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Epigenetic remodeling for regeneration progam activation in human cells [CUT&TAG]

ABSTRACT: Epigenetic remodeling for regeneration progam activation in human cells [CUT&TAG]

PROVIDER: PRJNA880586 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21573700_1.fastq.gz	Fastqsanger.gz
	SRR21573700_2.fastq.gz	Fastqsanger.gz
	SRR21573701_1.fastq.gz	Fastqsanger.gz
	SRR21573701_2.fastq.gz	Fastqsanger.gz
	SRR21573702_1.fastq.gz	Fastqsanger.gz

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Project description:Regeneration occurs naturally in certain lower vertebrates, but is highly restricted in humans with a stable epigenome. Recently, we demostrated that the small moleucles could reprogram the human somtic cells to pluripotent stem cells, relying on the activation of regeneration-like gene program. Here，by performing systematically epigenome analysis, we revealed that the establishment of this regeneration-like state relies on a hierarchical epigenetic regulation process. In additon, we also found the major barriers that inhibite the activation of regeneration program.

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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.

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Af-CUT&Tag: An Antibody-Free, High-Resolution Platform for Genome-Wide Profiling of Protein-DNA Interactions in Single Cells and Complex Tissues

Project description:Traditional antibody-based chromatin profiling methods are limited by antibody availability, cost, cell penetration, and protein modification susceptibility. To address these challenges, we present Af-CUT&Tag, a novel antibody-free approach for high-resolution chromatin profiling. By leveraging engineered binders (LgBiT/NbALFA) fused to Tn5 transposase and targeting CRISPR-integrated tags (HiBiT/ALFA), Af-CUT&Tag eliminates antibody dependence, achieving superior specificity and sensitivity with as few as 500 cells. This method outperforms antibody-based counterparts in signal-to-noise ratio, promoter enrichment, and library quality, while also enabling single-cell resolution (scAf-CUT&Tag). Applying Af-CUT&Tag to Hippo effectors (YAP1/TAZ) during liver regeneration revealed dynamic chromatin remodeling, including YAP1/TAZ-mediated control of lipid metabolism (e.g.,Lpin1, Fasn) and heme clearance (Hpx, Trf). We further identify miR-122 as a critical regulator of these processes, impacting liver regeneration. The versatility of Af-CUT&Tag in cell lines, bulk tissues, and single nuclei establishes it as a transformative tool for studying gene regulation in development, disease, and regeneration.

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