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Genetic data indicate that abrogation of Notch-Rbpj or Wnt-β-catenin pathways results in the loss of the intestinal stem cells (ISCs). However, whether the effect of Notch is direct or due to the aberrant differentiation of the transit-amplifying cells into post-mitotic goblet cells is unknown. To address this issue, we have generated composite tamoxifen-inducible intestine-specific genetic mouse models and analyzed the expression of intestinal differentiation markers. Importantly, we found that activation of β-catenin partially rescues the differentiation phenotype of Rbpj deletion mutants, but not the loss of the ISC compartment. Moreover, we identified Bmi1, which is expressed in the ISC and progenitor compartments, as a gene that is co-regulated by Notch and β-catenin. Loss of Bmi1 resulted in reduced proliferation in the ISC compartment accompanied by p16(INK4a) and p19(ARF) (splice variants of Cdkn2a) accumulation, and increased differentiation to the post-mitotic goblet cell lineage that partially mimics Notch loss-of-function defects. Finally, we provide evidence that Bmi1 contributes to ISC self-renewal. ; This work has been supported by the Instituto de Salud Carlos III [PI10/01128], Ministerio de Ciencia e Innovación [ACI2009-0918], Agència de Gestió d'Ajuts Universitaris i de Recerca-Convocatòria Estratègica-2010-0006 and Red Temática de Investigación Cooperativa en Cáncer [RD06/0020/0098, RD12/0036/0054]. The Mar Institute of Medical Research (IMIM) Foundation financed V.R., and she is a recipient of a European Molecular Biology Organization (EMBO) short-term fellowship [ASTF 20-2010]. E.L.-A. is funded by 'Fundación la Caixa' (2010) and the Department of Education, Universities and Research of the Basque Government [BFI-2011]. L.L.E. is an investigator of the Spanish National Health System (SNS) [CES08/006]