A single cell transcriptome atlas of the developing zebrafish hindbrain

Abstract

Segmentation of the vertebrate hindbrain leads to the formation of rhombomeres, each with a distinct anteroposterior identity. Specialised boundary cells form at segment borders that act as a source or regulator of neuronal differentiation. In zebrafish, there is spatial patterning of neurogenesis in which non-neurogenic zones form at bounderies and segment centres, in part mediated by Fgf20 signaling. To further understand the control of neurogenesis, we have carried out single cell RNA sequencing of the zebrafish hindbrain at three different stages of patterning. Analyses of the data reveal known and novel markers of distinct hindbrain segments, of cell types along the dorsoventral axis, and of the transition of progenitors to neuronal differentiation. We find major shifts in the transcriptome of progenitors and of differentiating cells between the different stages analysed. Supervised clustering with markers of boundary cells and segment centres, together with RNA-seq analysis of Fgf-regulated genes, has revealed new candidate regulators of cell differentiation in the hindbrain. These data provide a valuable resource for functional investigations of the patterning of neurogenesis and the transition of progenitors to neuronal differentiation.

Uncovering the genetic blueprint of theC. elegansnervous system

“…The presented framework offers guidance for future experiments: To apply SCM to these systems requires a matched connectome, contactome, and transcriptome, meaning that, for each cell, we need to know its connections, its physical contacts, and its gene expression. Partial neuronal transcriptomes and connectomes have been published recently for fly (54)(55)(56) and zebrafish (57,58). However, connectivity and gene expression were not profiled jointly; thus these datasets cannot offer cellular-level predictions.…”

Specification of axial identity by Hoxa2 distinguishes between a phenotypic and molecular ground state in mouse cranial neural crest cells

“…In recent years, scRNAseq experiments have been used to shed light on the dynamics of embryonic development, from whole-embryo studies (Cao et al 2019; Soldatov et al 2019) to in-depth characterization of particular developmental processes (Xu et al 2019; Tambalo et al 2020). Here, we took advantage of this approach to explore the heterogeneity of the PAs and characterize the role of HOXA2 in imparting PA2 NCC identity at single-cell resolution.…”

Primary culture of adult cortical neurons from reptile Gekko japonicus

“…Such exclusive features are governed by a different set of molecular programs with the non‐regenerative counterparts (Lee‐Liu et al, 2013). Several established methods, such as transgenic tracing, single cell sequencing, and immunostaining, can elucidate the states of in vivo axonal growth or gene expression profiles (Kunst et al, 2019; Tambalo et al, 2020; Tiklova et al, 2019), but an in vitro culture of primary neurons from the regenerative models is indispensable for investigating neuronal reactions to various stimuli and the basic mechanisms of differential functions.…”