Cell state dynamics underlying successful tissue regeneration are undercharacterized. In the intestine, damage prompts epithelial reprogramming into revival stem cells (revSCs) that reconstitute Lgr5⁺ intestinal stem cells (ISCs). Here single-nuclear multi-omics of mouse crypts regenerating from irradiation shows revSC chromatin accessibility overlaps with ISCs and differentiated lineages. While revSC genes themselves are accessible throughout homeostatic epithelia, damage-induced remodelling of chromatin in the crypt converges on Hippo and the transforming growth factor-beta (TGFβ) signalling pathway, which we show is transiently activated and directly induces functional revSCs. Combinatorial gene expression analysis further suggests multiple sources of revSCs, and we demonstrate TGFβ can reprogramme enterocytes, goblet and paneth cells into revSCs and show individual revSCs form organoids. Despite this, loss of TGFβ signalling yields mild regenerative defects, whereas interference in both Hippo and TGFβ leads to profound defects and death. Intestinal regeneration is thus poised for activation by a compensatory system of crypt-localized, transient morphogen cues that support epithelial reprogramming and robust intestinal repair.

成功组织再生的细胞状态动力学被低估了。在肠道中，损伤促使上皮重编程为重建干细胞 （revSC），这些细胞重建 Lgr5⁺ 肠道干细胞 （ISC）。在这里，从照射再生的小鼠隐窝的单核多组学显示 revSC 染色质可及性与 ISC 和分化谱系重叠。虽然 revSC 基因本身在整个稳态上皮细胞中都可以访问，但隐窝中染色质的损伤诱导重塑会聚集在 Hippo 和转化生长因子-β （TGFβ） 信号通路上，我们表明该途径是瞬时激活的，直接诱导功能性 revSCs。组合基因表达分析进一步表明 revSCs 的多种来源，我们证明 TGFβ 可以将肠上皮细胞、杯状细胞和潘氏细胞重编程为 revSCs，并显示单个 revSCs 形成类器官。尽管如此，TGFβ 信号的缺失会产生轻微的再生缺陷，而 Hippo 和 TGFβ 的干扰会导致严重的缺陷和死亡。因此，肠道再生准备通过隐窝定位的瞬时形态发生线索的代偿系统激活，该系统支持上皮重编程和强大的肠道修复。