Abstract
Recent single cell RNA-sequencing (scRNA-seq) studies of early stages of embryos or human embryonic stem (ES) cell-derived embryoid bodies (EBs) provided unprecedented information on the spatiotemporal heterogeneity of cells in embryogenesis 1–8. Nonetheless, these snapshots offer insufficient information on dynamic developmental processes due to inadvertently missing intermediate states and unavoidable batch effects. Blood and endothelial cells arise from hemangiogenic progenitors that are specified from FLK1-expressing mesoderm by the transcription factor ETV2 9, 10. To delineate the entire transcriptome dynamics from pluripotency to hemangiogenic lineage, we performed scRNA-seq of mouse ES cells in asynchronous EB differentiation. We found the exit from naïve pluripotency and hemangiogenic program activation were the two major transitions in the trajectory, while the intermediate gastrulation stages were gradually specified by ‘relay’-like highly overlapping transcription factor modules. Unexpectedly, we found smooth muscle lineage might be the ‘default’ fate of FLK1 mesoderm, from which ETV2 initiates the hemangiogenic commitment. We also identified cell adhesion signaling required for ETV2-mediated activation of the hemangiogenic program. This continuous transcriptome map will benefit both basic and applied studies of mesoderm and its derivatives.