Spatio-temporal mRNA tracking in the early zebrafish embryo

Abstract

Early stages of embryogenesis depend on subcellular localization and transport of maternal mRNA. However, systematic analysis of these processes is hindered by a lack of spatio-temporal information in single-cell RNA sequencing. Here, we combine spatially-resolved transcriptomics and single-cell RNA labeling to perform a spatio-temporal analysis of the transcriptome during early zebrafish development. We measure spatial localization of mRNA molecules within the one-cell stage embryo, which allows us to identify a class of mRNAs that are specifically localized at an extraembryonic position, the vegetal pole. Furthermore, we establish a method for high-throughput single-cell RNA labeling in early zebrafish embryos, which enables us to follow the fate of individual maternal transcripts until gastrulation. This approach reveals that many localized transcripts are specifically transported to the primordial germ cells. Finally, we acquire spatial transcriptomes of two xenopus species and compare evolutionary conservation of localized genes as well as enriched sequence motifs.

Mapping transcriptomic vector fields of single cells

“…In summary, we have built a general framework for the analysis of transcriptional dynamics that can be applied to numerous biological systems. More broadly, when coupled with remarkable experimental advances in single cell approaches including RNA metabolic labeling ( Holler et al, 2021 ), lineage tracing ( Chan et al, 2019 ; McKenna et al, 2016 ), RNA age ( Rodriques et al, 2020 ), signal pathway recording ( Sheth and Wang, 2018 ), as well as genetic perturbations ( Adamson et al, 2016 ; Dixit et al, 2016 ), dynamo will enable us to move towards holistic kinetic models and theories of the entire organism for cell atlas projects ( Cao et al, 2020a ), to understand how complex cell states arise from the combinatorial regulations of a limited number of factors, and finally to tackle the ultimate goal of converting between any cell types.…”

SLAMseq resolves the kinetics of maternal and zygotic gene expression in early zebrafish embryogenesis

“…S1c). We thereby extend on previous applications of the technology for spatiotemporal mapping of gene expression (Holler et al, 2021). Taken together, we provide a robust experimental framework in zebrafish embryos to accurately measure ZGA in the context of pre-existing maternal mRNAs at unprecedented accuracy, resolution and sensitivity.…”

When Bigger Is Better: 3D RNA Profiling of the Developing Head in the Catshark Scyliorhinus canicula

“…Since the initial description of RNA tomography (Junker et al, 2014), this technique has been applied to a limited number of systems, including limbs, the regenerating or pathological heart and aorta formation, in major model organisms including the zebrafish, mouse, chick, and Drosophila (Wu et al, 2016;Combs and Eisen, 2017;Burkhard and Bakkers, 2018;van den Brink et al, 2020;Yvernogeau et al, 2020;Holler et al, 2021). Most of these analyses have focused on characterizations along a single plane of interest, which is sufficient to identify genes differentially expressed along a polarity axis but does not provide a 3D spatial resolution.…”