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

beta-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/-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. Comparative gene expression profiling analysis of RNA seq data in the small intestine crypt of adult wild-type and ieCtnnb1 knockout mice依赖β-连环蛋白（beta-catenin）的经典Wnt信号通路在器官发育、组织稳态以及癌症发生发展中发挥着极为广泛的作用。本研究鉴定出了Ctnnb1的一个上游增强子——ieCtnnb1，其可调控肠道稳态。ieCtnnb1仅在小肠和大肠的隐窝中具有活性。单细胞测序结果显示，敲除ieCtnnb1（ieCtnnb1KO）会改变小肠隐窝的上皮细胞组成与功能，使其偏向吸收功能，而以分泌功能为代价。敲除ieCtnnb1会阻碍生理及再生状态下的上皮细胞更新。与之相反，敲除ieCtnnb1可阻断由Wnt/β-连环蛋白驱动的结直肠癌的发生与进展。人类的ieCTNNB1可特异性地在肠道隐窝中驱动报告基因表达，且其携带的一个单核苷酸多态性（SNP）位点与人类胃肠道上皮细胞中CTNNB1的表达水平相关。ieCTNNB1在结直肠癌组织中的增强子活性高于邻近正常组织，且与CTNNB1的表达水平呈正相关。本研究还鉴定出了结合ieCTNNB1并调控CTNNB1转录的关键反式作用因子。综上，本研究的发现揭示了一种依赖增强子的调控机制，该机制可控制Wnt信号通路的剂量，进而维持肠道上皮细胞的稳态。对成年野生型及ieCtnnb1敲除型小鼠小肠隐窝的RNA测序（RNA-seq）数据开展了比较基因表达谱分析。