Determination of 5-hydroxymethyl-2′-deoxycytidine in Rice by High-performance Liquid Chromatography–Tandem Mass Spectrometry with Isotope Dilution

References

• Bender, J. 2004. DNA methylation and epigenetics. Annual Review of Plant Biology 55:41–68. doi:10.1146/annurev.arplant.55.031903.141641
   PubMed Web of Science ®Google Scholar
• Ficz, G., M. R. Branco, S. Seisenberger, F. Santos, F. Krueger, T. A. Hore, C. J. Marques, S. Andrews, and W. Reik. 2011. Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature 473:398–402. doi:10.1038/nature10008
   PubMed Web of Science ®Google Scholar
• Finnegan, E. J., and K. A. Kovac. 2000. Plant DNA methyltransferases. Plant Molecular Biology 43:189–201.
   PubMed Web of Science ®Google Scholar
• Gao, Y., J. Chen, K. Li, T. Wu, B. Huang, W. Liu, X. Kou, Y. Zhang, H. Huang, Y. Jiang, C. Yao, X. Liu, Z. Lu, Z. Xu, L. Kang, J. Chen, H. Wang, T. Cai, and S. Gao. 2013. Replacement of Oct4 by Tet1 during iPSC induction reveals an important role of DNA methylation and hydroxymethylation in reprogramming. Cell Stem Cell 12:453–69. doi:10.1016/j.stem.2013.02.005
   PubMed Web of Science ®Google Scholar
• He, X. J., T. Chen, and J. K. Zhu. 2011. Regulation and function of DNA methylation in plants and animals. Cell Research 21:442–65. doi:10.1038/cr.2011.23
   PubMed Web of Science ®Google Scholar
• Hong, S., H. Hashimoto, Y. W. Kow, X. Zhang, and X. Cheng. 2014. The carboxy-terminal domain of ROS1 is essential for 5-methylcytosine DNA glycosylase activity. Journal of Molecular Biology 426:3703–12. doi:10.1016/j.jmb.2014.09.010
   PubMed Web of Science ®Google Scholar
• Ito, S., A. C. D’Alessio, O. V. Taranova, K. Hong, L. C. Sowers, and Y. Zhang. 2010. Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 466:1129–33. doi:10.1038/nature09303
   PubMed Web of Science ®Google Scholar
• Ito, S., L. Shen, Q. Dai, S. C. Wu, L. B. Collins, J. A. Swenberg, C. He, and Y. Zhang. 2011. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333:1300–303. doi:10.1126/science.1210597
   PubMed Web of Science ®Google Scholar
• Jin, S. G., X. Wu, A. X. Li, and G. P. Pfeifer. 2011. Genomic mapping of 5-hydroxymethylcytosine in the human brain. Nucleic Acids Research 39:5015–24. doi:10.1093/nar/gkr120
   PubMed Web of Science ®Google Scholar
• Kriaucionis, S., and N. Heintz. 2009. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324:929–30. doi:10.1126/science.1169786
   PubMed Web of Science ®Google Scholar
• Lewsey, M. G., T. Hardcastle, C. W. Melnyk, A. Molnar, A. Valli, M. A. Urich, J. R. Nery, D. C. Baulcombe, and J. R. Ecker. 2016. Mobile small RNAs regulate genome-wide DNA methylation. Proceedings of the National Academy of Sciences of the United States of America 113:E801–10. doi:10.1073/pnas.1515072113
   PubMed Web of Science ®Google Scholar
• Liu, S., T. L. Dunwell, G. P. Pfeifer, J. M. Dunwell, I. Ullah, and Y. Wang. 2013a. Detection of oxidation products of 5-methyl-2′-deoxycytidine in Arabidopsis DNA. PLoS ONE 8:e84620. doi:10.1371/journal.pone.0084620
   PubMed Web of Science ®Google Scholar
• Liu, S., J. Wang, Y. Su, C. Guerrero, Y. Zeng, D. Mitra, P. J. Brooks, D. E. Fisher, H. Song, and Y. Wang. 2013b. Quantitative assessment of Tet-induced oxidation products of 5-methylcytosine in cellular and tissue DNA. Nucleic Acids Research 41:6421–29. doi:10.1093/nar/gkt360
   PubMed Web of Science ®Google Scholar
• Liu, X., G. Zhang, Y. Yi, L. Xiao, M. Pei, S. Liu, Y. Luo, H. Zhong, Y. Xu, W. Zheng, and J. Shen. 2013c. Decreased 5-hydroxymethylcytosine levels are associated with TET2 mutation and unfavorable overall survival in myelodysplastic syndromes. Leukemia Lymphoma 54:2466–73. doi:10.3109/10428194.2013.778408
   PubMed Web of Science ®Google Scholar
• Münzel, M., D. Globisch, T. Brückl, M. Wagner, V. Welzmiller, S. Michalakis, M. Müller, M. Biel, and T. Carell. 2010. Quantification of the sixth DNA base hydroxymethylcytosine in the brain. Angewandte Chemie International Edition 49:5375–77. doi:10.1002/anie.201002033
   PubMed Web of Science ®Google Scholar
• Penterman, J., D. Zilberman, J. H. Huh, T. Ballinger, S. Henikoff, and R. L. Fischer. 2007. DNA demethylation in the Arabidopsis genome. Proceedings of the National Academy of Sciences of the United States of America 104:6752–57. doi:10.1073/pnas.0701861104
   PubMed Web of Science ®Google Scholar
• Schoft, V. K., N. Chumak, Y. Choi, M. Hannon, M. Garcia-Aguilar, A. Machlicova, L. Slusarz, M. Mosiolek, J. S. Park, G. T. Ark, R. L. Fischer, and H. Tamaru. 2011. Function of the DEMETER DNA glycosylase in the Arabidopsis thaliana male gametophyte. Proceedings of the National Academy of Sciences of the United States of America 108:8042–47. doi:10.1073/pnas.1105117108
   PubMed Web of Science ®Google Scholar
• Shi, J., A. Dong, and W. H. Shen. 2015. Epigenetic regulation of rice flowering and reproduction. Frontiers in Plant Science 5:803. doi:10.3389/fpls.2014.00803
   PubMed Web of Science ®Google Scholar
• Song, C. X., K. E. Szulwach, Y. Fu, Q. Dai, C. Yi, X. Li, Y. Li, C. H. Chen, W. Zhang, X. Jian, J. Wang, L. Zhang, T. J. Looney, B. Zhang, L. A. Godley, L. M. Hicks, B. T. Lahn, P. Jin, and C. He. 2011. Selective chemical labeling reveals genome-wide distribution of 5-hydroxymethylcytosine. Nature Biotechnology 29:68–72. doi:10.1038/nbt.1732
   PubMed Web of Science ®Google Scholar
• Szwagierczak, A., S. Bultmann, C. S. Schmidt, F. Pada, and H. Leonhardt. 2010. Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA. Nucleic Acids Research 38:e181. doi:10.1093/nar/gkq684
   PubMed Web of Science ®Google Scholar
• Tahiliani, M., K. P. Koh, Y. Shen, W. A. Pastor, H. Bandukwala, Y. Brudno, S. Agarwal, L. M. Iyer, D. R. Liu, L. Aravind, and A. Rao. 2009. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324: 930–35. doi:10.1126/science.1170116
   PubMed Web of Science ®Google Scholar
• Tan, L., and Y. G. Shi. 2012. Tet family proteins and 5-hydroxymethylcytosine in development and disease. Development 139:1895–902. doi:10.1242/dev.070771
   PubMed Web of Science ®Google Scholar
• Terragni, J., J. Bitinaite, Y. Zheng, and S. Pradhan. 2012. Biochemical characterization of recombinant β-glucosyltransferase and analysis of global 5-hydroxymethylcytosine in unique genomes. Biochemistry 51:1009–19. doi:10.1021/bi2014739
   PubMed Web of Science ®Google Scholar
• Uchiyama, R., H. Uhara, A. Uchiyama, E. Ogawa, Y. Takazawa, A. Ashida, H. Koga, K. Hayashi, Y. Kiniwa, and R. Okuyama. 2014. 5-Hydroxymethylcytosine as a useful marker to differentiate between malignant melanomas and benign melanocytic nevi. Journal of Dermatological Science 73:161–63. doi:10.1016/j.jdermsci.2013.09.008
   PubMed Web of Science ®Google Scholar
• Weinhold, B. 2006. Epigenetics: The science of change. Environmental Health Perspectives 114:A160–67. doi:10.1289/ehp.114-a160
   PubMed Web of Science ®Google Scholar
• Wu, S. C., and Y. Zhang. 2010. Active DNA demethylation: Many roads lead to Rome. Nature Reviews Molecular Cell Biology 11:607–20. doi:10.1038/nrm2950
   PubMed Web of Science ®Google Scholar
• Xing, M. Q., Y. J. Zhang, S. R. Zhou, W. Y. Hu, X. T. Wu, Y. J. Ye, X. Wu, Y. P. Xiao, X. Li, and H. W. Xue. 2015. Global analysis reveals the crucial roles of DNA methylation during rice seed development. Plant Physiology 168:1417–32. doi:10.1104/pp.15.00414
   PubMed Web of Science ®Google Scholar
• Yang, H., Y. Liu, F. Bai, J. Y. Zhang, S. H. Ma, J. Liu, Z. D. Xu, H. G. Zhu, Z. Q. Ling, D. Ye, K. L. Guan, and Y. Xiong. 2013. Tumor development is associated with decrease of TET gene expression and 5-methylcytosine hydroxylation. Oncogene 32:663–69. doi:10.1038/onc.2012.67
   PubMed Web of Science ®Google Scholar
• Yin, R., J. Mo, M. Lu, and H. Wang. 2015. Detection of human urinary 5-hydroxymethylcytosine by stable isotope dilution HPLC-MS/MS analysis. Analytical Chemistry 87:1846–52. doi:10.1021/ac5038895
   PubMed Web of Science ®Google Scholar
• Zhong, X., J. Du, C. J. Hale, J. Gallego-Bartolome, S. Feng, A. A. Vashisht, J. Chory, J. A. Wohlschlegel, D. J. Patel, and S. E. Jacobsen. 2014. Molecular mechanism of action of plant DRM de novo DNA methyltransferases. Cell 157:1050–60. doi:10.1016/j.cell.2014.03.056
   PubMed Web of Science ®Google Scholar
• Zhu, J. K. 2009. Active DNA demethylation mediated by DNA glycosylases. Annual Review of Genetics 43:143–66. doi:10.1146/annurev-genet-102108-134205
   PubMed Web of Science ®Google Scholar