Genome-wide Analysis Reveals TET- and TDG-Dependent 5-Methylcytosine Oxidation Dynamics

• Published in: Cell 2013-04, Vol.153 (3), p.692-706
• Main Authors: Shen, Li, Wu, Hao, Diep, Dinh, Yamaguchi, Shinpei, D’Alessio, Ana C., Fung, Ho-Lim, Zhang, Kun, Zhang, Yi
• Format: Article
• Language: English
• Subjects: 5-Methylcytosine - metabolism; Animals; antibodies; Cytosine - analogs & derivatives; Cytosine - metabolism; Dioxygenases - metabolism; DNA; DNA Methylation; DNA Repair; Embryonic Stem Cells; Epigenesis, Genetic; Genetic Techniques; Genome-Wide Association Study; Heterochromatin - chemistry; Heterochromatin - metabolism; loci; Mice; oxidation; Oxidation-Reduction; regulator genes; Regulatory Elements, Transcriptional; Thymine DNA Glycosylase - metabolism; thymine-DNA glycosylase
• ISSN: 0092-8674; 1097-4172
• DOI: 10.1016/j.cell.2013.04.002

TET dioxygenases successively oxidize 5-methylcytosine (5mC) in mammalian genomes to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC/5caC can be excised and repaired to regenerate unmodified cytosines by thymine-DNA glycosylase (TDG) and base excision repair (BER) pathway, but it is unclear to what extent and at which part of the genome this active demethylation process takes place. Here, we have generated genome-wide distribution maps of 5hmC/5fC/5caC using modification-specific antibodies in wild-type and Tdg-deficient mouse embryonic stem cells (ESCs). In wild-type mouse ESCs, 5fC/5caC accumulates to detectable levels at major satellite repeats but not at nonrepetitive loci. In contrast, Tdg depletion in mouse ESCs causes marked accumulation of 5fC and 5caC at a large number of proximal and distal gene regulatory elements. Thus, these results reveal the genome-wide view of iterative 5mC oxidation dynamics and indicate that TET/TDG-dependent active DNA demethylation process occurs extensively in the mammalian genome. [Display omitted] •Modification-specific antibodies reveals TET/TDG-mediated 5mC oxidation dynamics•A resource of genome-wide distribution for all oxidized forms of 5mC in mouse ESCs•Tdg depletion induces 5fC and 5caC accumulation at bivalent and silent promoters•TDG activity is preferentially recruited to distal cis-regulatory elements Modification-specific antibodies allow detection of the oxidized forms of 5-methylcytosine (5hmC, 5fC, and 5caC), which are intermediates in the demethylation pathway. Examining the distribution of these modified forms reveals active demethylation throughout the genome, in particular at transcriptionally repressed or poised promoters and at distal regulatory elements.