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

James A Briggs, Caleb Weinreb, Daniel E Wagner, Sean Megason, Leonid Peshkin, Marc W Kirschner*, Allon M Klein*​

Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
*Correspondence to: marc@hms.harvard.edu; Allon_Klein@hms.harvard.edu

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.