a, Wild-type or Clucre-ERT2/+;Rosa26lsl-DTA/+ (Cluless) mice were irradiated and analysed at 3 and 5 dpi. Small intestinal crypts were stained for the proliferation marker KI67 (green), and counterstained with EPCAM (red) and DAPI (blue). Nuclear KI67 staining, crypt numbers and crypt length were quantified (n = 49 images analysed; two-tailed Mann–Whitney test; box edges show 25th and 75th percentile, the central point is the median and whiskers represent minimum and maximum values. n.s., non-significant (P > 0.05); *P < 0.05, ***P < 0.001. b, Representative images of intestinal epithelia from wild-type or YAP1-mutant mice at 3 dpi visualized with EPCAM (red) and DAPI (blue) staining (left). Crypts per unit length of small intestine for the indicated mice and conditions are quantified (right; n = 16 images analysed across two mice each; two-tailed Mann–Whitney test; box edges show 25th and 75th percentile, the central point is the median and whiskers represent minimum and maximum values; the experiment was repeated once with similar results). c, Colons from wild-type and YAP1 mutants at 3 dpi or untreated (normal) were analysed by immunohistochemistry (representative images; n = 2 mice each). d, Images of non-irradiated, TAM-treated (10 days) wild-type and Cluless small intestines and colons stained for epithelial marker EPCAM (n = 2 mice each). e, Colons dissected from non-irradiated, wild-type or Cluless mice (compare with Fig. 4b) (n = 2 mice each). f, CLU+ revSCs are required for recovery from DSS. Mice of the indicated genotypes were treated with TAM in the presence or absence of DSS, as indicated (schematic, top). Body weight was measured daily and is plotted as change relative to starting weight (percentage ± s.d., n = 62 total mice tested). g, Kaplan–Meier survival curves for the indicated cohort of mice that were either exposed to DSS (2.5%) treatment or left untreated (number of mice of the corresponding genotype is indicated; two-sided log-rank test was applied to compare survival curves). h, Average crypt length in the small intestine is quantified (n = 22 crypts, two-tailed Mann–Whitney Test, box edges show 25th and 75th percentile, central point is median and whiskers represent minimum and maximum values). i, Representative images are shown of small intestinal and colonic tissues in the absence or presence of DSS treatment stained for endogenous Clu mRNA (red; white arrows) using smFISH (RNAScope), (n = 2, mice each). j, Representative images showing that non-DSS treated control mice that received nine TAM injections developed rare ribbon formation in the small intestine and colon. Quantification of tdTomato ribbons formed in the presence of the indicated TAM treatment either without (blue), or with DSS (red) treatment is plotted as percent of crypt–villus axes (n = 10 images each across two treated mice each; two-tailed Mann–Whitney Test; box edges show 25th and 75th percentile, central point is median and error bars represent minimum and maximum values, experiment was repeated once with similar results). Scale bars, 120 μm (b, left, c); 70 μm (d); 1.5 cm (e); 30 μm (i); 75 μm (j). Source data