CUT&Tag applied to zebrafish adult tail fins reveals a return of embryonic H3K4me3 patterns during regeneration

TL;DR

Researchers used a modified CUT&Tag method to study chromatin changes in regenerating zebrafish tail fins and found similarities to embryonic gene activation patterns.

Contribution

A modified CUT&Tag protocol enables high-resolution profiling of chromatin modifications in regenerating zebrafish tissues with improved efficiency and signal quality.

Findings

H3K4me3 levels increase at active gene promoters during fin regeneration.

Genes losing H3K4me3 become transcriptionally silent during regeneration.

Regeneration-associated H3K4me3 patterns mirror those seen in 24-h-old zebrafish embryos.

Abstract

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.

The online version contains supplementary material available at 10.1186/s13072-024-00547-5.

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