The DNA Methylation Machinery Regulates Treg Homeostasis in the Intestine

Colonization of newborn mice with gut microbiota induces vigorous proliferation of colonic regulatory T (Treg) cells, which critically contribute to establish intestinal symbiosis by suppressing inflammatory response to the microbiota. However, the molecular machinery controlling colonic Treg homeostasis remains largely unknown. Here we report that a DNA methylation adaptor Uhrf1/Np95 is essential for Treg expansion particularly during early life. Microbial colonization upregulated Uhrf1 in colonic Treg but not conventional T cells. Mice with T-cell-specific deletion of Uhrf1 (Cd4^creUhrf1^fl/fl) mice showed a defect in proliferation and functional maturation of colonic Treg cells. As a consequence, Cd4^creUhrf1^fl/fl mice spontaneously developed severe colitis. Such pathological changes are attributed to the impaired regulation of T-cell-intrinsic DNA methylation, because Cd4^creDnmt1^fl/fl mice also displayed the similar phenotype. DNA methylome analysis revealed that Uhrf1 deficiency de-repressed the cyclin-dependent kinase inhibitor Cdkn1a due to hypomethylation of its promoter region, leading to cell-cycle arrest of Treg cells. The knockdown or genetic deletion of Cdkn1a in Uhrf1-deficient Treg cells at least partially rescued the cell cycle arrest. Thus, DNA methylation-dependent epigenetic silencing of Cdkn1a is required for the maintenance of Treg homeostasis in the colon. Collectively, our findings demonstrated that the Uhrf1-Dnmt1 axis activated by microbial colonization is essential for the maintenance of gut immunological homeostasis.