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Nat Chem Biol. 2014 Jul;10(7):574-81. doi: 10.1038/nchembio.1532. Epub 2014 May 18.

Tet oxidizes thymine to 5-hydroxymethyluracil in mouse embryonic stem cell DNA.

Author information

1
1] Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany. [2].
2
Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany.
3
Charité Universitätsklinikum, Otto-Heubner-Centrum für Kinder und Jugendmedizin, Klinik für Allgemeine Pädiatrie, Labor für Pädiatrische Molekularbiologie, Berlin, Germany.
4
Department of Biomedicine, University of Basel, Basel, Switzerland.
5
Center for Integrated Protein Science at the Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-Universität München, München, Germany.
6
Center for Integrated Protein Science at the Department of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
7
Department of Molecular Cancer Research, Cancer Genomics Netherlands, Utrecht, The Netherlands.
8
1] Department of Molecular Cancer Research, Cancer Genomics Netherlands, Utrecht, The Netherlands. [2].

Abstract

Ten eleven translocation (Tet) enzymes oxidize the epigenetically important DNA base 5-methylcytosine (mC) stepwise to 5-hydroxymethylcytosine (hmC), 5-formylcytosine and 5-carboxycytosine. It is currently unknown whether Tet-induced oxidation is limited to cytosine-derived nucleobases or whether other nucleobases are oxidized as well. We synthesized isotopologs of all major oxidized pyrimidine and purine bases and performed quantitative MS to show that Tet-induced oxidation is not limited to mC but that thymine is also a substrate that gives 5-hydroxymethyluracil (hmU) in mouse embryonic stem cells (mESCs). Using MS-based isotope tracing, we show that deamination of hmC does not contribute to the steady-state levels of hmU in mESCs. Protein pull-down experiments in combination with peptide tracing identifies hmU as a base that influences binding of chromatin remodeling proteins and transcription factors, suggesting that hmU has a specific function in stem cells besides triggering DNA repair.

PMID:
24838012
DOI:
10.1038/nchembio.1532
[Indexed for MEDLINE]

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