Regulation of neurogenesis by FGF signaling and Neurogenin in the invertebrate chordate Ciona
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ABSTRACT:
PROVIDER: PRJNA634076 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11817083_1.fastq.gz | Fastqsanger.gz | |||
| SRR11817083_2.fastq.gz | Fastqsanger.gz | |||
| SRR11817084_1.fastq.gz | Fastqsanger.gz | |||
| SRR11817084_2.fastq.gz | Fastqsanger.gz | |||
| SRR11817085_1.fastq.gz | Fastqsanger.gz |
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Project description:We present a comprehensive proteome atlas of the model chordate Ciona, covering eight developmental stages and ~7k translated genes as well as a deep quantitative atlas of maternal proteins found in the Ciona egg.
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Project description:To profile gene expression associated with BTN neurogenesis we performed RNAseq of isolated BTN lineage cells in which BTN neurogenesis was enhanced or suppressed by perturbing Neurog function.
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Project description:Dynamic gene expression programs determine multipotent cell states and fate choices during development. Multipotent progenitors for cardiomyocytes and branchiomeric head muscles populate the pharyngeal mesoderm of vertebrate embryos, but the mechanisms underlying cardiopharyngeal multipotency and heart vs. head muscle fate choices remain elusive. The tunicate Ciona emerged as a simple chordate model to study cardiopharyngeal development with unprecedented spatio-temporal resolution. We analyzed the transcriptome of single cardiopharyngeal lineage cells isolated at successive time points encompassing the transitions from multipotent progenitors to distinct first and second heart, and pharyngeal muscle precursors. We reconstructed the three cardiopharyngeal developmental trajectories, and characterized gene expression dynamics and regulatory states underlying each fate choice. Experimental perturbations and bulk transcriptome analyses revealed that ongoing FGF/MAPK signaling maintains cardiopharyngeal multipotency and promotes the pharyngeal muscle fate, whereas signal termination permits the deployment of a full pan-cardiac program and heart fate specification. We identified the Dach1/2 homolog as a novel evolutionarily conserved second-heart-field-specific factor and demonstrate, through lineage tracing and CRISPR/Cas9 perturbations, that it operates downstream of Tbx1/10 to actively suppress the first heart lineage program. This data indicates that the regulatory state of multipotent cardiopharyngeal progenitors determines the first vs. second heart lineage choice, and that Tbx1/10 acts as a bona fide regulator of cardiopharyngeal multi potency. We performed bulk RNAseq to profile the FACS purified Ciona Robusta Truck Ventral Cells (TVCs) with FGF-MAPK perturbation conditions to address the question- What is the role of FGF signaling pathway during early cardiopharyngeal specification. we performed bulk RNA sequencing of FACS-purified cardiopharyngeal lineage cells isolated from embryos and larvae expressing either a dominant negative form the fibroblast growth factor receptor (dnFGFR), or a constitutively active form of M-Ras (caM-Ras), the sole Ras homolog in Ciona, under the control of TVC-specific enhancers.
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Project description:The notochord is the eponymous feature of the chordates and an essential organ in chordate development. The notochord of the invertebrate chordate Ciona consists of only 40 cells, and is a longstanding model for studying differentiation and morphogenesis in a small, simple embryo. Here we perform RNAseq analysis on flow-sorted notochord cells from multiple stages of development to define a comprehensive Ciona notochord transcriptome. We identify 1364 genes with enriched expression in the notochord and extensively validate the results by in situ hybridization. This notochord gene set is highly enriched for Gene Ontology codes related to the extracellular matrix, cell adhesion and cytoskeleton, and contains numerous genes with intriguing potential functions in morphogenesis. Orthologs of 112 of the Ciona notochord genes have known notochord expression in vertebrates, more than twice as many as would be predicted by chance alone. This set of putative effector genes with notochord expression conserved from tunicates to vertebrates will be invaluable for testing hypotheses about the evolution of the notochord.
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Project description:Ageing causes a progressive deterioration of the structure and function of vascular cells that results in a decline of vascular functionality. Impaired functionality of vascular cells is a key factor that triggers several age-related vascular diseases. Most of our understanding of this process comes from in vitro studies. Further understanding of the mechanism underlying vascular aging in vivo are needed to get new insights into the pathobiology of age-associated vascular diseases. Here we use a combination of transcriptomics, immunostaining, and in vivo pharmacological and regeneration assays coupled with the extracorporeal vasculature of the invertebrate chordate Botryllus schlosseri (which is large, transparent, accessible and easy to manipulate) and show that we can study morphological, transcriptional and functional age-associated changes of vascular cells that are similar to those of mammalian vascular cells from tissue culture and fixed vascular cells. We showed that age-associated changes in the cytoskeleton and the ECM reshape vascular cells into flatten and elongated form and heavily accumulate Collagen, rendering the vessels into more rigid and less responsive to pharmacological insults. These changes did not alter the regeneration potential of aged blood vessels and newly regenerated vascular cells retained the same aged phenotype. Furthermore, we found that a subset of blood circulating hemocytes showed reduced proliferation while increasing apoptosis in aged animals.
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Project description:Gene number can be considered a pragmatic measure of biological complexity, but reliable data is scarce. Estimates for vertebrates are 50-100,000 genes per haploid genome, whereas invertebrate estimates fall below 25,000. We wished to test the hypothesis that the origin of vertebrates coincided with extensive gene creation. A prediction is that gene number will differ sharply between invertebrate and vertebrate members of the chordate phylum. A gene number estimation method requiring limited sequence sampling of genomic DNA was developed and validated by using data for Caenorhabditis elegans. Using the method, we estimated that the invertebrate chordate Ciona intestinalis has 15,500 protein-coding genes (+/-3,700). This number is significantly lower than gene numbers of vertebrate chordates, but similar to those of invertebrates in distantly related phyla. The data indicate that evolution of vertebrates was accompanied by a dramatic increase in protein-coding capacity of the genome.
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