Multipotent stem cells maintain tissue homeostasis by producing distinct daughter cell types in defined proportions1,2, but how they coordinate type-specific ratios during repeated divisions remains unknown. Drosophila intestinal stem cells (ISCs) switch between producing enteroendocrine cells (EECs) and enterocytes (ECs)3,4, yet maintain a constant EEC:EC ratio despite rapid tissue turnover5–7. Here we show that ISCs intrinsically count self-renewal divisions through an epigenetic mechanism to control multipotency switching. After each asymmetrical division producing an enteroendocrine mother cell (EMC; which divides symmetrically to produce a pair of EECs), ISCs execute precisely eight divisions that generate ECs, before switching back to EMC production at the ninth division. This counting is driven by antagonistic histone modifications: Trithorax group (TrxG)-dependent active marks (H3K4me3 and H3K36me3) progressively decline, whereas Polycomb group (PcG)-dependent repressive marks (H3K27me3) accumulate over successive divisions, triggering fate switching at a threshold. The division count is tunable by modulating TrxG and PcG activities, but withstands acute injury. Crucially, EMC-derived transient Notch signalling establishes active marks in ISCs to initiate the count, designating each EMC production as the cycle’s start point. Our work identifies a histone-modification-based division counter that programs developmental fidelity in stem cells, with implications for engineered tissue growth and differentiation disorder therapies.
