Level of polyadenylated RNAs during regeneration of adult zebrafish brain
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ABSTRACT:
PROVIDER: PRJNA675638 | ENA |
REPOSITORIES: ENA
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Project description:For its remarkable ability to heal injuries of the adult central nervous system, the zebrafish has become an important model to investigate neural regeneration. Despite big progresses in our understanding of some of the underlying key processes, a comprehensive analysis of the changes of the transcriptome has not been reported yet. We analysed here the transcriptome of the regenerating telencephalon for changes in the expression of mRNAs, their splice variants and regulatory long non-coding RNAs and their putative targets.
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Project description:After heart injury, adult zebrafish can perfectly regenerate its heart without any scar tissue left. We performed 100bp*2, paired-end, strand-specific, polyA-positive RNA-seq on hearts from 2 group of adult zebrafish, in which one was sham group and the other 7 days after heart tip amputation (7dpa). We found pathways involving hydrogen peroxidate related functions significantly up-regulated in 7dpa group, indicating its role in heart regeneration. RNA-seq: hearts from sham or 7dpa adult zebrafish
2014-12-24 | E-GEOD-50203 | biostudies-arrayexpress
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2019-08-13 | GSE112498 | GEO
Project description:Ischemic cardiopathy is the leading cause of death in the world, for which efficient regenerative therapy is not currently available. In mammals, after a myocardial infarction episode, the damaged myocardium is replaced by scar tissue featuring collagen deposition and tissue remodelling with negligible cardiomyocyte proliferation. Zebrafish, in contrast, display an extensive regenerative capacity as they are able to restore completely lost cardiac tissue after partial ventricular amputation. Due to the lack of genetic lineage tracing evidence, it is not yet clear if new cardiomyocytes arise from existing contractile cells or from an uncharacterised set of progenitors cells. Nonetheless, several genes and molecules have been shown to participate in this process, some of them being cardiomyocyte mitogens in vitro. Though questions as what are the early signals that drive the regenerative response and what is the relative role of each cardiac cell in this process still need to be answered, the zebrafish is emerging as a very valuable tool to understand heart regeneration and devise strategies that may be of potential value to treat human cardiac disease. Here, we performed a genome-wide transcriptome profile analysis focusing on the early time points of zebrafish heart regeneration and compared our results with those of previously published data. Our analyses confirmed the differential expression of several transcripts, and identified additional genes the expression of which is differentially regulated during zebrafish heart regeneration. We validated the microarray data by conventional and/or quantitative RT-PCR. For a subset of these genes, their expression pattern was analyzed by in situ hybridization and shown to be upregulated in the regenerating area of the heart. The specific role of these new transcripts during zebrafish heart regeneration was further investigated ex vivo using primary cultures of zebrafish cardiomyocytes and/or epicardial cells. Our results offer new insights into the biology of heart regeneration in the zebrafish and, together with future experiments in mammals, may be of potential interest for clinical applications. In order to study zebrafish heart regeneration, a time course experiment was realized where amputated heart regenerating were compared to control heart. Samples in triplicate were extracted at 1, 3, 5 and 7 days post-amputation.
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Project description:Zebrafish kidney regeneration transcriptome
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Project description:Adult zebrafish regenerate about half of cerebrospinal axons by six weeks after a complete spinal cord transection. We isolated the two populations of neurons that successfully regenerated their axons versus those that did not and isolated the total RNA. Cerebrospinal neurons from unlesioned animals were also collected to serve as controls. Whole transcriptome microarray was performed to determine axonal regeneration-associated genes. For each condition (regenerated, non-regenerated and control neurons) we had 3 biological replicates that consisted of neurons pooled from 3 to 9 zebrafish. A complete spinal cord transection with Fluororuby retrograde tracing was performed at the 8th vertebra level in adult zebrafish. Fluororuby labeled all the neurons in the brain that project their axons to the 8th vertebra. Three weeks later Fluoroemerald was injected 4mm distally from the spinal cord transection site, thereby labeling all neurons that regenerated their axons to this level. The zebrafish were sacrificed 1 week after Fluoroemerald tracing, brain enzymatically dissociated and cells sorted using fluorescence-activated cell sorter. After sorting the total RNA was extracted, amplified and labeled with biotin and then hybridized to Affymetrix 3' IVT gene expression microarray. Unlesioned fish were traced with Fluororuby at the 8th vertebra level and labeled neurons isolated 1 week after to serve as control for gene expression microarray.
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Project description:Adult zebrafish, in contrast to mammals, are able to regenerate their hearts in response to injury or experimental amputation. Our understanding of the cellular and molecular bases that underlie this process, although fragmentary, has increased significantly over the last years. However, the role of the extracellular matrix (ECM) during zebrafish heart regeneration has been comparatively rarely explored. Here, we set out to characterize the ECM protein composition in adult zebrafish hearts, and whether it changed during the regenerative response. For this purpose, we first established a decellularization protocol of adult zebrafish ventricles that significantly enriched the yield of ECM proteins. We then performed proteomic analyses of decellularized control hearts and at different times of regeneration. Our results show a dynamic change in ECM protein composition, most evident at the earliest (7 days post-amputation) time-point analyzed. Regeneration associated with sharp increases in specific ECM proteins, and with an overall decrease in collagens and cytoskeletal proteins. We finally tested by atomic force microscopy that the changes in ECM composition translated to decreased ECM stiffness. Our cumulative results identify changes in the protein composition and mechanical properties of the zebrafish heart ECM during regeneration.
2019-08-26 | PXD010092 | Pride
Project description:Zebrafish spontaneously regenerate the retina after injury. Currently, studies have observed gene expression profiles in this species however this may be a poor reflection of protein function. To further address this and expand our understanding of the regenerative process in the zebrafish, we compared the proteomic profile of the retina during injury and upon regeneration. Ouabain was injected intravitreously to create a model of degeneration and regeneration of the retina which was extracted at 0, 3 and 18 days after injection. Differences in protein expression indicates reduced metabolic processing, and increase in fibrin clot formation, with significant upregulation of fibrinogen gamma polypeptide, apolipoproteins A-Ib and A-II, galectin-1, and vitellogenin-6 during degeneration when compared to normal retina. In addition, cytoskeleton and membrane transport proteins were considerably altered during regeneration, with the highest fold upregulation observed for tubulin beta 2A, histone H2B and brain type fatty acid binding protein. Key proteins identified in this study may play an important role in the regeneration of the zebrafish retina and investigations on the potential regulation of these proteins may support future investigations in this field.
2017-03-21 | PXD005843 | Pride
Project description:After heart injury, adult zebrafish can perfectly regenerate its heart without any scar tissue left. We performed 100bp*2, paired-end, strand-specific, polyA-positive RNA-seq on hearts from 2 group of adult zebrafish, in which one was sham group and the other 7 days after heart tip amputation (7dpa). We found pathways involving hydrogen peroxidate related functions significantly up-regulated in 7dpa group, indicating its role in heart regeneration.
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