Maintenance DNA methylation is essential for regulatory T cell development and stability of suppressive function [gene expression/RNA-seq]

Regulatory T (Treg) cells require Foxp3 expression and induction of a specific DNA hypomethylation signature during development, after which Treg cells persist as a self-renewing population that regulates immune system activation. Whether maintenance DNA methylation is required for Treg cell lineage development and stability and how methylation patterns are maintained during lineage self-renewal remain unclear. Here, we demonstrate that the epigenetic regulator Uhrf1 is essential for maintenance of methyl-DNA marks that stabilize Treg cellular identity by repressing effector T cell transcriptional programs. Constitutive and induced deficiency of Uhrf1 within Foxp3+ cells resulted in global yet non-uniform loss of DNA methylation, derepression of inflammatory transcriptional programs, destabilization of the Treg cell lineage, and spontaneous inflammation. These findings support a paradigm in which maintenance DNA methylation is required in distinct regions of the Treg cell genome for both lineage establishment and stability of identity and suppressive function. Overall design: Treg cells (CD25hiFoxp3-YFP+) from 8-week-old female Uhrf1fl/flFoxp3+/YFP-Cre (Uhrf1 chimeric knockout) or Uhrf1+/+Foxp3YFP-Cre/YFP-Cre (control) mice with n = 4 biological replicates per group; labeled Treg cells (Foxp3-GFP+tdTomato+), ex-Foxp3 cells (Foxp3-GFP–tdTomato+), and post-tamoxifen Treg cells (Foxp3-GFP+tdTomato–) from Uhrf1fl/flFoxp3GFP-CreERT2Rosa26SorCAG-tdTomato (a.k.a. iUhrf1fl/fl) or Uhrf1+/+Foxp3GFP-CreERT2Rosa26SorCAG-tdTomato (a.k.a iUhrf1+/+ control) mice with n = 6 (iUhrf1fl/fl) and 5 (iUhrf1+/+) biological replicates per cell type in 8-week-old mice that received tamoxifen chow for 2 weeks followed by standard chow for 4 weeks