5-hydroxymethyluracil in mouse embryonic stem cell DNA. Nat Chem Biol 10(7):574–581.
https://doi.org/10.1038/nchembio.1532
58. Tsuji M, Matsunaga H, Jinno D, Tsukamoto H, Suzuki N, Tomioka Y (2014) A validated
quantitative liquid chromatography-tandem quadrupole mass spectrometry method for monitoring isotopologues to evaluate global modified cytosine ratios in genomic DNA. J
Chromatogr B Analyt Technol Biomed Life Sci 953–954:38–47. https://doi.org/10.1016/j.
jchromb.2014.01.050
59. Liu S, Wang J, Su Y, Guerrero C, Zeng Y, Mitra D, Brooks PJ, Fisher DE, Song H, Wang Y
(2013) Quantitative assessment of Tet-induced oxidation products of 5-methylcytosine in
cellular and tissue DNA. Nucleic Acids Res 41(13):6421–6429
60. Gackowski D, Starczak M, Zarakowska E, Modrzejewska M, Szpila A, Banaszkiewicz Z,
Olinski R (2016) Accurate, direct, and high-throughput analyses of a broad Spectrum of
endogenously generated DNA base modifications with isotope-dilution two-dimensional
ultraperformance liquid chromatography with tandem mass spectrometry: possible clinical
implication. Anal Chem 88(24):12128–12136. https://doi.org/10.1021/acs.analchem.6b02900
61. Lin XC, Zhang T, Liu L, Tang H, Yu RQ, Jiang JH (2016) Mass spectrometry based
ultrasensitive DNA methylation profiling using target fragmentation assay. Anal Chem 88
(2):1083–1087. https://doi.org/10.1021/acs.analchem.5b04247
62. Le T, Kim KP, Fan G, Faull KF (2011) A sensitive mass spectrometry method for simultaneous quantification of DNA methylation and hydroxymethylation levels in biological samples. Anal Biochem 412(2):203–209. https://doi.org/10.1016/j.ab.2011.01.026
63. Hayatsu H, Wataya Y, Kazushige K (1970) The addition of sodium bisulfite to uracil and to
cytosine. J Am Chem Soc 92(3):724–726
64. Hayatsu H (2008) Discovery of bisulfite-mediated cytosine conversion to uracil, the key
reaction for DNA methylation analysis--a personal account. Proc Jpn Acad Ser B Phys Biol
Sci 84(8):321–330
65. Hayatsu H, Shiragami M (1979) Reaction of bisulfite with the 5-hydroxymethyl group in
pyrimidines and in phage DNAs. Biochemistry 18(4):632–637
66. Clark SJ, Statham A, Stirzaker C, Molloy PL, Frommer M (2006) DNA methylation:
bisulphite modification and analysis. Nat Protoc 1(5):2353–2364. https://doi.org/10.1038/
nprot.2006.324
67. Deng J, Shoemaker R, Xie B, Gore A, LeProust EM, Antosiewicz-Bourget J, Egli D,
Maherali N, Park IH, Yu J, Daley GQ, Eggan K, Hochedlinger K, Thomson J, Wang W,
Gao Y, Zhang K (2009) Targeted bisulfite sequencing reveals changes in DNA methylation
associated with nuclear reprogramming. Nat Biotechnol 27(4):353–360. https://doi.org/10.
1038/nbt.1530
68. Taub FE, DeLeo JM, Thompson EB (1983) Sequential comparative hybridizations analyzed
by computerized image processing can identify and quantitate regulated RNAs. DNA 2
(4):309–327. https://doi.org/10.1089/dna.1983.2.309
69. Gitan RS, Shi H, Chen CM, Yan PS, Huang TH (2002) Methylation-specific oligonucleotide
microarray: a new potential for high-throughput methylation analysis. Genome Res 12
(1):158–164. https://doi.org/10.1101/gr.202801
70. Yan PS, Wei SH, Huang TH (2004) Methylation-specific oligonucleotide microarray.
Methods Mol Biol 287:251–260. https://doi.org/10.1385/1-59259-828-5:251
71. Dedeurwaerder S, Defrance M, Calonne E, Denis H, Sotiriou C, Fuks F (2011) Evaluation of
the Infinium methylation 450K technology. Epigenomics 3(6):771–784. https://doi.org/10.
2217/epi.11.105
72. Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S,
Hori F, Ishikawa-Kato S, Mungall CJ, Arner E, Baillie JK, Bertin N, Bono H, de Hoon M,
Diehl AD, Dimont E, Freeman TC, Fujieda K, Hide W, Kaliyaperumal R, Katayama T,
Lassmann T, Meehan TF, Nishikata K, Ono H, Rehli M, Sandelin A, Schultes EA, t’Hoen
PA, Tatum Z, Thompson M, Toyoda T, Wright DW, Daub CO, Itoh M, Carninci P,
Hayashizaki Y, Forrest AR, Kawaji H, Consortium F (2015) Gateways to the FANTOM5
Experimental Methodologies for Detection and Mapping of Epigenetic DNA Marks
517
https://doi.org/10.1038/nchembio.1532
58. Tsuji M, Matsunaga H, Jinno D, Tsukamoto H, Suzuki N, Tomioka Y (2014) A validated
quantitative liquid chromatography-tandem quadrupole mass spectrometry method for monitoring isotopologues to evaluate global modified cytosine ratios in genomic DNA. J
Chromatogr B Analyt Technol Biomed Life Sci 953–954:38–47. https://doi.org/10.1016/j.
jchromb.2014.01.050
59. Liu S, Wang J, Su Y, Guerrero C, Zeng Y, Mitra D, Brooks PJ, Fisher DE, Song H, Wang Y
(2013) Quantitative assessment of Tet-induced oxidation products of 5-methylcytosine in
cellular and tissue DNA. Nucleic Acids Res 41(13):6421–6429
60. Gackowski D, Starczak M, Zarakowska E, Modrzejewska M, Szpila A, Banaszkiewicz Z,
Olinski R (2016) Accurate, direct, and high-throughput analyses of a broad Spectrum of
endogenously generated DNA base modifications with isotope-dilution two-dimensional
ultraperformance liquid chromatography with tandem mass spectrometry: possible clinical
implication. Anal Chem 88(24):12128–12136. https://doi.org/10.1021/acs.analchem.6b02900
61. Lin XC, Zhang T, Liu L, Tang H, Yu RQ, Jiang JH (2016) Mass spectrometry based
ultrasensitive DNA methylation profiling using target fragmentation assay. Anal Chem 88
(2):1083–1087. https://doi.org/10.1021/acs.analchem.5b04247
62. Le T, Kim KP, Fan G, Faull KF (2011) A sensitive mass spectrometry method for simultaneous quantification of DNA methylation and hydroxymethylation levels in biological samples. Anal Biochem 412(2):203–209. https://doi.org/10.1016/j.ab.2011.01.026
63. Hayatsu H, Wataya Y, Kazushige K (1970) The addition of sodium bisulfite to uracil and to
cytosine. J Am Chem Soc 92(3):724–726
64. Hayatsu H (2008) Discovery of bisulfite-mediated cytosine conversion to uracil, the key
reaction for DNA methylation analysis--a personal account. Proc Jpn Acad Ser B Phys Biol
Sci 84(8):321–330
65. Hayatsu H, Shiragami M (1979) Reaction of bisulfite with the 5-hydroxymethyl group in
pyrimidines and in phage DNAs. Biochemistry 18(4):632–637
66. Clark SJ, Statham A, Stirzaker C, Molloy PL, Frommer M (2006) DNA methylation:
bisulphite modification and analysis. Nat Protoc 1(5):2353–2364. https://doi.org/10.1038/
nprot.2006.324
67. Deng J, Shoemaker R, Xie B, Gore A, LeProust EM, Antosiewicz-Bourget J, Egli D,
Maherali N, Park IH, Yu J, Daley GQ, Eggan K, Hochedlinger K, Thomson J, Wang W,
Gao Y, Zhang K (2009) Targeted bisulfite sequencing reveals changes in DNA methylation
associated with nuclear reprogramming. Nat Biotechnol 27(4):353–360. https://doi.org/10.
1038/nbt.1530
68. Taub FE, DeLeo JM, Thompson EB (1983) Sequential comparative hybridizations analyzed
by computerized image processing can identify and quantitate regulated RNAs. DNA 2
(4):309–327. https://doi.org/10.1089/dna.1983.2.309
69. Gitan RS, Shi H, Chen CM, Yan PS, Huang TH (2002) Methylation-specific oligonucleotide
microarray: a new potential for high-throughput methylation analysis. Genome Res 12
(1):158–164. https://doi.org/10.1101/gr.202801
70. Yan PS, Wei SH, Huang TH (2004) Methylation-specific oligonucleotide microarray.
Methods Mol Biol 287:251–260. https://doi.org/10.1385/1-59259-828-5:251
71. Dedeurwaerder S, Defrance M, Calonne E, Denis H, Sotiriou C, Fuks F (2011) Evaluation of
the Infinium methylation 450K technology. Epigenomics 3(6):771–784. https://doi.org/10.
2217/epi.11.105
72. Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S,
Hori F, Ishikawa-Kato S, Mungall CJ, Arner E, Baillie JK, Bertin N, Bono H, de Hoon M,
Diehl AD, Dimont E, Freeman TC, Fujieda K, Hide W, Kaliyaperumal R, Katayama T,
Lassmann T, Meehan TF, Nishikata K, Ono H, Rehli M, Sandelin A, Schultes EA, t’Hoen
PA, Tatum Z, Thompson M, Toyoda T, Wright DW, Daub CO, Itoh M, Carninci P,
Hayashizaki Y, Forrest AR, Kawaji H, Consortium F (2015) Gateways to the FANTOM5
Experimental Methodologies for Detection and Mapping of Epigenetic DNA Marks
517