SINGLE-NUCLEI MULTIOME ANALYSIS IDENTIFIES CELL SUBTYPE-SPECIFIC MITOTIC TRANSCRIPTOME AND BOOKMARKING FACTORS IN THE DEVELOPING FOREBRAIN

Mitotic bookmarking (MB), the retention of transcriptional and chromatin features through mitosis, is emerging as a key mechanism for maintaining cell identity during cell division. However, the identification of MB factors and their regulatory mechanisms in neural progenitor subtypes in developing brains remains unexplored.
Using single-nuclei multiomic analysis on sorted mitotic cells from developing mouse forebrain, we identified two distinct mitotic populations: quiescent-like (QMCs) and active-like (AMCs), with AMCs showing higher global transcription and chromatin accessibility. Lineage-resolved analyses revealed that mitotic cells are already fate-committed, including toward excitatory or inhibitory neurons, Cajal–Retzius cells, intermediate progenitors (IPCs), and basal radial glia. We uncovered widespread MB of regulatory elements enriched for neurogenic genes and mapped general and lineage-specific transcription factors with potential bookmarking activity. Notably, Neurog2 displayed genome-wide mitotic chromatin occupancy in IPCs, and its mitosis-specific degradation impaired neuronal differentiation, enhanced progenitor proliferation, and increased apoptosis.These findings demonstrate that fate specification is encoded during mitosis and highlight mitotic bookmarking as a regulatory mechanism, ensuring balanced neurogenesis in the developing brain.