Tet1 and Tet2 Protect DNA Methylation Canyons against Hypermethylation

Abstract

DNA methylation is a dynamic epigenetic modification with an important role in cell fate specification and reprogramming. The Ten eleven translocation (Tet) family of enzymes converts 5-methylcytosine to 5-hydroxymethylcytosine, which promotes passive DNA demethylation and functions as an intermediate in an active DNA demethylation process. Tet1/Tet2 double-knockout mice are characterized by developmental defects and epigenetic instability, suggesting a requirement for Tet-mediated DNA demethylation for the proper regulation of gene expression during differentiation. Here, we used whole-genome bisulfite and transcriptome sequencing to characterize the underlying mechanisms. Our results uncover the hypermethylation of DNA methylation canyons as the genomic key feature of Tet1/Tet2 double-knockout mouse embryonic fibroblasts. Canyon hypermethylation coincided with disturbed regulation of associated genes, suggesting a mechanistic explanation for the observed Tet-dependent differentiation defects. Based on these results, we propose an important regulatory role of Tet-dependent DNA demethylation for the maintenance of DNA methylation canyons, which prevents invasive DNA methylation and allows functional regulation of canyon-associated genes.

Supplemental material for this article may be found at http://dx.doi.org/10.1128/MCB.00587-15.

ACKNOWLEDGMENTS

We thank the DKFZ Genomics and Proteomics Core Facility for sequencing services and Tobias Reber for highly competent information technology support.

A.B., R.J., and F.L. conceived the study. A.B., L.W., and F.L. designed the experiments and interpreted the results. M.M.D. and R.J. provided cell lines. L.W., T.M., and A.B. performed the experiments. G.R. performed the bioinformatics analyses. A.B. and F.L. wrote the manuscript, with contributions from all.

We declare that we have no conflict of interest.

Additional information

Funding

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.