Temporally distinct CDX programmes preconfigure vagal and trunk neural crest
Neural crest cells (NCCs) are progenitor cells vital in establishing the head, heart, gut and peripheral nervous system of vertebrate embryos. Disruptions to NCC development underlie neurocristopathies, which constitute a wide array of congenital anomalies. Yet how NCCs acquire defined regional identities that enable them to generate distinct derivatives along the body axis remains unclear. Here, we identify an epiblast progenitor population in mouse embryos that transiently contributes to vagal neural crest cells and trunk-to-tail derivatives. Using single-cell spatial transcriptomics across successive stages of neural crest migration, we generate a cervicothoracic cell atlas that resolves vagal and trunk neural crest cells in situ. Combining in vivo lineage tracing with in vitro models of neural crest induction, we show that despite transiently sharing a lineage, vagal and trunk neural crest arise through separate mechanisms. Temporally discrete regionalisation events mediated by CDX transcription factors establish HOX states that define vagal versus trunk identity. These findings revise models of NCC formation by demonstrating that temporally separate epiblast regionalisation events preconfigure neural crest and neural progenitor identities. More broadly, the results suggest that primary regionalisation events coordinately govern multiple cell lineages at the cervicothoracic transition, with implications for understanding neurocristopathies involving combined enteric and trunk derivatives.