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. 2019 Jun 20;47(11):5522-5529.
doi: 10.1093/nar/gkz395.

DNA repair enzymes ALKBH2, ALKBH3, and AlkB oxidize 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine in vitro

Ke Bian  1 , Stefan A P Lenz  2 , Qi Tang  1 , Fangyi Chen  1 , Rui Qi  1 , Marco Jost  3 , Catherine L Drennan  3   4   5   6 , John M Essigmann  3   5   7 , Stacey D Wetmore  2 , Deyu Li  1
Affiliations

DNA repair enzymes ALKBH2, ALKBH3, and AlkB oxidize 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine in vitro

Ke Bian et al. Nucleic Acids Res. .

Abstract

5-Methylcytosine (5mC) in DNA CpG islands is an important epigenetic biomarker for mammalian gene regulation. It is oxidized to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) by the ten-eleven translocation (TET) family enzymes, which are α-ketoglutarate (α-KG)/Fe(II)-dependent dioxygenases. In this work, we demonstrate that the epigenetic marker 5mC is modified to 5hmC, 5fC, and 5caC in vitro by another class of α-KG/Fe(II)-dependent proteins-the DNA repair enzymes in the AlkB family, which include ALKBH2, ALKBH3 in huamn and AlkB in Escherichia coli. Theoretical calculations indicate that these enzymes may bind 5mC in the syn-conformation, placing the methyl group comparable to 3-methylcytosine, the prototypic substrate of AlkB. This is the first demonstration of the AlkB proteins to oxidize a methyl group attached to carbon, instead of nitrogen, on a DNA base. These observations suggest a broader role in epigenetics for these DNA repair proteins.

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Figures

Figure 1.
Figure 1.
Reaction pathway of the AlkB family DNA repair enzymes modifying 5mC and 3mC.
Figure 2.
Figure 2.
High resolution ESI-TOF MS analyses of 16mer DNA oligonucleotides containing 5mC and oxidized products. The observed m/z values represent the oligonucleotides under their –3 charge state. (A) 5mC; (B) 5mC (in ds-DNA) + ALKBH2; (C) 5mC (in ss-DNA) + ALKBH3 and (D) 5mC (in ss-DNA) + AlkB.
Figure 3.
Figure 3.
Product distribution and strand preference (in univariate scatterplot) for the oxidation of 5mC by the AlkB family enzymes. Reaction products (5hmC, 5fC and 5caC) generated from the reactions of 5mC with the AlkB family enzymes in (A) ds-DNA and (B) ss-DNA. (C) Total product percentage from reactions of the AlkB family enzymes oxidizing 5mC in ds- and ss-DNA.
Figure 4.
Figure 4.
Representative molecular dynamics structures of the ALKBH2 (A–C) or AlkB (D–F) complex bound to anti-5mC (A, D), syn-5mC (B, E), or anti-3mC (C, F). The distance between the oxo-moiety and methyl groups is highlighted with dashed lines.
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References

    1. Wu X., Zhang Y.. TET-mediated active DNA demethylation: mechanism, function and beyond. Nat. Rev. Genet. 2017; 18:517–534. - PubMed
    1. Smith Z.D., Meissner A.. DNA methylation: roles in mammalian development. Nat. Rev. Genet. 2013; 14:204–220. - PubMed
    1. Li E., Zhang Y.. DNA methylation in mammals. Cold Spring Harb. Perspect. Biol. 2014; 6:a019133. - PMC - PubMed
    1. Law J.A., Jacobsen S.E.. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 2010; 11:204–220. - PMC - PubMed
    1. Hausinger R.P., Schofield C.J.. 2-Oxoglutarate-Dependent Oxygenases. 2015; Cambridge: Royal Society of Chemistry.

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