Early stages of embryogenesis depend heavily on subcellular localization and transport of maternally deposited mRNA. However, systematic analysis of these processes is currently hindered by a lack of spatio-temporal information in single-cell RNA sequencing. Here, we combined spatially-resolved transcriptomics and single-cell RNA labeling to study the spatio-temporal dynamics of the transcriptome during the first few hours of zebrafish development. We measured spatial localization of mRNA molecules with sub-single-cell resolution at the one-cell stage, which allowed us to identify a class of mRNAs that are specifically localized at an extraembryonic position, the vegetal pole. Furthermore, we established a method for high-throughput single-cell RNA labeling in early zebrafish embryos, which enabled us to follow the fate of individual maternal transcripts until gastrulation. This approach revealed that many localized transcripts are specifically transported to the primordial germ cells. Finally, we acquired spatial transcriptomes of two xenopus species, and we compared evolutionary conservation of localized genes as well as enriched sequence motifs. In summary, we established sub-single-cell spatial transcriptomics and single-cell RNA labeling to reveal principles of mRNA localization in early vertebrate development.

中文翻译：

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早期斑马鱼胚胎的时空mRNA动态。

胚胎发生的早期严重依赖于亚细胞定位和母体沉积的mRNA的运输。但是，目前由于单细胞RNA测序缺乏时空信息而阻碍了对这些过程的系统分析。在这里，我们结合了空间分辨的转录组学和单细胞RNA标记，以研究斑马鱼发育的最初几个小时的转录组的时空动态。我们在单细胞阶段用亚单细胞分辨率测量了mRNA分子的空间定位，这使我们能够识别一类专门位于胚外位置（植物极）的mRNA。此外，我们建立了一种在斑马鱼早期胚胎中进行高通量单细胞RNA标记的方法，这使我们能够追踪各个母体转录本的命运，直到精胃为止。这种方法表明，许多本地化的成绩单被专门运输到原始生殖细胞。最后，我们获得了两个非洲爪蟾物种的空间转录组，并比较了局部基因和丰富序列基序的进化保守性。总之，我们建立了亚单细胞空间转录组学和单细胞RNA标记，以揭示早期脊椎动物发育中mRNA定位的原理。