Discovery of bisulfite-mediated cytosine conversion to uracil, the key reaction for DNA methylation analysis - A personal account

Proceedings of the Japan Academy Series B: Physical and Biological Sciences

Volumn 84, Issue 8, 2008, Pages 321-330

  Hayatsu, Hikoya ^a  

^a OKAYAMA UNIVERSITY   (Japan)

Author keywords

5 methylcytosine; Bisulfite; Chemical modification; Concentration dependency; Deamination of cytosine

Indexed keywords

CYTOSINE; SULFITE; URACIL;

DNA METHYLATION; METABOLISM; REVIEW;

CYTOSINE; DNA METHYLATION; SULFITES; URACIL;

EID: 54249091549     PISSN: 03862208     EISSN: 13492896     Source Type: Journal    
DOI: 10.2183/pjab.84.321     Document Type: Review

References (29)

1. Calladine, C.R., Drew, H.R., Luisi, B.F. and Travers, A.A. (2004) Understanding DNA, the Molecule and How it Works, 3rd ed., Elsevier, Amsterdam, pp. 270-294.
2. Shapiro, R., Servis, R.E. and Welcher, M. (1970) Reactions of uracil and cytosine derivatives with sodium bisulfite. A specific deamination method. J. Am. Chem. Soc. 92, 422-424.
3. Hayatsu, H., Wataya, Y. and Kai, K. (1970) The addition of sodium bisulfite to uracil and cytosine. J. Am. Chem. Soc. 92, 724-726.
4. Frommer, M., McDonald, L.E., Millar, D.S., Collis, C.M., Watt, F., Grigg, G.W., Molloy, P.L. and Paul, C.L. (1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl. Acad. Sci. USA 80, 1579-1583.
5. Hayatsu, H. and Ukita, T. (1967) The selective degradation of pyrimidines in nucleic acids by permanganate oxidation. Biochem. Biophys. Res. Commun. 29, 556-561.
6. Hayatsu, H. and Yano, M. (1969) Permanganate oxidation of 4-thiouracil derivatives. Isolation and properties of 1-substituted-2-pyrimidone-4- sulfonates. Tetrahedron Lett. 9, 755-758.
7. Hayatsu, H. (1969) The oxygen-catalyzed reaction between 4-thiouridine and sodium sulfite. J. Am. Chem. Soc. 91, 5693-5694.
8. Hayatsu, H. and Inoue, M. (1971) The oxygen-mediated reaction between 4-thiouracil derivatives and bisulfite. Isolation and characterization of 1-methyluracil-4-thiosulfonate as an intermediate in the formation of 1-methyluracil-4-sulfonate. J. Am. Chem. Soc. 93, 2301-2306.
9. Hayatsu, H., Wataya, Y., Kai, K. and Iida, S. (1970) Reaction of sodium bisulfite with uracil, cytosine and their derivatives. Biochemistry 9, 2858-2865.
10. Hall, R. (1971) The Modified Nucleosides in Nucleic Acids. Columbia University Press, New York, pp. 282-286.
11. Kuo, T., Huang, T. and Teng, M. (1968) 5-Methylcytosine replacing cytosine in the deoxyribonucleic acid of a bacteriophage for Xanthomonas oryzae. J. Mol. Biol. 34, 373-375.
12. Hayatsu, H. and Shiragami, M. (1979) Reaction of bisulfite with 5-hydroxymethyl group in pyrimidines and in phage DNAs. Biochemistry 18, 632-637.
13. Shiragami, M., Iida, S., Kudo, I. and Hayatsu, H. (1975) Formation of diastereomers of 5,6-dihydrothymine-6-sulfonate by deamination of 5-methylcytosine with bisulfite. Chem. Pharm. Bull. 23, 3027-3029.
14. Newman, M.S. (1956) Steric Effects in Organic Chemistry. Wiley, New York.
15. Wang, R.Y., Gehrke, C.W. and Ehrlich, M. (1980) Comparison of bisulfite modification of 5-methyldeoxycytidine and deoxycytidine residues. Nucleic Acids Res. 8, 4777-4790.
16. Inoue, M., Hayatsu, H. and Tanooka, H. (1972) Concentration effect of bisulfite on the inactivation of transforming activity of DNA. Chem. Biol. Interactions 5, 85-95.
17. Hayatsu, H. and Miller, R.C. (1972) The cleavage of DNA by the oxygen-dependent reaction of bisulfite. Biochem. Biophys. Res. Commun. 46, 120-124.
18. Freese, E. and Freese, E.B. (1965) The oxygen effect on deoxyribonucleic acid inactivation by hydroxylamine. Biochemistry 4, 2419-2433.
19. Sono, M., Wataya, Y. and Hayatsu, H. (1973) Role of bisulfite in the deamination and the hydrogen isotope exchange of cytidylic acid. J. Am. Chem. Soc. 95, 4745-4749.
20. Shapiro, R., DiFate, V. and Welcher, M. (1974) Deamination of cytosine derivatives by bisulfite. Mechanism of the reaction. J. Am. Chem. Soc. 96, 906-912.
21. Hayatsu, H. (1976) Bisulfite modification of nucleic acids and their constituents. Progress in Nucleic Acid Res. and Mol. Biol. 16, 75-124.
22. Eads, C.A. and Laird, P.W. (2002) In DNA Methylation Protocols. Methods in Molecular Biology (eds. Millis, K.I. and Ramsahoye, B.H.). vol. 200, Humana Press, NJ, USA, pp. 71-85.
23. Clark, S.J., Stathem, A., Stirzaker, C., Molloy, P.L. and Frommer, M. (2006) DNA methylation: Bisulfite modification and analysis. Nature Protocols 1, 2353-2364.
24. Hayatsu, H., Negishi, K. and Shiraishi, M. (2004) DNA methylation analysis: speedup of bisulfite-mediated deamination of cytosine in the genomic sequencing procedure. Proc. Jpn. Acad., Ser B 80, 189-194.
25. Shiraishi, M. and Hayatsu, H. (2004) High-speed conversion of cytosine to uracil in bisulfite genomic sequencing analysis of DNA methylation. DNA Res. 11, 409-415.
26. Hayatsu, H. (2006) Bisufite modification of cytosine and 5-methylcytosine as used in epigenetic studies. Genes and Environment 28, 1-8.
27. Hayatsu, H. (2008) The bisulfite genomic sequencing used in the analysis of epigenetic states, a technique in the emerging environmental genotoxicology research. Mutat. Res. 659, 77-82.
28. Hayatsu, H., Shiraishi, M. and Negishi, K. (2008) Bisulfite modification of DNA for analyzing 5-methylcytosine and cytosine. Current Protocols in Nucleic Acid Chemistry 33, 6.10.1-6.10.15, Wiley, NC, USA.
29. Kai, K., Tsuruo, T. and Hayatsu, H. (1974) The effect of bisulfite modification on the template activity of DNA for DNA polymerase I. Nucleic Acids Res. 1, 889-899.