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Spatio-temporal mRNA tracking in the early zebrafish embryo

Author

Listed:
  • 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
    Humboldt University)

  • Markus Landthaler

    (Max Delbrück Center for Molecular Medicine
    Humboldt University)

  • Jan Philipp Junker

    (Max Delbrück Center for Molecular Medicine)

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.

Suggested Citation

  • Karoline Holler & Anika Neuschulz & Philipp Drewe-Boß & Janita Mintcheva & Bastiaan Spanjaard & Roberto Arsiè & Uwe Ohler & Markus Landthaler & Jan Philipp Junker, 2021. "Spatio-temporal mRNA tracking in the early zebrafish embryo," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-23834-1
    DOI: 10.1038/s41467-021-23834-1
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    Cited by:

    1. Lior Fishman & Avani Modak & Gal Nechooshtan & Talya Razin & Florian Erhard & Aviv Regev & Jeffrey A. Farrell & Michal Rabani, 2024. "Cell-type-specific mRNA transcription and degradation kinetics in zebrafish embryogenesis from metabolically labeled single-cell RNA-seq," Nature Communications, Nature, vol. 15(1), pages 1-20, December.

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