Wnt signaling dosage controlled by a Ctnnb1 enhancer balances homeostasis and tumorigenesis of intestinal epithelia [scRNA-Seq]

β-catenin-dependent canonical Wnt signaling plays a plethora of roles in organ development, tissue homeostasis and cancer. Here we identified an upstream enhancer of Ctnnb1 - ieCtnnb1 - that controls intestinal homeostasis. ieCtnnb1 is specifically active in crypts of small and large intestines. Single-cell sequencing revealed that ieCtnnb1 knockout (ieCtnnb1KO) biased epithelial composition and functions of small intestinal crypts – leaning toward absorptive functions at the expense of secretive roles. Deletion of ieCtnnb1 hampered epithelial turnovers in physiologic and regenerative conditions. In contrast, deletion of ieCtnnb1 prevents occurrence and progression of Wnt/β-catenin driving colorectal cancers. The human ieCTNNB1 specifically drives reporter in intestinal crypts and contains a SNP that is associated with CTNNB1 expression levels in human gastrointestinal epithelia. The enhancer activity of ieCTNNB1 in colorectal cancer tissues is higher than that in adjacent normal tissues and positively correlates with CTNNB1 expression levels. Key trans-factors that bind to ieCTNNB1 and regulate CTNNB1 transcription were identified. Together, these findings revealed an enhancer-dependent mechanism that controls the dosage of Wnt signaling, hence homeostasis of intestinal epithelia.