory factors, because chicken myogenic factors do not bind to the MLC box. A cis element identified at about 150 bp upstream from the cap site of cardiac MLC gene suppresses the cardiac MLC gene expression in skeletal muscle cells but not in cardiac muscle cells. The protein(s) bound to NRE might be identical with one of proteins bound to SRE. NRE may block the function of MLC box and resultantly inhibits the expression of cardiac MLC1 gene in skeletal muscle cells. Skeletal muscle enhancer at -2 kb of skeletal MLC1f gene is composed of two subelements P and D, cooperative action between them is required for sufficient enhancer activity. CMD1 and myogenin bind to the enhancer sequences of skeletal MLC1 gene and MCK gene and transactivate these genes preferentially in skeletal muscle cells. In addition to the CMD1 responsible enhancer, another cis-element is required for transactivation of the MLC1f gene by cMyogenin. An E-box adjacent to MLC box may co-work with the enhancer to increase the expression of MLC1f gene. Muscle specific and developmentally regulated expression of MLC gene family is regulated by the combination of these cis and trans-acting elements.
Animals↗
Exploring Hox Genes and Their Temporal Expression in an Embryonic Model of Freshwater Crustaceans.
Hox genes have been investigated in various Arthropod species, resulting in the identification of ten Hox genes, organized in a colinear arrangement within the genome. Among arthropods, crustaceans exhibit a remarkable diversity of body shapes, which are associated with a variety of egg types, embryonic development patterns, and importantly, with the modulation of Hox genes to specify the identity of body segments along the antero-posterior axis of the embryo. Although there are more than 52,000 species of crustaceans described, their genomic resources are relatively limited, making it challenging to employ several molecular tools for studying embryonic development. In this regard, we present a protocol for identifying Hox genes in a freshwater prawn using degenerate primers and transcriptome analysis. This method enables the study of specific functions of Hox genes, thereby contributing to the evolutionary understanding of the diversity of body shapes in crustaceans.
Animals↗
Sexually dimorphic expression and hormonal responsiveness of steroidogenic Cyp genes during gonadal differentiation in mandarin fish.
Steroid hormones play a pivotal role in fish sex differentiation, yet the dynamic expression patterns of key steroidogenic enzymes during this process remain incompletely characterized. Here, we combined genome-wide identification, time series transcriptomes spanning gonadal development (5-360 days post-hatch), and multiple hormone treatment experiments (17α-methyltestosterone, estrone, and etonogestrel) to investigate the Cyp11, Cyp17, Cyp19, and Cyp21 subfamilies in mandarin fish (Siniperca chuatsi). Seven steroidogenic Cyp genes were identified, showing teleost-specific expansion, with one duplicated pair (cyp17a2 and cyp2u1) exhibiting strong purifying selection. Expression profiling revealed pronounced sexually dimorphic and stage-specific patterns: During female differentiation (20-30 days), cyp19a1a and associated genes were highly expressed, coinciding with ovarian differentiation; during male differentiation (30-60 days), cyp17a2 and related genes were upregulated, aligning with testicular development. Exogenous hormone treatments further demonstrated that these genes are dynamically responsive: cyp19a1a and cyp17a2 were highly responsive to androgenic and progestogenic treatments, and their expression changes correlated closely with gonadal sex reversal phenotypes observed histologically. Collectively, this study provides a comprehensive expression atlas of steroidogenic Cyp genes during gonadal differentiation and identifies key hormonally responsive candidates for sex control in aquaculture.
Animals↗
Spatially guided in vivo single-cell functional genomics of postnatal heart.
Understanding how spatial organization and cell-cell interactions shape gene regulatory programs is central to decoding tissue development and function. The transition at birth, marked by increased circulatory demands and rapid tissue growth, requires precise spatiotemporal coordination of cardiac maturation. In this study, we generated a high-resolution spatial and temporal atlas of the postnatal mouse heart by integrating single-nucleus RNA sequencing with image-based spatial transcriptomics. This framework revealed dynamic cellular interactions, niche-specific signaling and transcriptional programs guiding cardiomyocyte maturation. To functionally test prioritized regulators in vivo and at scale, we developed PIP-seq (probe-based indel-detectable Perturb-seq), a high-throughput platform that detects single guide RNA identity, infers gene editing and profiles transcription from fixed nuclei. Applying PIP-seq to the developing postnatal heart, we identified 21 previously uncharacterized regulators of cardiomyocyte maturation, including genes essential for sarcomere assembly, metabolic reprogramming and electrophysiological transitions. Together, our findings define how microenvironmental signals and intrinsic gene programs cooperate to guide heart maturation and establish a broadly applicable framework for functional genomics in complex tissues.
Animals↗
Zfp-37, a new murine zinc finger encoding gene, is expressed in a developmentally regulated pattern in the male germ line.
To begin to examine the function in the mouse testis of genes containing the zinc finger motif, we have screened an adult mouse total testis cDNA library with probes to a conserved region of zinc fingers. We have isolated cDNAs for a new murine zinc finger encoding gene that has been designated Zfp-37. Northern blot hybridization analysis revealed Zfp-37 transcripts at high levels in the testis, the only adult tissue in which Zfp-37 expression was observed. Zfp-37 was also expressed at lower levels in the mid-gestation embryo and placenta. The major testicular transcripts are 2.3 and 2.6 kb. A 4.0 kb transcript was detected at lower levels in the testis as well as in embryo and placenta. Northern blot and in situ hybridization analysis revealed that expression of Zfp-37 was most abundant in germ cells which have completed meiosis and are undergoing the complex morphogenetic changes of spermiogenesis. The pattern of expression of Zfp-37 and the presence of the zinc finger domain suggest that Zfp-37 may have a role in regulating spermiogenesis.
Amino Acid Sequence↗
Molting in Pancrustacea Is Characterized by Both Deeply Conserved and Recently Evolved Gene Modules.
Arthropods such as insects and crustaceans, which together form the monophyletic group Pancrustacea, possess a rigid chitinous exoskeleton that must be periodically shed through molting to allow growth and morphological change. Although molting is a deeply conserved developmental process across Arthropoda, our understanding of its molecular mechanisms is still largely derived from insect model species. Lineage-specific innovations and losses of molting-related genes raise fundamental questions about the extent of its conservation outside noninsect arthropods. Here, we investigate the evolutionary conservation of molting gene expression across five representative pancrustacean species using publicly available transcriptomic datasets. Changes in gene expression during molting are characterized by both deeply conserved and lineage-specific gene modules. Temporal gene expression analyses reveal that these lineage-specific signatures are not uniformly distributed across the molting process: the middle transitional phase is more lineage-specific, thereby exhibiting an inverse hourglass pattern. This is likely due to life-history-specific processes, development of the cuticle, and specialized structures of the exoskeleton. Overall, this study provides evidence for both the evolutionary conservation and divergence of this key postembryonic developmental process and highlights the modular architecture of the molting program.
Animals↗
Identification of a set of genes with developmentally down-regulated expression in the mouse brain.
Using a subtraction cloning approach, we have isolated a set of cDNA clones from mouse neural precursor cells whose respective mRNA levels are down-regulated during the development of mouse brain. Single stranded DNA prepared from neuronal precursor cell cDNA library in lambda Zap vector was subtracted with poly (A)+ RNA prepared from postnatal and adult mouse brain to obtain several clones which show developmental down-regulation of expression. Their patterns of expression indicate that these genes may play important roles during the embryonic development and differentiation of central nervous system.
Aging↗
Dynamic allelic expression in mouse mammary glands across the adult developmental cycle.
The mammary gland, which primarily develops postnatally, undergoes significant changes during pregnancy and lactation to facilitate milk production. Through the generation and analysis of 480 transcriptomes, we provide the most detailed allelic expression map of the mammary gland, cataloguing cell-type-specific expression from ex-vivo purified cell populations over 10 developmental stages, enabling comparative analysis. The work identifies genes involved in the mammary gland cycle, parental-origin-specific and genetic background-specific expression at cellular and temporal resolution, genes associated with human lactation disorders and breast cancer. Genomic imprinting, a mechanism regulating gene expression based on parental origin, is crucial for controlling gene dosage and stem cell potential throughout development. The analysis identified 25 imprinted genes monoallelically expressed in the mammary gland, with several showing allele-specific expression in distinct cell types. No novel imprinted genes were identified and the absence of biallelically expressed imprinted genes suggests that, unlike in brain, selective absence of imprinting does not regulate gene dosage in the mammary gland. This research highlights transcriptional dynamics within mammary gland cells and identifies novel candidate genes potentially significant in the tissue during pregnancy and lactation. Overall, this comprehensive atlas represents a valuable resource for future studies on expression and transcriptional dynamics in mammary cells.
Animals↗
Characterization of a Xenopus oocyte factor that binds to a developmentally regulated cis-element in the TFIIIA gene.
TFIIIA mRNA expression is developmentally regulated during Xenopus oogenesis. We have identified a positive-acting cis-element in the TFIIIA gene located between -671 and -629 with respect to the mRNA initiation site, termed element 3. Element 3 contributes to the efficient transcription of the TFIIIA gene in stage III oocytes, but is inactive in the normal context of the TFIIIA gene in stage VI oocytes. A trans-acting factor, termed B3, in immature ovary extracts binds to a region within element 3 containing four repeats of the consensus nucleotide sequence 5' (T/A)GGTTACT. We discuss how the developmental regulation of B3-element 3 function could be achieved in the context of the TFIIIA gene during oogenesis.
Animals↗