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CUT&Tag Reveals a Return of Embryonic H3K4me3 Patterns During Zebrafish Tail Fin Regeneration (RNA-Seq)

ABSTRACT: The regenerative potential is governed by a complex process of transcriptional reprogramming, involving nuclear reorganization and dynamics in transcription factor binding patterns throughout the genome. The degree to which chromatin and epigenetic changes influence this process remains only partially understood. Here we provide a modified CUT&Tag protocol suitable for improved characterization and interrogation of epigenetic changes during of zebrafish caudal fin regeneration. Data generated from our protocol recapitulates results from previously published ChIP-Seq methods, requires far fewer cells as input, and significantly improves signal to noise ratios during profiling. We deliver high-resolution enrichment maps for H3K4me3 at 0 days post amputation (DPA) and 2DPA using tissue isolated from caudal fins. During regeneration, we find that H3K4me3 levels increase over gene promoters which become transcriptionally active and H3K4me3 is lost at genes which are silenced. Remarkably, these epigenetic alterations partially recapitulate H3K4me3 patterns that occur normally in 24 hour old embryos. Our results demonstrate that the CUT&Tag method is an effective tool for profiling chromatin landscapes in regenerating fins, and that changes in genomic H3K4me3 patterns during fin regeneration occur in a manner consistent with reactivation of developmental programming.

ORGANISM(S): Danio rerio

PROVIDER: GSE261539 | GEO | 2024/05/01

REPOSITORIES: GEO

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CUT&Tag Reveals a Return of Embryonic H3K4me3 Patterns During Zebrafish Adult Tail Fin Regeneration (CUT&Tag)

Project description:Regenerative potential is governed by a complex process of transcriptional reprogramming, involving chromatin reorganization and dynamics in transcription factor binding patterns throughout the genome. The degree to which chromatin and epigenetic changes contribute to this process remains partially understood. Here we provide a modified CUT&Tag protocol suitable for improved characterization and interrogation of epigenetic changes during adult fin regeneration in zebrafish. Data generated from our protocol recapitulates results from previously published ChIP-Seq methods, requires far fewer cells as input, and significantly improves signal to noise ratios. We deliver high-resolution enrichment maps for H3K4me3 of uninjured and regenerating fin tissues. During regeneration, we find that H3K4me3 levels increase over gene promoters which become transcriptionally active and H3K4me3 is lost at genes which become silenced . Interestingly, these epigenetic reprogramming events recapitulate the H3K4me3 patterns observed in developing fin folds of 24 hour old zebrafish embryos. Our results indicate that changes in genomic H3K4me3 patterns during fin regeneration occur in a manner consistent with reactivation of developmental programs, demonstrating CUT&Tag to be an effective tool for profiling chromatin landscapes in regenerating tissues.

2024-05-01 | GSE261538 | GEO

Transcription profiling of zebrafish adult and larval fin to investigate mechanisms of regeneration

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

Transcription profiling of zebrafish larval regenerating fin tissue after exposure to TCDD in order to identify genes differentially regulated after Ahr activation

Project description:Exposures to dioxin, including 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) cause a wide array of toxicities in vertebrates and is mostly considered to be mediated through the inappropriate activation of the aryl hydrocarbon receptor (Ahr) signaling pathway. Although transcriptional regulation by Ahr is widely studied, the molecular mechanisms responsible for the adverse outcomes after Ahr activation are largely unknown. To identify the important events downstream of AHR activation that play an actual role in the toxic responses, we employed the zebrafish caudal fin regeneration models since Ahr activation blocks the regenerative process. Zebrafish regenerate their caudal fins by an orchestrated progression of cell migration, differentiation and proliferation controlled by a multitude of signaling pathways. This complex process was exploited as an in vivo platform to identify cross talk between Ahr and other signaling pathways. Global genomic analysis was performed in the larval regenerating fin tissue after exposure to TCDD in order to identify genes differentially regulated after Ahr activation. Comparative toxicogenomic analysis revealed that both adult and larval fins respond to TCDD during regeneration with mis-expression of Wnt signaling pathway members and Wnt target genes. Experiment Overall Design: The caudal fin of zebrafish larvae at 2days post fertilization were amputated and exposed to vehicle control alone or TCDD. Regenerating fins were isolated at 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-10184 | biostudies-arrayexpress

CUT&Tag Reveals a Return of Embryonic H3K4me3 Patterns During Zebrafish Adult Tail Fin Regeneration (CUT&Tag)

Project description:CUT&Tag Reveals a Return of Embryonic H3K4me3 Patterns During Zebrafish Adult Tail Fin Regeneration (CUT&Tag)

| PRJNA1087402 | ENA

CUT&Tag Reveals a Return of Embryonic H3K4me3 Patterns During Zebrafish Tail Fin Regeneration

Project description:CUT&Tag Reveals a Return of Embryonic H3K4me3 Patterns During Zebrafish Tail Fin Regeneration

| PRJNA1087399 | ENA

Transcription profiling of zebrafish fin regeneration

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

Single-cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae

Project description:Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single-cell RNA-sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation. Methods: 150 of regenerating caudal fin (cut) and intact caudal fine (uncut) samples were dissociated and loaded into the 10x Genomics Chromium Platform, and sequenced using Illumina NovaSeq 6000. Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single-molecule-based sequencing technology for high-throughput profiling of both intact (uncut) and regenerating caudal fin samples (cut) at 24hpA. We confirmed the presence of macrophage subsets, previously described by our group to govern zebrafish fin regeneration, and identified a novel blastemal cell population.

2021-07-17 | GSE158851 | GEO

Transcription profiling of Zebrafish 1 Day post amputation vehicle or beclomethasone exposed to study regeneration

Project description:Zebrafish caudal fin regeneration is an established model to study tissue regeneration. In order to identify novel molecular signaling pathways critical for regeneration, we developed a rapid throughput in vivo regeneration assay. We screened a 2000 member structurally diverse small molecule library, followed by assessment of regenerative progression at three days post amputation. A cluster of glucocorticoids was identified among the âpositive hitsâ. To identify the molecular targets of the activated glucocorticoid receptor, microarray analysis was performed using RNA isolated from the regenerates of control and glucocorticoid exposed zebrafish. We identified 673 transcripts that were differentially regulated. The level of expression and spatial expression pattern of select genes were completed by qPCR and by in situ hybridization, respectively. Altogether, these studies demonstrate the power of chemical genetics to identify chemical probes and their targets which will provide a path towards defining conserved regenerative pathways. Experiment Overall Design: The caudal fin of zebrafish larvae at 2days post fertilization were amputated and exposed to vehicle control alone or Beclomethasone . Regenerating fins were isolated at 1days post amputation. Three replicates were collected at each time point. 150 fins were pooled to comprise one replicate.

2009-02-08 | E-GEOD-10766 | biostudies-arrayexpress

Effect of swim-training on caudal fin development in zebrafish larvae

Project description:Genome-wide microarray analysis of the effects of swim-training on caudal fin development in zebrafish larvae. Zebrafish were subjected to swim-training from 5 days post fertilization (dpf) until 10 dpf. Subsequently, we performed a genome-wide microarray analysis on the caudal fins of control and trained fish at 10 dpf. The goal of the project was to investigate the effects of swim-training on the gene expression level during caudal fin development in zebrafish larvae. Two-condition experiment: control vs trained fish. RNA was isolated from pooled caudal fins of 15 control fish (in duplo: pooled control samples (C2 and C3)) and of 15 trained fish (in duplo: pooled trained samples( T2 and T3)). Subsequently, each pooled RNA sample of control and trained caudal fins was labeled with Cy3 and Cy5 in order to correct for dye bias. We included a technical replicate of the labeled C2 and T2 samples.

2014-07-17 | E-GEOD-44395 | biostudies-arrayexpress

Glucocorticoid treatment leads to aberrant ion and macromolecular transport mechanisms in regenerating zebrafish fins.

Project description:Bone is a highly regenerative tissue but it can be permanently lost due to severe trauma and as a result of disease. In zebrafish, which are capable of complex organ regeneration, intramembranous bones of the fins and skull regenerate rapidly even after profound loss. The fin regenerate, albeit being composed of different tissues is a structure of modest complexity which, together with the fact that it is easy to access and monitor, makes it a useful system to study bone formation, wound healing and metabolic disease. Glucocorticoids are powerful drugs used in anti-inflammatory and immunosuppressive therapy. Despite their unmistakable advantages and usefulness, long term treatment with glucocorticoids can cause a variety of adverse effects such as insulin resistance, high blood pressure and bone fragility. Here we made use of proteomics to study the fin regeneration by sampling zebrafish caudal fins without prior injury and regenerated tissue 4 days post amputation at normal and perturbed conditions (prednisolone-treatment).

2019-09-26 | PXD013552 | Pride

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