Chromatin Remodelling in Damaged Intestinal Crypts Orchestrates Redundant TGFß and Hippo Signalling to Drive Regeneration
Regenerative cell state dynamics are under-characterized.  Intestinal damage prompts reprogramming into revival stem cells (revSCs) that reconstitute Lgr5+ intestinal stem cells (ISCs). Here, single nuclear multiomics of crypts regenerating from irradiation shows revSC epigenetic profiles overlap with ISCs and differentiated lineages.  RevSC genes themselves are accessible throughout homeostatic epithelia, while damage-induced crypt remodelling converges on the Hippo and TGFß pathway that is transiently activated in the crypt and directly induces functional revSCs.  Combinatorial analysis of gene expression suggests multiple sources of revSCs, and we show TGFb can reprogram Enterocytes, Goblet, and Paneth cells into revSCs, further demonstrating individual revSCs form organoids.  Despite this, loss of TGFß signalling yielded mild regenerative defects, whereas interference in both Hippo and TGFß led to rapid intestinal collapse with no detectable revSCs or ISCs. Regenerative signalling is thus poised for activation by a compensatory system of crypt-localized, transient morphogen cues that support robust intestinal regeneration. Overall design: Mouse small intestine at 0, 1, and 2 days following 12Gy irradiation