Expression profiling of zebrafish fin regeneration: role of hypoxia
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PROVIDER: PRJNA252908 | ENA |
REPOSITORIES: ENA
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Project description:Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non-coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation, we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Small RNA and mRNA gene expression profiling during 0 and 4 days post amputation.
2016-06-01 | E-GEOD-74415 | 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:Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non-coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation, we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing.
2016-06-01 | GSE74415 | GEO
Project description:Zebrafish have the remarkable ability to regenerate body parts including the heart, spinal cord and fins by a process referred to as epimorphic regeneration. Recent studies have illustrated that similar to adult zebrafish, early life stage-larvae also possess the ability to regenerate the caudal fin. A comparative genomic analysis was used to determine the degree of conservation in gene expression among the regenerating adult caudal fin, adult heart and larval fin. Results indicate that these tissues respond to amputation/injury with strikingly similar genomic responses. Comparative analysis revealed raldh2, a rate-limiting enzyme for the synthesis of Retinoic acid (RA), as one of the highly induced genes across the three regeneration platforms. Experiment Overall Design: The caudal fin of zebrafish larvae at 2days post fertilization were amputated. Caudal fin tissue at 2dpf and regenerating fins were isolated at 1, 2and 3 days post amputation. Three replicates were collected at each time point. 150 fins were pooled to comprise one replicate.
2008-04-07 | E-GEOD-10188 | biostudies-arrayexpress
Project description:Planarian flatworms regenerate their heads and tails from anterior or posterior wounds and this blastema regeneration polarity is controlled by Wnt/β-catenin signaling. It is well known that a regeneration blastema of appendages of vertebrates such as fish and amphibians grows distally. However, it remains unclear whether a regeneration blastema in vertebrate appendages can grow proximally. Here, we show that a regeneration blastema in zebrafish fins can grow proximally along the proximodistal axis by calcineurin inhibition. We used fin excavation in adult zebrafish to observe the unidirectional regeneration, from the anterior cut edge (ACE) to the posterior cut edge (PCE) of the cavity and this unidirectional regeneration polarity occurs as the PCE fails to build blastemas. Furthermore, we found that calcineurin activities in the ACE were greater than in the PCE. Calcineurin inhibition induced the PCE blastemas, and calcineurin hyperactivation suppressed fin regeneration. Collectively, these findings identify calcineurin as a molecular switch to specify the PCE blastema of the proximodistal axis and regeneration polarity in zebrafish fin.
2020-10-20 | GSE159560 | GEO
Project description:We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins
2016-04-08 | GSE76564 | GEO
Project description:Aim: In this study, we aim to establish a diabetic zebrafish model and examine the effects of high glucose on inflammation and tissue regeneration. Materials and Methods: Tübingen strain zebrafish (wild type, WT), Tg (mpo: EGFP), and Tg (coro1a: EGFP) zebrafish were employed. Caudal fin amputation was performed to study tissue regeneration and inflammation. Results: Our results showed that high glucose increased the recruitment of neutrophils and macrophages after amputation. Most importantly, limb regeneration was severely impaired after amputation in zebrafish larvae exposed to 222 mM glucose for 14 days. In addition, inflammatory factors IL-1β, IL-6, TNF-α, VCAM-1, and MCP-1, which are closely related to the development of diabetic wound, increased significantly in caudal fin amputation after glucose exposure. The p38 inhibitor SB203580 can reduce the expression of inflammatory factors and promote regeneration in high glucose. It showed that caudal fin amputation after glucose exposure resulted in genes enrichment of several pathways involved in amino acid metabolism, lipid metabolism, and inflammation based on high-throughput transcriptome sequencing. Conclusions: Overall, this experimental system using zebrafish larvae provides a wide spectrum of genetic and molecular profile recapitulating human diabetes which will be beneficial for basic research of inflammation and regeneration in diabetic background and promote translational research for diabetes therapy.
2025-09-01 | GSE260718 | GEO
Project description:Background/Aims:The ability of regeneration varies widely from invertebrates to vertebrates. Some animals, for example, flatworms, newts, salamanders, and lower vertebrates have the outstanding ability to regenerate all the organs even the whole individual. Unfortunately, the regenerative capacity of humans extremely attenuates along with the biological evolution and this makes it difficult for humans to recover from damaged or missing organs or tissues, and even cause serious loss of function or death. However, the research on regeneration mechanisms is limited and incomplete so far. Here, we investigated the biological mechanisms of zebrafish caudal fin regeneration. Methods:The zebrafish was used as the research object to analyze the differences of mRNA and ncRNA expressed in new tissues at 0d, 3d, and 7d after caudal fin removal, and analyzed the molecular mechanism of caudal fin regeneration from the perspective of the whole transcriptome. Results: We observed that the amputated caudal fin went through a complex genetic change, especially at 3 dpa. This result showed that genes related to response to cell cycle and wounding might play a role in caudal fin regeneration.The up regulated DEGs at 3 dpa (blastema outgrowth stage) were dramatically enriched in 20 Biological Processes (FDR < 0.05), three of which were cell cycle (GO:0007049), mitotic cell cycle (GO:0000278), and cell cycle process (GO:0022402), one was response to wounding (GO:0009611), etc. Conclusion: Taken together, the results revealed that the DEGs were enriched in numerous biological processes, molecular function, cellular component, and signaling pathways, suggesting that the caudal fin regeneration is a highly complicated process of the molecular mechanism.
2022-04-04 | GSE160909 | GEO
Project description:Teleost fish have the remarkable ability to regenerate their body parts including heart, spinal cord, and the caudal fin, while many higher vertebrates including us humans have only a limited ability. To facilitate molecular and genetic approaches for regeneration, we previously established an assay using the fin fold of early stage larvae, which regenerate their caudal fin folds as in adult regeneration. Here, we performed transcriptional profiling of regenerating larval fin folds and identified genes with differential expression during regeneration. Gene expression profiling of zebrafish larval fin-fold regeneration was performed by comparing amputated fin fold and uncut control. Keywords: Stress response, injury response.
2008-10-01 | GSE11391 | GEO
Project description:Olsen et al (2010) have shown that induced Diabetes mellitus (DM) in adult Zebrafish results in an impairment of tissue regeneration as monitored by caudal fin regeneration. In those studies, streptozocin was used to induce hyperglycemia in adult zebrafish, and then, following streptozocin withdrawal, a recovery phase was allowed to re-establish euglycemia, due to pancreatic b-cell regeneration. DM-associated impaired fin regeneration continued indefinitely in the metabolic memory state (MM); allowing for subsequent molecular analysis of the underlying mechanisms of MM. This study focuses on elucidating the molecular basis explaining DM-associated impaired fin regeneration and why it persists into the MM state. The analysis of microarray data indicated that of the 14,900 transcripts analyzed, aberrant expression of 71 genes relating to tissue developmental and regeneration processes were identified in DM fish and the aberrant expression of these 71 genes persisted into the MM state. Key regulatory genes of major signal transduction pathways were identified among this group of 71; and therefore, these findings provide a possible explanation for how hyperglycemia induces impaired fin regeneration and why it continues into the MM state. Total RNA was extracted from caudal fin at 0, 12, 24 and 48 hours post amputation from untreated controls and metabolic memory zebrafish.
2012-11-01 | E-GEOD-37163 | biostudies-arrayexpress