The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution.

IF: 63.714

Cited by: 402

Abstract

Time series of single-cell transcriptome measurements can reveal dynamic features of cell differentiation pathways. From measurements of whole frog embryos spanning zygotic genome activation through early organogenesis, we derived a detailed catalog of cell states in vertebrate development and a map of differentiation across all lineages over time. The inferred map recapitulates most if not all developmental relationships and associates new regulators and marker genes with each cell state. We find that many embryonic cell states appear earlier than previously appreciated. We also assess conflicting models of neural crest development. Incorporating a matched time series of zebrafish development from a companion paper, we reveal conserved and divergent features of vertebrate early developmental gene expression programs.

Keywords

Spatial reconstruction

Gene Expression

MeSH terms

Animals

Cell Differentiation

Embryonic Development

Gene Expression Profiling

Gene Expression Regulation, Developmental

Genetic Variation

Neural Crest

Neurogenesis

Pluripotent Stem Cells

Sequence Analysis, RNA

Single-Cell Analysis

Transcription Factors

Transcriptome

Xenopus

Zebrafish

Zygote

Authors

Briggs, James A

Weinreb, Caleb

Wagner, Daniel E

Megason, Sean

Peshkin, Leonid

Kirschner, Marc W

Klein, Allon M

Recommend literature

1. Spatiotemporal Patterning of Zygotic Genome Activation in a Model Vertebrate Embryo.

2. Spatial reconstruction of single-cell gene expression data.

3. MorphoSeq: Full Single-Cell Transcriptome Dynamics Up to Gastrulation in a Chordate.

4. Developmental scRNAseq Trajectories in Gene- and Cell-State Space-The Flatworm Example.

5. Molecular recording of mammalian embryogenesis.

Similar data

1. The dynamics of gene expression in vertebrate embryogenesis at single cell resolution

2. Systematic mapping of cell state trajectories, cell lineage, and perturbations in the zebrafish embryo using single cell transcriptomics

3. Embryonic transcription is controlled by maternally defined chromatin state

4. Pseudo-temporal ordering of individual cells reveals regulators of differentiation

5. Spatial reconstruction of single-cell gene expression