Detection of oxidation products of 5-methyl-2'-deoxycytidine in Arabidopsis DNA.

Abstract

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-2'-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-2'-deoxycytidine (5-FodC), 5-carboxyl-2'-deoxycytidine (5-CadC), 5-hydroxymethyl-2'-deoxyuridine (5-HmdU), and the (5'S) diastereomer of 8,5'-cyclo-2'-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 10(6) 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 Tet-family dioxygenase enzymes in Arabidopsis.

• Authors: Shuo Liu, Thomas L Dunwell, Gerd P Pfeifer, Jim M Dunwell, Ihsan Ullah, Yinsheng Wang
• Journal: PloS one (PLoS One) Vol. 8 Issue 12 Pg. e84620 ( 2013) ISSN: 1932-6203 [Electronic] United States
• PMID: 24391970 (Publication Type: Journal Article, Research Support, N.I.H., Extramural)

Chemical References

• 5-carboxyl-2'-deoxycytidine
• 5-formyl-2'-deoxycytidine
• DNA, Plant
• Fluoresceins
• Nucleosides
• Deoxycytidine
• Deoxycytidine Monophosphate
• 5-hydroxymethyldeoxycytidylic acid
• 5-hydroxymethyl-2'-deoxyuridine
• 5-carboxyfluorescein diacetate
• 5-methyldeoxycytidine
• Thymidine

Topics

• Arabidopsis (chemistry, physiology)
• Chromatography, High Pressure Liquid
• DNA, Plant (chemistry)
• Deoxycytidine (analogs & derivatives, chemistry, genetics, metabolism)
• Deoxycytidine Monophosphate (analogs & derivatives, chemistry, metabolism)
• Epigenesis, Genetic (genetics, physiology)
• Fluoresceins (chemistry, metabolism)
• Isotope Labeling
• Molecular Structure
• Nucleosides (metabolism)
• Oxidation-Reduction
• Tandem Mass Spectrometry
• Thymidine (analogs & derivatives, chemistry, metabolism)