Frequency encoding regulates cell type composition in the small intestine.

Intestinal homeostasis requires tight regulation of stem cell maintenance and differentiation to absorptive and secretory cell types, two major intestinal lineages. Key signaling pathways have been identified, but how they balance cell type composition remains unclear. We uncovered oscillatory expression of the Notch-target protein Hes1 (hairy and enhancer of split 1) that controls cell fate specification in a frequency-dependent manner. An endogenous fluorescent Hes1 reporter revealed distinct, cell type-specific oscillation frequencies forming a gradient along the crypt-villus axis, which was modulated by cell cycle phase as well as Wnt (wingless-related integration site)-signaling and Notch-signaling activity. We developed a microfluidic system to modulate Notch-signaling oscillations in organoids and found the oscillation frequency to regulate the balance of cell type composition. This study provides evidence that information for cell fate specification is encoded in the frequency of an oscillatory signal.