ZFIN ID: ZDB-PUB-180428-1
Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis
Farrell, J.A., Wang, Y., Riesenfeld, S.J., Shekhar, K., Regev, A., Schier, A.F.
Date: 2018
Source: Science (New York, N.Y.)   360(6392): (Journal)
Registered Authors: Farrell, Jeffrey, Schier, Alexander
Keywords: none
Microarrays: GEO:GSE106466, GEO:GSE106474, GEO:GSE106587, GEO:GSE112824
MeSH Terms:
  • Animals
  • Blastula/embryology
  • Blastula/metabolism
  • Embryo, Nonmammalian/embryology
  • Embryo, Nonmammalian/metabolism
  • Embryonic Development/genetics*
  • Gene Expression Regulation, Developmental*
  • High-Throughput Nucleotide Sequencing
  • Signal Transduction
  • Single-Cell Analysis
  • Transcription, Genetic
  • Transcriptome
  • Zebrafish/embryology*
  • Zebrafish/genetics*
  • Zebrafish Proteins/genetics*
PubMed: 29700225 Full text @ Science
During embryogenesis, cells acquire distinct fates by transitioning through transcriptional states. To uncover these transcriptional trajectories during zebrafish embryogenesis, we sequenced 38,731 cells and developed URD, a simulated diffusion-based computational reconstruction method. URD identified the trajectories of 25 cell types through early somitogenesis, gene expression along them, and their spatial origin in the blastula. Analysis of Nodal signaling mutants revealed that their transcriptomes were canalized into a subset of wild-type transcriptional trajectories. Some wild-type developmental branchpoints contained cells expressing genes characteristic of multiple fates. These cells appeared to trans-specify from one fate to another. These findings reconstruct the transcriptional trajectories of a vertebrate embryo, highlight the concurrent canalization and plasticity of embryonic specification, and provide a framework to reconstruct complex developmental trees from single-cell transcriptomes.