Multi-layered regulation of neuroectoderm differentiation by retinoic acid in a primitive streak-like context

The formation of the primitive streak (PS) and the subsequent induction of neuroectoderm are hallmarks of gastrulation. Combining an in vitro reconstitution of this process based on mouse embryonic stem cells (mESCs) with a collection of knockouts in reporter mESC lines, we identified retinoic acid (RA) as a critical mediator of early neural induction triggered by TGFβ or Wnt signaling inhibition. Single-cell RNA sequencing analysis captured the temporal unfolding of cell type diversification, up to the emergence of somite and neural fates. In the absence of the RA-synthesizing enzyme Aldh1a2, a sensitive RA reporter revealed a hitherto unidentified residual RA signaling that specified neural fate. Genetic evidence showed that the RA-degrading enzyme Cyp26a1 protected PS-like cells from neural induction, even in the absence of TGFβ and Wnt antagonists. Overall, we characterized a multi-layered control of RA levels that regulates early neural differentiation in an in vitro PS-like system. •In vitro reconstitution of neural induction by primitive streak-like cells•Retinoic acid mediates neural induction triggered by TGFβ or Wnt signaling inhibition•A sensitive activity reporter reveals Aldh1a2-independent retinoic acid signaling•Cyp26a1 protects primitive streak-like cells from neural induction Russo and colleagues show that retinoic acid mediates early neural induction triggered by TGFβ or Wnt signaling inhibition using an mESC-based reconstitution. In Aldh1a2 null cells, a sensitive activity reporter revealed a hitherto unidentified residual retinoic acid signaling that specified neural fate. Cyp26a1 protects primitive streak-like cells from neural induction, even in the absence of TGFβ and Wnt antagonists.