The mammalian intestinal mucosa is to form villi and crypts. YAP1 activity is highest at the bottom of the crypt, where ISCs and Paneth cells reside. The villus consists of differentiated cells. ISCs in the crypt base differentiate into transit amplifying cells, which further differentiate along a secretory lineage (into goblet cells, enteroendocrine cells and Paneth cells) or an absorptive lineage (into enterocytes). After differentiation, Paneth cells move down to the stem cell niche and reside beside ISCs at the bottom of the crypt. YAP1, Wnt signalling and Notch signalling play important parts in stem cell self-renewal and progenitor cell differentiation. YAP1 interacts with KLF4 to induce progenitor cell differentiation into goblet cells, whereas Wnt signalling is involved in Paneth cell differentiation, and high Notch signalling induces differentiation along the absorptive lineage. ISC, intestinal stem cell; KLF4, krueppel-like factor 4; TEAD, TEA domain family member; YAP1, Yes-associated protein 1.