Temporal effects of BMP4 on mouse embryonic and extraembryonic development

The developing placenta, originated in the mouse through the extra-embryonic ectoderm (ExE), is essential for mammalian embryonic development. Yet, unbiased characterization of ExE differentiation dynamics and interaction with the embryo proper remains incomplete. Here, we develop a temporal single-cell model of mouse gastrulation that maps continuous and parallel differentiation in embryonic and extraembryonic lineages. This is matched with a 3-way perturbation approach to target signaling from the embryo proper, the ExE alone, or both. We show that ExE specification involves early spatial and transcriptional bifurcation of uncommitted ectoplacental cone cells (EPCs) and chorion progenitors. Early BMP4 signaling from chorion progenitors is required for proper differentiation of uncommitted EPCs and later for their specification towards trophoblast giant cells. We also find bi-phasic regulation by BMP4 in the embryo. The early ExE-originating BMP4 signal is necessary for proper endo-mesoderm bifurcation, allantois, and primordial germ cells (PGCs) specification. However, commencing at E7.5, embryonic-derived BMP4 source restricts PGC pool size by favoring differentiation of their extraembryonic mesoderm precursors towards an allantois fate. ExE and embryonic tissues are therefore entangled in time, space, and signaling axes, highlighting the importance of their integrated understanding and modeling in vivo and in vitro. Overall design: We individually imaged each embryo and performed index-sorting for them with subsequent plate-based scRNA-seq (MARS-seq). For ex utero cultured embryos, we pooled 5 embryos and performed 10x single-cell RNA-seq on them for two time points (late streak and head fold stage embryos). For further analysis of mutant/perturbation data, query data was compared to an already established dataset [Mittnenzweig et al. Cell 2021] that was further enriched in this study. The projection of query cells over the atlas resulted in best matching WT embryos that were used to calculate time, cell state composition and differential gene expression between query and atlas cells.