PROJECT ID: GSE158849

Data source GEO: GSE158849
Description We performed spatially resolved transcriptomics with sub-single-cell resolution in zebrafish embryos at the one-cell stage, which allowed us to identify a class of mRNAs that is specifically localized at an extraembryonic position in the yolk sac, the vegetal pole. The 3’ UTRs of these localized genes are enriched in specific sequence motifs. Comparison to two frog species revealed relatively low conservation of localized genes, but high conservation of sequence motifs. In vivo RNA labeling followed by scRNA-seq revealed that a large number of the localized transcripts are specifically transported to the primordial germ cells.
Key word genome-wide expression; spatial transcriptomics; xenopus 00cytes; global analysis; seq reveals; localization; translation; cells; translocation; tomography
Publication Holler K, Neuschulz A, Drewe-Boß P, Mintcheva J et al. Spatio-temporal mRNA tracking in the early zebrafish embryo. Nat Commun 2021 Jun 7;12(1):3358. PMID: 34099733
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. 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.


Dataset Information

Dataset ID Species Tissue / Organ Experiment type Sample Source dataset ID
1. GSE158849 (labeled) Danio rerio embryo baseline 6hpf, WT, 4sUTP injected (labeled) GEO: GSM4812182
2. GSE158849 (unlabeled) Danio rerio embryo baseline 6hpf, WT, 4sUTP injected (unlabeled) GEO: GSM4812182

Clustering Result

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Ectoderm cells -- (h2afva) marker DOI:10.1038/s41467-021-23834-1
1 Ectoderm cells ENSDARG00000032866 (erh) marker DOI:10.1038/s41467-021-23834-1
1 Ectoderm cells ENSDARG00000099859 (CR383676.1) marker DOI:10.1038/s41467-021-23834-1
4 Non-axial mesoderm cells ENSDARG00000068761 (mespab) marker DOI:10.1038/s41467-021-23834-1
4 Non-axial mesoderm cells ENSDARG00000070546 (msgn1) marker DOI:10.1038/s41467-021-23834-1
4 Non-axial mesoderm cells ENSDARG00000017078 (mespaa) marker DOI:10.1038/s41467-021-23834-1
4 Non-axial mesoderm cells ENSDARG00000034610 (insb) marker DOI:10.1038/s41467-021-23834-1
5 Ectoderm cells -- (h2afva) marker DOI:10.1038/s41467-021-23834-1
5 Ectoderm cells ENSDARG00000032866 (erh) marker DOI:10.1038/s41467-021-23834-1
6 Axial mesoderm cells ENSDARG00000006110 (chrd) marker DOI:10.1038/s41467-021-23834-1
6 Axial mesoderm cells ENSDARG00000059073 (gsc) marker DOI:10.1038/s41467-021-23834-1
6 Axial mesoderm cells ENSDARG00000012788 (foxa3) marker DOI:10.1038/s41467-021-23834-1
7 Enveloping layer cells ENSDARG00000093584 (zgc:193505) marker DOI:10.1038/s41467-021-23834-1
7 Enveloping layer cells ENSDARG00000104181 (tmsb1) marker DOI:10.1038/s41467-021-23834-1
7 Enveloping layer cells ENSDARG00000017624 (krt4) marker DOI:10.1038/s41467-021-23834-1
7 Enveloping layer cells ENSDARG00000055046 (ponzr5) marker DOI:10.1038/s41467-021-23834-1
7 Enveloping layer cells ENSDARG00000043442 (zgc:153665) marker DOI:10.1038/s41467-021-23834-1
7 Enveloping layer cells ENSDARG00000036834 (krt92) marker DOI:10.1038/s41467-021-23834-1
7 Enveloping layer cells ENSDARG00000000212 (krt97) marker DOI:10.1038/s41467-021-23834-1
9 Primordial germ cells ENSDARG00000096095 (buc) marker DOI:10.1038/s41467-021-23834-1
9 Primordial germ cells ENSDARG00000060917 (anln) marker DOI:10.1038/s41467-021-23834-1

Cluster Cell type Gene id (symbol) Marker class Evidence
2 Ectoderm cells ENSDARG00000041065 (hspb1) marker DOI:10.1038/s41467-021-23834-1
5 Ectoderm cells ENSDARG00000041065 (hspb1) marker DOI:10.1038/s41467-021-23834-1
8 Enveloping layer cells ENSDARG00000093584 (zgc:193505) marker DOI:10.1038/s41467-021-23834-1
8 Enveloping layer cells ENSDARG00000036834 (krt92) marker DOI:10.1038/s41467-021-23834-1
8 Enveloping layer cells ENSDARG00000000212 (krt97) marker DOI:10.1038/s41467-021-23834-1
8 Enveloping layer cells ENSDARG00000055046 (ponzr5) marker DOI:10.1038/s41467-021-23834-1
8 Enveloping layer cells ENSDARG00000017624 (krt4) marker DOI:10.1038/s41467-021-23834-1
8 Enveloping layer cells ENSDARG00000104181 (tmsb1) marker DOI:10.1038/s41467-021-23834-1
8 Enveloping layer cells ENSDARG00000043442 (zgc:153665) marker DOI:10.1038/s41467-021-23834-1
9 Primordial germ cells ENSDARG00000096095 (buc) marker DOI:10.1038/s41467-021-23834-1