Spatio-temporal mRNA tracking in the early zebrafish embryo

Karoline Holler, Anika Neuschulz, Philipp Drewe-Boß, Janita Mintcheva, Bastiaan Spanjaard, Roberto Arsiè, Uwe Ohler, Markus Landthaler and Jan Philipp Junker ()
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Karoline Holler: Max Delbrück Center for Molecular Medicine
Anika Neuschulz: Max Delbrück Center for Molecular Medicine
Philipp Drewe-Boß: Max Delbrück Center for Molecular Medicine
Janita Mintcheva: Max Delbrück Center for Molecular Medicine
Bastiaan Spanjaard: Max Delbrück Center for Molecular Medicine
Roberto Arsiè: Max Delbrück Center for Molecular Medicine
Uwe Ohler: Max Delbrück Center for Molecular Medicine
Markus Landthaler: Max Delbrück Center for Molecular Medicine
Jan Philipp Junker: Max Delbrück Center for Molecular Medicine

Nature Communications, 2021, vol. 12, issue 1, 1-13

Abstract: 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.

Date: 2021
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DOI: 10.1038/s41467-021-23834-1

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