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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

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

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2016-06-01 | E-GEOD-74415 | biostudies-arrayexpress

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