Detection of Oxidation Products of 5-Methyl-2′-Deoxycytidine in Arabidopsis DNA

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Liu, S., Dunwell, T. L., Pfeifer, G. P., Dunwell, J. M. orcid id iconORCID: https://orcid.org/0000-0003-2147-665X, Ullah, I. and Wang, Y. (2013) Detection of Oxidation Products of 5-Methyl-2′-Deoxycytidine in Arabidopsis DNA. PLoS ONE, 8 (12). ISSN 1932-6203 doi: 10.1371/journal.pone.0084620

Abstract/Summary

Epigenetic regulations play important roles in plant development and adaptation to environmental stress. Recent studies from mammalian systems have demonstrated the involvement of ten-eleven translocation (Tet) family of dioxygenases in the generation of a series of oxidized derivatives of 5-methylcytosine (5-mC) in mammalian DNA. In addition, these oxidized 5-mC nucleobases have important roles in epigenetic remodeling and aberrant levels of 5-hydroxymethyl-29-deoxycytidine (5-HmdC) were found to be associated with different types of human cancers. However, there is a lack of evidence supporting the presence of these modified bases in plant DNA. Here we reported the use of a reversed-phase HPLC coupled with tandem mass spectrometry method and stable isotope-labeled standards for assessing the levels of the oxidized 5-mC nucleosides along with two other oxidatively induced DNA modifications in genomic DNA of Arabidopsis. These included 5- HmdC, 5-formyl-29-deoxycytidine (5-FodC), 5-carboxyl-29-deoxycytidine (5-CadC), 5-hydroxymethyl-29-deoxyuridine (5- HmdU), and the (59S) diastereomer of 8,59-cyclo-29-deoxyguanosine (S-cdG). We found that, in Arabidopsis DNA, the levels of 5-HmdC, 5-FodC, and 5-CadC are approximately 0.8 modifications per 106 nucleosides, with the frequency of 5-HmdC (per 5-mdC) being comparable to that of 5-HmdU (per thymidine). The relatively low levels of the 5-mdC oxidation products suggest that they arise likely from reactive oxygen species present in cells, which is in line with the lack of homologous Tetfamily dioxygenase enzymes in Arabidopsis.

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Item Type Article
URI https://reading-clone.eprints-hosting.org/id/eprint/35609
Identification Number/DOI 10.1371/journal.pone.0084620
Refereed Yes
Divisions Interdisciplinary centres and themes > Centre for Food Security
Life Sciences > School of Agriculture, Policy and Development > Department of Crop Science
Publisher Public Library of Science
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