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Open Access

Genome-wide analysis reveals TET-and TDG-mediated 5-methylcytosine oxidation dynamics

  • Li Shen1,
  • Hao Wu1,
  • Dinh Diep1,
  • Ana C D’Alessio1,
  • Alan Fung1,
  • Kun Zhang1 and
  • Yi Zhang1
Contributed equally
Epigenetics & Chromatin20136(Suppl 1):P75

Published: 18 March 2013


Mouse Embryonic Stem CellMarked AccumulationComprehensive MappingDynamic CyclingHydroxymethylcytosine

Recent studies suggest that DNA demethylation can be achieved through ten-eleven translocation (Tet) family of DNA deoxygenates mediated oxidation followed by thymine DNA glycosylase (TDG) mediated excision and repair, but it is unclear to what extent such active demethylation processes take place. Here, we generated genome-wide distribution maps of 5-methylcytosine(5mC),5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5- carboxylcytosine (5caC) in wild-type and Tdg-deficient mouse embryonic stem cells. We observe that the steady state 5fC and 5caC are preferentially detected at repetitive sequences in wild-type cells. Depletion of TDG causes marked accumulation of 5fC and 5caC at a large number of distal gene regulatory elements and transcriptionally repressed/poised gene promoters, suggesting that Tet/TDG- dependent dynamic cycling of 5mC oxidation states may be involved in regulating the function of these regions. Thus, comprehensive mapping of 5mC oxidation and BER pathway activity provides a promising approach for better understanding of DNA methylation and demethylation dynamics in development and diseases.


Authors’ Affiliations

Harvard Medical School and Boston Childrens Hospital, Boston, USA


© Shen et al; licensee BioMed Central Ltd. 2013

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.