biostudies-literatureFeng JNIDCR NIH HHS4396https://www.ebi.ac.uk/biostudies/studies/S-EPMC12069723biostudies-literatureUnknown16(1)The differentiation of post-migratory cranial neural crest cells (CNCCs) into distinct mesenchymal lineages is crucial for craniofacial development. Here we report a high-resolution spatiotemporal transcriptomic and cell-type atlas of CNCC-derived mesenchymal lineage diversification during mouse palatogenesis. We systematically defined each mesenchymal cell type by mapping their transcriptomic profiles to spatial identities. Integrative analysis of spatial transcriptomic data from E12.5 to E15.5 further revealed mesenchymal lineage establishment at or prior to initiation of palatogenesis. We also identified a heterogeneous Sox9+ mesenchymal progenitor population at the onset of palatal development, with subpopulations already activating early lineage-specific markers. In vivo lineage traciNature communicationsHigh-resolution spatial transcriptomics and cell lineage analysis reveal spatiotemporal cell fate determination during craniofacial development.PMC12069723R01 DE012711U01 DE028729Ho TVFeng JAraujo-Villalba ALiu MGeng JJJaneckova EGuo TZiaei HZhang MChai YCha SfalseHigh-resolution spatial transcriptomics and cell lineage analysis reveal spatiotemporal cell fate determination during craniofacial development.The differentiation of post-migratory cranial neural crest cells (CNCCs) into distinct mesenchymal lineages is crucial for craniofacial development. Here we report a high-resolution spatiotemporal transcriptomic and cell-type atlas of CNCC-derived mesenchymal lineage diversification during mouse palatogenesis. We systematically defined each mesenchymal cell type by mapping their transcriptomic profiles to spatial identities. Integrative analysis of spatial transcriptomic data from E12.5 to E15.5 further revealed mesenchymal lineage establishment at or prior to initiation of palatogenesis. We also identified a heterogeneous Sox9+ mesenchymal progenitor population at the onset of palatal development, with subpopulations already activating early lineage-specific markers. In vivo lineage traci2025-01-01T00:00:00Z2025 May2026-05-29T19:03:08.498Z2026-04-08T05:44:26.48ZS-EPMC120697234035546210.1038/s41467-025-59206-2