Project description:Here we describe a base-resolution DNA methylation map of Xenopus laevis gastrula (st.10.5) embryos generated by whole genome bisulfite sequencing
Project description:Animal embryos have the remarkable property of self-organization. Over 125 years ago Hans Driesch separated the two blastomeres of sea urchin embryos and obtained twins, in what was the foundational experiment of experimental embryology. Since then, embryonic twinning has been obtained experimentally in many animals by diverse methods. In a recent study, we developed bisection methods that generate identical twins reliably from Xenopus blastula embryos. In the present study we investigated the transcriptome of regenerating half-embryos after sagittal and dorsal-ventral (D-V) bisections. Individual embryos were operated at midblastula with an eyelash hair and cultured until early gastrula (stage 10.5) or late gastrula (Stage 12) and analyzed the transcriptome of each half-embryo by RNAseq. Because many genes are activated by wound healing, stringent analyses were used to identify genes upregulated in identical twins but not in either dorsal or ventral fragments. At early gastrula cell division-related genes such as histones were identified, whereas at late gastrula pluripotency genes (such as sox2) and germ layer determining genes (such as eomesodermin, ripply2 and activing receptor ACVRI) and a number of secretory pathway components (serpinH1, fucoleptin and sialyl transferase). These findings are consistent with a model in which cell division is required to heal damage, while maintaining pluripotency to permit formation of the organizer with a displacement of 900 from its original site. In addition, the extensive transcriptomic data presented here (30 RNA-seq libraries of individual whole or regenerating half-embryos) provides a useful resource for data mining gene expression during early vertebrate development.
Project description:Transcriptional profiling of Xenopus laevis embryos and ectoderm (animal caps) comparing embryos injected with control morpholino with embryos injected with the morpholino mixture PVD2, which knocks down all three Xenopus PouV proteins. Whole embryos (WE) or animal caps (AC) were collected at late blastula (9) or early gastrula (10) stages from Control and PVD2 morphants.
Project description:The Notch signaling pathway functions in a number of processes during embryologic development, especially the maintenance or aquisition of cell fate. We purturb the Notch signalling pathway in embryonic Xenopus laevis in order to 1) better characterize the downstream targets of Notch signalling, and 2) determine the extent to which early embryos can recover from transient purturbations to critical signalling pathways, if at all. Xenopus laevis embryos were unilaterally injected at the two cell stage with either GFP, GFP and ICD (Notch intracellular domain, an up-regulator of the Notch pathway), or GFP and DBM (domain-binding mutant, a downregulator of the Notch pathway). At stages 18, 28, and 38, for each injection, pooled total RNA from 10 embryos was extracted. Extraction was performed for three biological replicates for each time/injection condition. cDNA from total RNA was hybridized on Affymetrix Xenopus laevis Genome 2.0 arrays.
Project description:Xenopus laevis tadpoles differ in their regenerative potential according to their developmental stage. Here, we focus on tail regeneration following amputation. By comparing the regenerative response during the naturally occurring regeneration-competent and -incompetent stages, scRNAseq can reveal cell type changes that are required for successful regeneration.
Project description:In this experiment, we revealed the critical steps for regeneration initiation. We discovered Regeneration Initiating Cells (RICs) using single cell and spatial transcriptomics of the regenerating Xenopus laevis tail. RICs are formed transiently from the basal epidermal cells and are critical for the modification of the surrounding extracellular matrix to allow for migration of other cell types that promote regeneration. Absence or deregulation of RICs leads to excessive extracellular matrix deposition and regeneration defects.
Project description:In this experiment, we revealed the critical steps for regeneration initiation. We discovered Regeneration Initiating Cells (RICs) using single cell and spatial transcriptomics of the regenerating Xenopus laevis tail. RICs are formed transiently from the basal epidermal cells and are critical for the modification of the surrounding extracellular matrix to allow for migration of other cell types that promote regeneration. Absence or deregulation of RICs leads to excessive extracellular matrix deposition and regeneration defects.
Project description:Xenopus laevis tadpoles display a decreasing capacity to regenerate their limbs following injury according to developmental stage. By comparing the regenerative response during the naturally occurring regeneration-competent, -restricted and -incompetent stages, scRNAseq can reveal cell type changes that are required for successful regeneration.