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Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility (RNA-seq)

ABSTRACT: Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility (RNA-seq)

PROVIDER: PRJNA523009 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8587730_1.fastq.gz	Fastqsanger.gz
	SRR8587730_2.fastq.gz	Fastqsanger.gz
	SRR8587740_1.fastq.gz	Fastqsanger.gz
	SRR8587740_2.fastq.gz	Fastqsanger.gz
	SRR8587731_1.fastq.gz	Fastqsanger.gz

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Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility

Project description:Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility

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Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility (WGBS)

Project description:Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility (WGBS)

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Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility (ATAC-seq)

Project description:Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility (ATAC-seq)

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Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility.

Project description:BackgroundZebrafish can faithfully regenerate injured fins through the formation of a blastema, a mass of proliferative cells that can grow and develop into the lost body part. After amputation, various cell types contribute to blastema formation, where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored.ResultsWe produce epigenome maps, including DNA methylation and chromatin accessibility, as well as transcriptomes, of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes, coupled with stably maintained lineage-specific DNA methylation. The epigenetic signatures also reveal many novel regeneration-specific enhancers, which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map, and a knockout of a predicted upstream regulator disrupts normal regeneration, validating our prediction.ConclusionOur study shows that lineage-specific DNA methylation signatures are stably maintained during regeneration, and regeneration enhancers are preset as hypomethylated before injury. In contrast, chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis.

| S-EPMC7047409 | biostudies-literature

Regenerating zebrafish fin fold vs. uncut control

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. Two time points, 18-24 hours post amputation (hpa) and 48 hpa, of regenerating fin fold were analyzed. We performed one replicate per each time point. For microarray expression profiling, total RNA was extracted from regenerating and uncut caudal fin folds of AB strain larvae. Tail tissues of 16-24 hpa, 48 hpa, and uncut siblings of the respective stages including 3-5 posterior somite segments were collected on ice. Total RNA was extracted by using TRIzol reagent (Invitrogen, Carlsbad, California, United States) according to the manufacturerâs instruction. The quantity and quality of total RNA were assessed by absorbance at 260 nm and 280 nm and by gel electrophoresis. Approx. 9 Î¼g of total RNA was recovered from ~250 tail tissues at 16-24 hpa or uncut control tissues; and approx. 5 Î¼g, from ~130 tail tissues at 48 hpa or uncut control tissues. Probes for microarray analysis were labeled with cy3 (amputated fin fold at 16-24 hpa and uncut control at 48 hpa) or cy5 (uncut control at 16-24 hpa and amputated fin fold at 48 hpa), and used for hybridization.

2010-05-19 | E-GEOD-11391 | biostudies-arrayexpress

Regenerating Zebrafish fins: Controls vs. regenerating fins (3 days following fin amputation)

Project description:Transcriptional profiling of zebrafish rergenerating fins comparing control fins and regenerating fins (3 days following fin amputation)

2017-02-09 | GSE58567 | GEO

Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility (WGBS)

Project description:Background: Zebrafish can faithfully regenerate injured fins through the formation of a blastema, a mass of proliferative cells that can grow and develop into the lost body part. After amputation, various cell types contribute to blastema formation, where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. Results: We produce epigenome maps, including DNA methylation and chromatin accessibility, as well as transcriptomes, of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes, coupled with stably maintained lineage-specific DNA methylation. The epigenetic signatures also reveal many novel regeneration-specific enhancers, which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map, and a knockout of a predicted upstream regulator disrupts normal regeneration, validating our prediction. Conclusion: Our study shows that lineage-specific DNA methylation signatures are stably maintained during regeneration, and regeneration enhancers are preset as hypomethylated before injury. In contrast, chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis.

2020-01-20 | GSE126702 | GEO

Cellular diversity of the regenerating caudal fin

Project description:single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell-type-specific genetic program during regeneration

2020-08-12 | GSE137971 | GEO

Regenerating zebrafish fin fold vs. uncut control

2008-10-01 | GSE11391 | GEO

Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility (RNA-seq)

2020-01-20 | GSE126701 | GEO