Rapidly cycling stem cells regenerate the intestine independent of Lgr5 high cells

The +4 cells in intestinal crypts are DNA damage-resistant and contribute to regeneration. However, their exact identity and the mechanism underlying +4 cell-mediated regeneration remain unclear. Using lineage tracing, we show that cells marked by an reporter () are enriched at the +4 position in intestinal crypts and exhibit DNA damage resistance. Single-cell RNA sequencing reveals that the cells are heterogeneous with the majority being intestinal stem cells (ISCs). The DNA damage-resistant subpopulation of cells is characterized by low-to-negative expression and is more rapidly cycling than radio-sensitive crypt base columnar stem cells (CBCs); they enable fast repopulation of the intestinal epithelium independent of CBCs that are largely depleted after irradiation. Furthermore, relative to CBCs, cells preferentially produce Paneth cells during homeostasis and upon radiation repair. Together, we demonstrate that the DNA damage-resistant cells are rapidly cycling ISCs that maintain and regenerate the intestinal epithelium.