PUBLICATION
Mapping the chromatin accessibility landscape of zebrafish embryogenesis at single-cell resolution by SPATAC-seq
- Authors
- Sun, K., Liu, X., Xu, R., Liu, C., Meng, A., Lan, X.
- ID
- ZDB-PUB-240709-20
- Date
- 2024
- Source
- Nature cell biology 26(7): 1187-1199 (Journal)
- Registered Authors
- Meng, Anming
- Keywords
- none
- Datasets
- GEO:GSE243256
- MeSH Terms
-
- Animals
- Cell Differentiation/genetics
- Cell Lineage/genetics
- Chromatin*/genetics
- Chromatin*/metabolism
- Embryo, Nonmammalian/metabolism
- Embryonic Development*/genetics
- Enhancer Elements, Genetic
- Gene Expression Regulation, Developmental*
- Green Fluorescent Proteins/genetics
- Green Fluorescent Proteins/metabolism
- Single-Cell Analysis*/methods
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transposases/genetics
- Transposases/metabolism
- Zebrafish*/embryology
- Zebrafish*/genetics
- Zebrafish*/metabolism
- Zebrafish Proteins/genetics
- Zebrafish Proteins/metabolism
- PubMed
- 38977847 Full text @ Nat. Cell Biol.
Citation
Sun, K., Liu, X., Xu, R., Liu, C., Meng, A., Lan, X. (2024) Mapping the chromatin accessibility landscape of zebrafish embryogenesis at single-cell resolution by SPATAC-seq. Nature cell biology. 26(7):1187-1199.
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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping