BET activity plays an essential role in control of stem cell attributes in Xenopus
Ontology highlight
ABSTRACT:
ORGANISM(S): Xenopus laevis
PROVIDER: GSE221330 | GEO | 2024/06/19
REPOSITORIES: GEO
Similar Datasets
Project description:Gene expression was analysed in normally developing Xenopus laevis embryos from early blastula to early neurula stages
2009-03-01 | E-MEXP-2059 | biostudies-arrayexpress
Project description:Purpose: Study the developing neural cell fate of the D1 blastomere in the 8-cell embryo. Determine what transcripts are dependant on cell/cell signaling and which are inherit to the single cell and do not depend on the rest of the embryo. Methods: D1 blastomere was either injected with fluorescent dye or explanted away from the developing embryo. Transcript profile was taken at 7 time points: 8-cell, 16-cell, 32-cell, blastula, gastrula, early neurula, and mid/late neurula. 3 biological triplicates were taken at each time point for both the dissect and explant condition. Results: Up until blastula stage, dissect and explant transcript profiles remain fairly similar. But following this the profiles completely diverge, with the dissect tissue heading towards the neural fate while the explant samples head towards an ectoderm/epithelial fate.
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2024-06-21 | GSE205436 | GEO
Project description:Retinoid signaling is important for patterning the vertebrate hindbrain and midaxial regions. We recently showed that signaling through retinoic acid receptors (RARs) is essential for anteroposterior patterning along the entire body axis. To further investigate the mechanisms through which RARs act, we employed microarray analysis to investigate the effects of modulating RAR activity on target gene expression. We identified 334 upregulated genes (92% of which were validated) including known RA responsive genes, known genes that have never been proposed as RA targets and many hypothetical and unidentified genes (n = 166). 67 validated downregulated genes were identified including known RA responsive genes and anterior marker genes. The expression patterns of selected upregulated genes (n = 45) were examined at neurula stages using whole mount in situ hybridization. We found that most of these genes were expressed in the neural tube and many were expressed in anterior tissues such as neural crest, brain, eye anlagen, and cement gland. Some were expressed in tissues such as notochord, somites, pronephros and blood islands, where retinoic acid (RA) plays established roles in organogenesis. Members of this set of newly identified RAR target genes are likely to play important roles in neural patterning and organogenesis under the control of RAR signaling pathways and their further characterization will expand our understanding of RA signaling during development. Keywords = retinoid Keywords = microarray Keywords = RAR Keywords = neurula Keywords = anteroposterior patterning Keywords = and organogenesis
2010-06-10 | E-GEOD-2295 | biostudies-arrayexpress
Project description:Neural crest cells are multipotent cells that delaminate from the neuroepithelium, migrating throughout the embryo. Aberrant migration causes developmental defects. Animal models are improving our understanding of neural crest anomalies, but in vivo migration behaviours are poorly understood. Here, we demonstrate that murine neural crest cells display actin-based lamellipodia and filopodia in vivo. Using neural crest-specific knockouts or inhibitors, we show that the serine-threonine kinase Glycogen Synthase Kinase-3 (GSK3), and the cytoskeletal regulator Lamellipodin (Lpd), are required for lamellipodia formation whilst preventing focal adhesion maturation. Lpd is a novel substrate of GSK3 and phosphorylation of Lpd favours interactions with the Scar/WAVE complex (lamellipodia formation) at the expense of VASP and Mena interactions (adhesion maturation and filopodia formation). This improved understanding of cytoskeletal regulation in mammalian neural crest migration has general implications for neural crest anomalies and cancer.
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Project description:During vertebrate neurulation, the embryonic ectoderm is patterned into lineage progenitors for neural plate, neural crest, placodes and epidermis. Here, we use Xenopus laevis embryos to analyze the spatial and temporal transcriptome of distinct ectodermal domains in the course of neurulation, during the establishment of cell lineages. In order to define the transcriptome of small groups of cells from a single germ layer, and to retain spatial information, dorsal and ventral ectoderm was subdivided along the anterior-posterior and medial-lateral axes by microdissections. Principal Component Analysis on the transcriptomes of these ectoderm fragments primarily identifies embryonic axes and temporal dynamics. This provides a genetic code to define positional information of any ectoderm sample along the anterior-posterior and dorsal-ventral axes, directly from its transcriptome. In parallel, we use Non-Negative Matrix Factorization to predict enhanced gene expression maps onto early and mid-neurula embryos, and specific signatures for each ectoderm area. The clustering of spatial and temporal datasets allowed detection of multiple biologically relevant groups (e.g. Wnt signaling, neural crest development, sensory placode specification, ciliogenesis, germ layer specification). We provide an interactive network interface, EctoMap, for exploring synexpression relationships among genes expressed in the neurula, and suggest several strategies to use this comprehensive dataset to address questions in developmental biology as well as stem cell or cancer research.
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Project description:Retinoid signaling is important for patterning the vertebrate hindbrain and midaxial regions. We recently showed that signaling through retinoic acid receptors (RARs) is essential for anteroposterior patterning along the entire body axis. To further investigate the mechanisms through which RARs act, we employed microarray analysis to investigate the effects of modulating RAR activity on target gene expression. We identified 334 upregulated genes (92% of which were validated) including known RA responsive genes, known genes that have never been proposed as RA targets and many hypothetical and unidentified genes (n = 166). 67 validated downregulated genes were identified including known RA responsive genes and anterior marker genes. The expression patterns of selected upregulated genes (n = 45) were examined at neurula stages using whole mount in situ hybridization. We found that most of these genes were expressed in the neural tube and many were expressed in anterior tissues such as neural crest, brain, eye anlagen, and cement gland. Some were expressed in tissues such as notochord, somites, pronephros and blood islands, where retinoic acid (RA) plays established roles in organogenesis. Members of this set of newly identified RAR target genes are likely to play important roles in neural patterning and organogenesis under the control of RAR signaling pathways and their further characterization will expand our understanding of RA signaling during development. Keywords = retinoid Keywords = microarray Keywords = RAR Keywords = neurula Keywords = anteroposterior patterning Keywords = and organogenesis Keywords: repeat sample
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Project description:The transcription factors Pax3 and Zic1 are among the earliest genes activated at the neural plate border. Pax3 and Zic1 in combination promote neural crest fate, while Zic1 alone regulate cranial placode progenitor formation. We used microarrays to identify the global repertoire of genes activated by these facors individually or in combination to gain insights into the molecular mechanisms underlying cell fate decision at the neural plate border. Xenopus laevis embryos were injected at the 2-cell stage with mRNA encoding Pax3GR and Zic1GR , the hormone-inducible version of Pax3 and Zic1, alone or in combination. At the blastula stage (stage 9), animal cap explants were dissected and cultured for 8 hours in the presence of dexamethasone. A glucocorticoid receptor (GR) mRNA was also injected as negative control.
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Project description:Neural crest cells exemplify cellular diversification from a multipotent progenitor population. However, the full sequence of molecular choices governing the emergence of neural crest heterogeneity from the ectoderm remains elusive. Gene regulatory networks govern these steps of embryonic development and cell specification towards definitive neural crest. Here, we combine ultra-dense single cell transcriptomes with machine-learning strategies and experimental validation to provide a comprehensive gene regulatory network driving vertebrate neural crest fate diversification, from induction to early migration stages. Transcription factor connectome and bifurcation analyses demonstrate emergence of early neural crest fates at the neural plate stage, alongside an unbiased multipotent neural crest lineage persisting until after epithelial-mesenchymal transition. We also define a new and transient neural border zone state, preceding choice between neural crest and placodes during gastrulation. Theis combination of experimental tests, with Machine Learning broadly applicable to single cell transcriptomics, deciphers the circuits driving cranial and vagal neural crest formation and provides a general model for investigating vertebrate GRNs in development, evolution and disease.
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