Neural stem cells epigenomes and fate bias are temporally coordinated during corticogenesis [scATAC-seq]

The cerebral cortex orchestrates complex cognitive functions, yet how its distinct temporal lineages are molecularly patterned during development remains unresolved. Here, we integrate single-cell transcriptomics and chromatin accessibility, together with genome-wide profiling of DNA methylation and 3D chromosomal contact across mouse corticogenesis (E13–E18) to elucidate cell fate transitions. We reveal using metacell flow analysis that neural stem cells (NSC) progressively shift from an intermediate progenitor–biased state toward an astrocytic lineage and that his process is accompanied with DNA methylation programming and chromosomal insulation changes. A model integrating transcription factor motif affinities with epigenetic features, identifies key regulators of cis-regulatory element (CRE) activation. In vivo reporter assays further decouple the intrinsic regulatory potential of CREs from context-dependent synergistic activation. Collectively, our findings uncover temporal epigenomic reprogramming that underlies the evolving differentiation potential of NSC, providing insights into the intrinsic and extrinsic mechanisms that pattern cortical lineages.