ArticleNature cell biology2024
Mapping the chromatin accessibility landscape of zebrafish embryogenesis at single-cell resolution by SPATAC-seq.
Article in Nature cell biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Article
- CREsted: modeling genomic and synthetic cell-type-specific enhancers across tissues and species.Nature methods · 2026Article
- Single-cell ATAC-seq analysis of human embryoid bodies reveals crucial transcription factor networks involved in early germ layer specification.Cell & bioscience · 2026Article
- Single-cell chromatin profiling reveals dynamic regulatory logic and enhancer elements in brain and retina development.bioRxiv : the preprint server for biology · 2026Article
- Evaluating single-cell ATAC-seq atlasing technologies using sequence-to-function modeling.Nature communications · 2026Article
- Epigenetic remodeling during early embryonic development.Frontiers in cell and developmental biology · 2026Review
- Next-generation molecular tools in veterinary parasitology: advances, challenges, and perspectives in the diagnosis of emerging parasites.Revista brasileira de parasitologia veterinaria = Brazilian journal of veterinary parasitology : Orgao Oficial do Colegio Brasileiro de Parasitologia Veterinaria · 2026Review
- Article
- Cell type-independent timekeeping gene modules enable embryonic stage prediction in zebrafish.bioRxiv : the preprint server for biology · 2025Article
- Dynamic Chromatin Accessibility and Transcriptional Regulation in the Eyes of Red Tilapia (Oreochromis sp.) in Response to Wintering Stress.Marine biotechnology (New York, N.Y.) · 2025Article
- Dissecting the regulatory logic of specification and differentiation during vertebrate embryogenesis.bioRxiv : the preprint server for biology · 2024Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Currently, the dynamic accessible elements that determine regulatory programs responsible for the unique identity and function of each cell type during zebrafish embryogenesis lack detailed study. Here we present SPATAC-seq: a split-pool ligation-based assay for transposase-accessible chromatin using sequencing. Using SPATAC-seq, we profiled chromatin accessibility in more than 800,000 individual nuclei across 20 developmental stages spanning the sphere stage to the early larval protruding mouth stage. Using this chromatin accessibility map, we identified 604 cell states and inferred their developmental relationships. We also identified 959,040 candidate cis-regulatory elements (cCREs) and delineated development-specific cCREs, as well as transcription factors defining diverse cell identities. Importantly, enhancer reporter assays confirmed that the majority of tested cCREs exhibited robust enhanced green fluorescent protein expression in restricted cell types or tissues. Finally, we explored gene regulatory programs that drive pigment and notochord cell differentiation. Our work provides a valuable open resource for exploring driver regulators of cell fate decisions in zebrafish embryogenesis.
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