Transient epigenetic reprogramming during adult zebrafish muscle regeneration
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA565138 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genomic reprogramming and cellular dedifferentiation are critical to the success of de novo tissue regeneration in lower vertebrates such as zebrafish and axolotl. ChIP-seq of the histone modifications H3K27Ac, H3K27me3, and H3K4me3 was used to characterize early epigenetic changes in a zebrafish in vivo model of adult muscle regeneration.
2019-12-06 | GSE137304 | GEO
Project description:label-free relative quantitation based on nLC-MS/MS performed on heart tissues in a clinically relevant zebrafish model of cardiac tissue regeneration . Each of the six samples (2dp Cl, 2dpS, 7dp Cl, 7dpS, 14dp Cl, 14dpS,) has been analysed in two technical replicates.
dpci = days post cryoinjury; dps = days post sham
2022-11-14 | MSV000090703 | MassIVE
Project description:PurposeGenomic reprogramming and cellular dedifferentiation are critical to the success of de novo tissue regeneration in lower vertebrates such as zebrafish and axolotl. In tissue regeneration following injury or disease, differentiated cells must retain lineage while assuming a progenitor-like identity in order to repopulate the damaged tissue. Understanding the epigenetic regulation of programmed cellular dedifferentiation provides unique insights into the biology of stem cells and cancer and may lead to novel approaches for treating human degenerative conditions.MethodsUsing a zebrafish in vivo model of adult muscle regeneration, we utilized chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) to characterize early changes in epigenetic signals, focusing on three well-studied histone modifications-histone H3 trimethylated at lysine 4 (H3K4me3), and histone H3 trimethylated or acetylated at lysine 27 (H3K27me3 and H3K27Ac, respectively).ResultsWe discovered that zebrafish myocytes undergo a global, rapid, and transient program to drive genomic remodeling. The timing of these epigenetic changes suggests that genomic reprogramming itself represents a distinct sequence of events, with predetermined checkpoints, to generate cells capable of de novo regeneration. Importantly, we uncovered subsets of genes that maintain epigenetic marks paradoxical to changes in expression, underscoring the complexity of epigenetic reprogramming.ConclusionsWithin our model, histone modifications previously associated with gene expression act for the most part as expected, with exceptions suggesting that zebrafish chromatin maintains an easily editable state with a number of genes paradoxically marked for transcriptional activity despite downregulation.
| S-EPMC6890397 | biostudies-literature
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
Project description:Adult zebrafish are able to regenerate many organs such as their caudal fin in only few days post amputation. To explore the landscape and dynamic of the genes involed in regeneration, we performed a global transcriptomic analysis using RNA-seq during zebrafish caudal fin regeneration.
2019-08-13 | GSE112498 | GEO
Project description:In adult mammals, tissue damage after myocardial infarction induces myofibroblast differentiation and the formation of a permanent, functionally inert scar. However, the molecular mechanisms that govern myofibroblast differentiation and scarring remain poorly understood. Some vertebrates like zebrafish display a remarkable regenerative potential with only limited and transient fibrosis after tissue damage, including in the heart. Here, employing comparative expression profiling coupled with loss-of-function approaches, we identified the canonical Interleukin-11/Stat3 signaling axis as a core component of regeneration in zebrafish. Notably, animals with loss of Interleukin-11 receptor (Il11ra) function reach adulthood without overt developmental defects, but exhibit strongly impaired cardiac regeneration with increased myofibroblast differentiation and the formation of a permanent collagenous scar, similar to what is observed in adult mammals. Using zebrafish fate-mapping approaches, reporter lines and human primary cell culture methods, we provide evidence that Interleukin-11 signaling limits endothelial-to-myofibroblast transdifferentiation and maintains a pro-regenerative niche to promote cardiac regeneration. Altogether, our data reveal a vital role for endothelial Interleukin-11/Stat3 signaling in containing injury-induced cardiac fibrosis.
2021-09-10 | GSE161647 | GEO
Project description:label-free relative quantitation based on nLC-MS/MS performed on heart tissues in a clinically relevant zebrafish model of cardiac tissue regeneration . Each of the six samples (2dp Cl, 2dpS, 7dp Cl, 7dpS, 14dp Cl, 14dpS,) has been analysed in two technical replicates.
dpci = days post cryoinjury; dps = days post sham
2022-11-14 | MSV000090703 | GNPS
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.
2010-03-09 | E-GEOD-17993 | biostudies-arrayexpress
Project description:Zebrafish kidney regeneration transcriptome
| PRJNA789561 | ENA
Project description:Transient induction of pluripotent reprogramming factors has been reported to reverse some features of aging in mammalian cells and tissues. However, the impact of transient reprogramming on somatic cell identity programs and the necessity of individual pluripotency factors remain unknown. Here, we mapped trajectories of transient reprogramming in young and aged cells from multiple murine cell types using single cell transcriptomics to address these questions. We found that transient reprogramming restored youthful gene expression in adipogenic cells and mesenchymal stem cells but also temporarily suppressed somatic cell identity programs. We further screened Yamanaka Factor subsets and found that many combinations had an impact on aging gene expression and suppressed somatic identity, but that these effects were not tightly entangled. We also found that a transient reprogramming approach inspired by amphibian regeneration restored youthful gene expression in aged myogenic cells. Our results suggest that transient pluripotent reprogramming poses a neoplastic risk, but that restoration of youthful gene expression can be achieved with alternative strategies.
2022-06-10 | GSE176206 | GEO