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

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.

Current best practices in single‐cell RNA‐seq analysis: a tutorial

“…In recent years, single‐cell RNA sequencing (scRNA‐seq) has significantly advanced our knowledge of biological systems. We have been able to both study the cellular heterogeneity of zebrafish, frogs and planaria (Briggs et al , ; Plass et al , ; Wagner et al , ) and discover previously obscured cellular populations (Montoro et al , ; Plasschaert et al , ). The great potential of this technology has motivated computational biologists to develop a range of analysis tools (Rostom et al , ).…”

Microfluidic Single‐Cell Omics Analysis

“…The main cerebellar lineages were identified to uncover the engine behind these processes at different branching points, which enhanced the knowledge of neurodevelopment . Similar technologies were also applied to investigate the differentiation and growth dynamics of other species, such as Zebrafish, Xenopus laevis , and Arabidopsis, etc.…”

Advancing genetic and genomic technologies deepen the pool for discovery in Xenopus tropicalis

“…The genome assembly is now available at chromosome‐level (version 9.1 as of this writing) and gene models and annotations are well‐suited to RNA‐Seq analysis. An exciting frontier in X. tropicalis , as in other model systems, is the potential for cell type discovery and type‐specific transcriptomic profiling through single‐cell RNA‐Seq, which has recently been leveraged to show that many cell types acquire their identity much earlier than previously appreciated . Both bulk and single‐cell RNA‐Seq are expected to continue to provide critical unbiased insight into the effects of developmental, genetic or pharmacological perturbations, and into the molecular basis of cell identity and differentiation.…”

“…When the neural fold finishes zippering, the embryo begins to elongate. During early tailbud stages (19)(20)(21)(22)(23)(24) the embryo develops morphologically well-defined anterior structures including the pharyngeal arches, sensory placodes, and eyecup, while elongating along the anterior-posterior axis. Elongation, development of tail fin, resecting of gut, and development of refined organs then takes place over the rest of tailbud and early tadpole development.…”