Spatio-temporal mRNA tracking in the early zebrafish embryo

• Published in: Nature communications Vol. 12; no. 1; p. 3358
• Main Authors: Holler, Karoline, Neuschulz, Anika, Drewe-Boß, Philipp, Mintcheva, Janita, Spanjaard, Bastiaan, Arsiè, Roberto, Ohler, Uwe, Landthaler, Markus, Junker, Jan Philipp
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 07.06.2021; Nature Publishing Group; Nature Portfolio
• Subjects: 38; 38/91; 631/136/756; 631/1647/2217/2218; 631/1647/334/1874/763; 631/61/212/2019; 631/80/85/2361; 64/116; Animals; Cell Tracking - methods; Conserved sequence; Danio rerio; Embryo, Nonmammalian - cytology; Embryo, Nonmammalian - embryology; Embryo, Nonmammalian - metabolism; Embryogenesis; Embryonic growth stage; Embryos; Evolutionary conservation; Female; Gastrulation; Gene expression; Gene Expression Regulation, Developmental; Gene sequencing; Germ cells; Humanities and Social Sciences; Labeling; Localization; multidisciplinary; Oocytes - cytology; Oocytes - metabolism; Ribonucleic acid; RNA; RNA transport; RNA, Messenger - genetics; RNA, Messenger - metabolism; Science; Science (multidisciplinary); Single-Cell Analysis - methods; Spatial analysis; Spatial discrimination; Spatio-Temporal Analysis; Species Specificity; Tracking; Transcriptome - genetics; Transcriptomes; Transcriptomics; Wildlife conservation; Xenopus - embryology; Xenopus - genetics; Xenopus laevis - embryology; Xenopus laevis - genetics; Zebrafish; Zebrafish - embryology; Zebrafish - genetics
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-021-23834-1

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. Early stages of embryogenesis are known to depend on subcellular localization and transport of maternal mRNA, but systematic analyses have been hindered by a lack of methods for tracking of RNA. Here the authors combine spatially-resolved transcriptomics and single-cell RNA labeling to perform a spatio-temporal analysis of the transcriptome during early zebrafish development, revealing insights into this process.