ArticleDevelopmental dynamics : an official publication of the American Association of Anatomists2022
Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag.
Article in Developmental dynamics : an official publication of the American Association of Anatomists, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 29 citations in OpenAlex.
- Genomic Profiling of Chromatin State Using CUT&Tag.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Motif-Cluster: Motif driven prioritization of transcription factor binding clusters.PLoS computational biology · 2026Article
- HES3-dependent regulatory functions in development and fusion-positive rhabdomyosarcoma.bioRxiv : the preprint server for biology · 2026Article
- From two to one: spatiotemporal mapping of chromatin remodelling in the protamine-lacking early zygote of zebrafish.Epigenetics & chromatin · 2026Article
- Article
- Epigenetic Biomarkers for Predicting Nucleoside Analog Drug Response and Resistance in Cancer.Biomolecules · 2026Review
- ChIP happens: from biochemical origins to the modern omics toolbox for understanding steroid hormone receptors.The Biochemical journal · 2026Review
- How ATP-Dependent Chromatin Remodeling Complexes Regulate Vertebrate Embryonic Development.International journal of molecular sciences · 2026Review
- CUT&Tag for Chromatin Profiling in Cancer Tissue.Methods in molecular biology (Clifton, N.J.) · 2026Article
- H3K4me2 distinguishes a distinct class of enhancers during the maternal-to-zygotic transition.PLoS biology · 2025Article
- From morphology to single-cell molecules: high-resolution 3D histology in biomedicine.Molecular cancer · 2025Review
- Canonical and Variant Nucleosome Reprogramming from Sperm to Blastula.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Cut&tag: a powerful epigenetic tool for chromatin profiling.Epigenetics · 2024Review
- Article
- CUT&Tag applied to zebrafish adult tail fins reveals a return of embryonic H3K4me3 patterns during regeneration.Epigenetics & chromatin · 2024Article
- Improving rigor and reproducibility in chromatin immunoprecipitation assay data analysis workflows with Rocketchip.bioRxiv : the preprint server for biology · 2024Article
- The emerging H3K9me3 chromatin landscape during zebrafish embryogenesis.bioRxiv : the preprint server for biology · 2024Article
- CUT&Tag Applied to Zebrafish Adult Tail Fins Reveals a Return of Embryonic H3K4me3 Patterns During Regeneration.Research square · 2024Article
- Anp32e protects against accumulation of H2A.Z at Sox motif containing promoters during zebrafish gastrulation.Developmental biology · 2024Article
- Competition for H2A.Z underlies the developmental impacts of repetitive element de-repression.Development (Cambridge, England) · 2023Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundCell fate decisions are governed by interactions between sequence-specific transcription factors and a dynamic chromatin landscape. Zebrafish offer a powerful system for probing the mechanisms that drive these cell fate choices, especially in the context of early embryogenesis. However, technical challenges associated with conventional methods for chromatin profiling have slowed progress toward understanding the exact relationships between chromatin changes, transcription factor binding, and cellular differentiation during zebrafish embryogenesis.
resultsTo overcome these challenges, we adapted the chromatin profiling methods Cleavage Under Targets and Release Using Nuclease (CUT&RUN) and CUT&Tag for use in zebrafish and applied these methods to generate high-resolution enrichment maps for H3K4me3, H3K27me3, H3K9me3, RNA polymerase II, and the histone variant H2A.Z using tissue isolated from whole, mid-gastrula stage embryos. Using this data, we identify a subset of genes that may be bivalently regulated during both zebrafish and mouse gastrulation, provide evidence for an evolving H2A.Z landscape during embryo development, and demonstrate the effectiveness of CUT&RUN for detecting H3K9me3 enrichment at repetitive sequences.
conclusionsOur results demonstrate the power of combining CUT&RUN and CUT&Tag methods with the strengths of the zebrafish system to define emerging chromatin landscapes in the context of vertebrate embryogenesis.
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