5mC Oxidation by Tet2 Modulates Enhancer Activity and Timing of Transcriptome Reprogramming during Differentiation

Abstract

Summary In mammals, cytosine methylation (5mC) is widely distributed throughout the genome, but is notably depleted from active promoters and enhancers. While the role of DNA methylation in promoter silencing has been well documented, the function of this epigenetic mark at enhancers remains unclear. Recent experiments have demonstrated that enhancers are enriched for 5-hydroxymethylcytosine (5hmC), an oxidization product of the Tet family of 5mC dioxygenases and an intermediate of DNA demethylation. These results support the involvement of Tet proteins in regulation of dynamic DNA methylation at enhancers. By mapping DNA methylation and hydroxymethylation at base resolution, we find that deletion of Tet2 causes extensive loss of 5hmC at enhancers, accompanied by enhancer hypermethylation, reduction of enhancer activity, and delayed gene induction in the early steps of differentiation. Our results reveal that DNA demethylation modulates enhancer activity, and its disruption influences the timing of transcriptome reprogramming during cellular differentiation.

Tet1 and Tet2 Protect DNA Methylation Canyons against Hypermethylation

“…Our unbiased analysis of genome-wide methylation patterns showed widespread hypermethylation in DKO MEFs, which included promoter and enhancer regions. These findings are consistent with recent studies of Tet-deficient mouse ESCs (11,12) and provide a mechanistic explanation for the epigenetic regulatory defects of Tet-deficient cells.…”

“…S2 in the supplemental material). Significant (P Ͻ 0.01; Wilcoxon rank sum test) hypermethylation was detected for both promoter and enhancer regions, consistent with recent findings in Tet-deficient mouse ESCs (11,12). As Tet-dependent methylation changes at promoters appeared more prominent (Fig.…”

“…DKO mice are characterized by global DNA hypermethylation and developmental plasticity, suggesting an important role of Tet1/Tet2 in the epigenetic regulation of developmental genes (8). In agreement with this notion, recent studies have shown a role of Tet-mediated demethylation in the modulation of enhancer activity (10)(11)(12).…”

“…Recent publications have suggested distinct roles for Tet1 and Tet2 in mouse embryonic stem cells, particularly with respect to the subgenomic localization of Tet1-or Tet2-dependent 5hmC and the degree of hypermethylation in Tet1-or Tet2-deficient cell lines (12,33). We therefore analyzed the same canyons in Tet1 and Tet2 single-knockout MEFs.…”

Tet proteins influence the balance between neuroectodermal and mesodermal fate choice by inhibiting Wnt signaling

“…Besides their functionally redundant roles in the generation of oxi-mC, TET-family members also display distinct roles, in part because they are expressed in different cellular locations or at different developmental stages (18,32), and regulate oxi-mC levels at different genomic locations (55,56). Although there is some overlap, Tet1 primarily regulates 5hmC levels at gene promoters and TSSs, whereas Tet2 mainly regulates 5hmC levels in gene bodies (55).…”