Xenopus laevis
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ABSTRACT:
PROVIDER: PRJNA400602 | ENA |
REPOSITORIES: ENA
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Project description:Targets of Pax3 and Zic1 in neural crest and cranial placode progenitors
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Project description:Pax3 and Zic1 trigger the early neural crest gene regulatory network by the direct activation of multiple key neural crest specifiers [Xenopus_laevis]
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Project description:Pax3 and Zic1 trigger the early neural crest gene regulatory network by the direct activation of multiple key neural crest specifiers [X_laevis_2]
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Project description:microRNAs associated with early neural crest development in Xenopus laevis
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Project description:It was shown that neil2 is required for neural crest development in Xenopus (Schomacher et al. 2016; doi:10.1038/nsmb.3151). To gain further insights into the underlying molecular mechanism leading to neural crest defects and microcephaly in neil2 Morpholino injected Xenopus embryos, we performed RNA-seq transcriptome analysis of neil2 Morpholino versus control Morpholino injected embryos.
2019-09-16 | GSE130079 | GEO
Project description:Pregnane X receptor (PXR) is generally considered the most important sensor of natural and anthropogenic xenobiotics in vertebrates. In Xenopus, however, PXR plays a role in neural development and it is irresponsive to xenobiotics. We report a first broad-spectrum amphibian xenobiotic receptor, which is an ortholog of the mammalian constitutive androstane receptor (CAR). The low basal activity and pronounced responsiveness to activators such as drugs and steroids displayed by the Xenopus CAR resemble PXR, which both trace back to a common ancestor early in the divergence of land vertebrates. The constitutive activity of CAR emerged first in Sauropsida (reptiles and birds) and it is common to all fully terrestrial land vertebrates (Amniota). This activity can be mimicked by humanizing just two amino acids of the Xenopus CAR. These results demonstrate a remarkable plasticity of CAR which enabled its employment as Xenopus xenosensors. They open way to toxicogenomic and bioaugmentation studies in amphibians, a critically endangered taxon of land vertebrates. Taken together, we provide evidence for a much earlier origin of CAR, for its conservation in tetrapods which exceeds that of PXR, and for its remarkable functional plasticity which enabled its role as a PXR-like xenosensor in Amphibia.
2011-10-11 | GSE28510 | GEO
Project description:Pregnane X receptor (PXR) is generally considered the most important sensor of natural and anthropogenic xenobiotics in vertebrates. In Xenopus, however, PXR plays a role in neural development and it is irresponsive to xenobiotics. We report a first broad-spectrum amphibian xenobiotic receptor, which is an ortholog of the mammalian constitutive androstane receptor (CAR). The low basal activity and pronounced responsiveness to activators such as drugs and steroids displayed by the Xenopus CAR resemble PXR, which both trace back to a common ancestor early in the divergence of land vertebrates. The constitutive activity of CAR emerged first in Sauropsida (reptiles and birds) and it is common to all fully terrestrial land vertebrates (Amniota). This activity can be mimicked by humanizing just two amino acids of the Xenopus CAR. These results demonstrate a remarkable plasticity of CAR which enabled its employment as Xenopus xenosensors. They open way to toxicogenomic and bioaugmentation studies in amphibians, a critically endangered taxon of land vertebrates. Taken together, we provide evidence for a much earlier origin of CAR, for its conservation in tetrapods which exceeds that of PXR, and for its remarkable functional plasticity which enabled its role as a PXR-like xenosensor in Amphibia. We used microarrays to detect global transcriptional changes in Xenopus laevis livers following pregnenolone and artemisinin treatment in order to identify target genes of xlCAR. Arteminisin or pregnenolone were injected intraperitoneally into three frogs on two consecutive days. The control group received in parallel two DMSO injections. All frogs were sacrificed 24 h after the second injection by decapitation, and livers were immediately frozen in liquid nitrogen. After RNA isolation, specimens within the same experimental group were pooled.
2011-10-10 | E-GEOD-28510 | biostudies-arrayexpress
Project description:In the embryo, inductive cues are interpreted by competent tissues in a spatially and temporally restricted manner, and the mechanisms for the loss of responsiveness are not well understood. To test the hypothesis that loss of competence is associated with changes in chromatin accessibility, we adapted the assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) for use in Xenopus laevis to evaluate genome-wide changes in chromatin accessibility in early and late gastrula stages. ATAC-seq was performed on presumptive ectoderm (animal caps) explanted at the blastula stage and cultured until siblings reached early (stage 10) or late (stage 12) gastrula stage. Approximately 70,000 accessible regions were identified at intergenic regions, introns, promoters, and transcription termination sites at both stages. Accessibility decreased from stage 10 to stage 12 at 279 promoters, including developmental regulators such as Foxh1, chordin, and VegT. Accessible chromatin domains overlap extensively with previously reported p300 binding sites, consistent with putative cis-regulatory modules (pCRMs), and these pCRMs are enriched for binding motifs for pluripotency factors, including Sox, Oct/Pou, and KLF binding motifs. Dorsal Wnt target gene promoters are not accessible after the loss of competence, but inhibition of histone deacetylases increases acetylation at these promoters and extends competence for dorsal gene induction by Wnt signaling. In contrast, the promoters for genes involved in mesoderm and neural crest development remain open through gastrulation, and histone deacetylase inhibition does not extend competence for mesoderm or neural crest induction. These data suggest that chromatin state regulates the loss of competence to inductive signals in a context-dependent manner.
2020-02-26 | GSE138905 | GEO
Project description:Geminin-regulated genes in the Xenopus laevis embryonic ectoderm
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