A Single-Cell Transcriptomic Atlas of Epithelial Cell Heterogeneity During the Crown-to-Root Transition in the Mouse Molar

The mechanisms driving the crown-to-root transition in tooth development remain incompletely understood, particularly the functional heterogeneity of dental epithelium. To address this gap and deconstruct this complexity, we aimed to analyze dental epithelial heterogeneity during this critical transition and to identify subpopulation-specific programs relevant to root development. We therefore established a single-cell transcriptomic atlas of the mouse molar at postnatal days 3.5 and 7.5, integrating 30,951 cells to profile the pan-tissue landscape and performing an in-depth analysis of 4323 dental epithelial cells. Our results reveal that the dental epithelium is composed of seven distinct subpopulations with a clear lineage hierarchy, originating from multipotent progenitors and bifurcating into self-renewing and differentiating trajectories. The identified particular functions of each subcluster include the following: structural maintaining progenitor that inhibits mineralization (Cluster 4), proliferation driver (Cluster 0), key signaling center (Cluster 1), terminally differentiated executing enamel formation (Cluster 3 and Cluster 6), and extracellular matrix-organizing hub (Cluster 5), communicating extensively via the Bmp, Tgf-β, and Wnt pathways. Our work defines dental epithelium as a dynamic and heterogeneous orchestrator of root morphogenesis, providing a foundational framework for understanding developmental biology and pioneering future regenerative strategies based on precise epithelial cell functions.