It is generally accepted that epiblast cells ingress into the primitive streak by epithelial-to-mesenchymal transition (EMT) to give rise to the mesoderm; however, it is less clear how the endoderm acquires an epithelial fate. Here, we used embryonic stem cell and mouse embryo knock‐in reporter systems to combine time-resolved lineage labelling with high-resolution single-cell transcriptomics. This allowed us to resolve the morphogenetic programs that segregate the mesoderm from the endoderm germ layer. Strikingly, while the mesoderm is formed by classical EMT, the endoderm is formed independent of the key EMT transcription factor Snail1 by mechanisms of epithelial cell plasticity. Importantly, forkhead box transcription factor A2 (Foxa2) acts as an epithelial gatekeeper and EMT suppressor to shield the endoderm from undergoing a mesenchymal transition. Altogether, these results not only establish the morphogenetic details of germ layer formation, but also have broader implications for stem cell differentiation and cancer metastasis.

人们普遍认为，外胚层细胞通过上皮间质转化（EMT）进入原条形成中胚层；然而，尚不清楚内胚层如何获得上皮命运。在这里，我们使用胚胎干细胞和小鼠胚胎敲入报告系统将时间分辨谱系标记与高分辨率单细胞转录组学相结合。这使我们能够解决将中胚层与内胚层胚层分离的形态发生程序。引人注目的是，中胚层是由经典的 EMT 形成的，而内胚层是通过上皮细胞可塑性机制独立于关键的 EMT 转录因子 Snail1 形成的。重要的，叉头盒转录因子 A2 (Foxa2) 充当上皮守门员和 EMT 抑制因子，以保护内胚层免受间充质转化。总之，这些结果不仅确定了胚层形成的形态发生细节，而且对干细胞分化和癌症转移具有更广泛的意义。