CUT&Tag Reveals a Return of Embryonic H3K4me3 Patterns During Zebrafish Tail Fin Regeneration (RNA-Seq)
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1087403 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28335985_1.fastq.gz | Fastqsanger.gz | |||
| SRR28335985_2.fastq.gz | Fastqsanger.gz | |||
| SRR28335986_1.fastq.gz | Fastqsanger.gz | |||
| SRR28335986_2.fastq.gz | Fastqsanger.gz |
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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
Project description:CUT&Tag Reveals a Return of Embryonic H3K4me3 Patterns During Zebrafish Tail Fin Regeneration
| PRJNA1087399 | ENA
Project description: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.
2024-05-01 | GSE261539 | GEO
Project description:CUT&Tag Reveals a Return of Embryonic H3K4me3 Patterns During Zebrafish Adult Tail Fin Regeneration (CUT&Tag)
| PRJNA1087402 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2024-05-01 | GSE261540 | GEO
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 only partially understood. Here we provide a modified CUT&Tag protocol suitable for improved characterization and interrogation of changes in chromatin modifications during adult fin regeneration in zebrafish. Our protocol generates data that 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 genes which lose H3K4me3 become silenced. Interestingly, these reprogramming events recapitulate the H3K4me3 patterns observed in developing fin folds of 24-h 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.
| S-EPMC11264793 | biostudies-literature
Project description:The goal of this study is to find skate pectoral fin motor neuron markers. Total RNA was extracted from manually sorted pectoral fin MNs, which were retrogradely labeled and tail spinal cord cells. By comparing RNA expression profiles of pectoral fin MNs and tail spinal cord neurons, we could identity general MN, MN columnar, and subset MN pool markers for fin MNs.
2018-02-08 | GSE105156 | GEO
Project description:Using genome-wide transcriptional profiling and whole-mount expression analyses of zebrafish larvae, we have identified hyaluronan synthase 3 (has3) as an upregulated gene during caudal fin regeneration. has3 expression is induced in the wound epithelium within hours after tail amputation, and its onset and maintenance requires fibroblast growth factor, phosphoinositide 3-kinase, and transforming growth factor-β signaling. Inhibition of hyaluronic acid (HA) synthesis by the small molecule 4-methylumbelliferone (4-MU) impaired tail regeneration in zebrafish larvae by preventing injury-induced cell proliferation. In addition, 4-MU reduced the expression of genes associated with wound epithelium and blastema function. Treatment with the glycogen synthase 3-kinase inhibitors rescued 4-MU-induced defects in cell proliferation and tail regeneration, even though only a subset of wound epithelium and blastema markers was restored. Our findings uncover a role for HA biosynthesis in zebrafish tail regeneration and its epistatic relationships with other regenerative processes.
2017-03-10 | GSE72422 | 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. 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 μg of total RNA was recovered from ~250 tail tissues at 16-24 hpa or uncut control tissues; and approx. 5 μg, 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
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