A sensitive mass spectrometry method for simultaneous quantification of DNA methylation and hydroxymethylation levels in biological samples

Analytical Biochemistry

Volumn 412, Issue 2, 2011, Pages 203-209

  Le, Thuc ^a   Kim, Kee Pyo ^a,b   Fan, Guoping ^a   Faull, Kym F ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

5 Hydroxymethyl cytosine (5hmC); 5 Methyl cytosine (5mC); DNA hydroxymethylation; DNA methylation; Induced pluripotent stem cells (iPSCs); Mass spectrometry; Multiple reaction monitoring (MRM)

Indexed keywords

ALKYLATION; CELL CULTURE; ELECTROSPRAY IONIZATION; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; METHYLATION; STEM CELLS; THIN LAYER CHROMATOGRAPHY;

5-HYDROXYMETHYL-CYTOSINE (5HMC); 5-METHYL-CYTOSINE (5MC); DNA METHYLATION; HYDROXYMETHYLATION; INDUCED PLURIPOTENT STEM CELLS; MULTIPLE REACTION MONITORING;

DNA;

5 HYDROXYMETHYL CYTOSINE; 5 METHYL CYTOSINE; CYTOSINE; GENOMIC DNA; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; BIOLOGICAL MONITORING; CHEMICAL MODIFICATION; CONTROLLED STUDY; DNA DETERMINATION; DNA EXTRACTION; DNA METHYLATION; ELECTROSPRAY MASS SPECTROMETRY; EMBRYONIC STEM CELL; FIBROBLAST; GLYCOSYLATION; HUMAN; HUMAN CELL; HYDROLYSIS; LIQUID CHROMATOGRAPHY; MOUSE; MULTIPLE REACTION MONITORING; NICK END LABELING; NONHUMAN; NUCLEOTIDE SEQUENCE; PLURIPOTENT STEM CELL; PRIORITY JOURNAL; PROTEIN ANALYSIS; REGULATORY MECHANISM; SENSITIVITY ANALYSIS; VALIDATION STUDY;

EID: 79953217366     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2011.01.026     Document Type: Article

References (34)

1. S.H. Cross, R.R. Meehan, X. Nan, and A. Bird A component of the transcriptional repressor MeCP1 shares a motif with DNA methyltransferase and HRX proteins Nat. Genet. 16 1997 256 259
2. X. Nan, F.J. Campoy, and A. Bird MeCP2 is a transcriptional repressor with abundant binding sites in genomic chromatin Cell 88 1997 471 481 (Pubitemid 27154412)
3. P.L. Jones, G.J. Veenstra, P.A. Wade, D. Vermaak, S.U. Kass, N. Landsberger, J. Strouboulis, and A.P. Wolffe Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription Nat. Genet. 19 1998 187 191 (Pubitemid 28248804)
4. X. Nan, H.H. Ng, C.A. Johnson, C.D. Laherty, B.M. Turner, R.N. Eisenman, and A. Bird Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex Nature 393 1998 386 389 (Pubitemid 28269714)
5. K. Martinowich, D. Hattori, H. Wu, S. Fouse, F. He, Y. Hu, G. Fan, and Y.E. Sun DNA methylation-related chromatin remodeling in activity-dependent BDNF gene regulation Science 302 2003 890 893 (Pubitemid 37339633)
6. G. Fan, K. Martinowich, M.H. Chin, F. He, S.D. Fouse, L. Hutnick, D. Hattori, W. Ge, Y. Shen, H. Wu, J. ten Hoeve, K. Shuai, and Y.E. Sun DNA methylation controls the timing of astrogliogenesis through regulation of JAK-STAT signaling Development 132 2005 3345 3356 (Pubitemid 41246111)
7. G. Fan, C. Beard, R.Z. Chen, G. Csankovszki, Y. Sun, M. Siniaia, D. Biniszkiewicz, B. Bates, P.P. Lee, R. Kuhn, A. Trumpp, C. Poon, C.B. Wilson, and R. Jaenisch DNA hypomethylation perturbs the function and survival of CNS neurons in postnatal animals J. Neurosci. 21 2001 788 797 (Pubitemid 32163120)
8. L.K. Hutnick, P. Golshani, M. Namihira, Z. Xue, A. Matynia, X.W. Yang, A.J. Silva, F.E. Schweizer, and G. Fan DNA hypomethylation restricted to the murine forebrain induces cortical degeneration and impairs postnatal neuronal maturation Hum. Mol. Genet. 18 2009 2875 2888
9. J. Feng, Y. Zhou, S.L. Campbell, T. Le, E. Li, J.D. Sweatt, A.J. Silva, and G. Fan Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons Nat. Neurosci. 13 2010 423 430
10. M. Tahiliani, 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 Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1 Science 324 2009 930 935
11. N.W. Penn, R. Suwalski, C. O'Riley, K. Bojanowski, and R. Yura The presence of 5-hydroxymethylcytosine in animal deoxyribonucleic acid Biochem. J. 126 1972 781 790
12. S. Kriaucionis, and N. Heintz The nuclear DNA base 5- hydroxymethylcytosine is present in Purkinje neurons and the brain Science 324 2009 929 930
13. S. Ito, A.C. D'Alessio, O.V. Taranova, K. Hong, L.C. Sowers, and Y. Zhang Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal, and inner cell mass specification Nature 466 2010 1129 1133
14. E. Privat, and L.C. Sowers Photochemical deamination and demethylation of 5-methylcytosine Chem. Res. Toxicol. 9 1996 745 750 (Pubitemid 26181625)
15. Z. Liutkeviciute, G. Lukinavicius, V. Masevicius, D. Daujotyte, and S. Klimasauskas Cytosine-5-methyltransferases add aldehydes to DNA Nat. Chem. Biol. 5 2009 400 402
16. Y. Huang, W.A. Pastor, Y. Shen, M. Tahiliani, D.R. Liu, and A. Rao The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing PLoS ONE 5 2010 e8888
17. A. Szwagierczak, S. Bultmann, C.S. Schmidt, F. Spada, and H. Leonhardt Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA Nucleic Acids Res. 38 2010 e181
18. B.A. Flusberg, D.R. Webster, J.H. Lee, K.J. Travers, E.C. Olivares, T.A. Clark, J. Korlach, and S.W. Turner Direct detection of DNA methylation during single-molecule, real-time sequencing Nat. Methods 7 2010 461 465
19. D.G. Burke, K. Griffiths, Z. Kassir, and K. Emslie Accurate measurement of DNA methylation that is traceable to the international system of units Anal. Chem. 81 2009 7294 7301
20. R.M. Kok, D.E. Smith, R. Barto, A.M. Spijkerman, T. Teerlink, H.J. Gellekink, C. Jakobs, and Y.M. Smulders Global DNA methylation measured by liquid chromatography-tandem mass spectrometry: analytical technique, reference values, and determinants in healthy subjects Clin. Chem. Lab. Med. 45 2007 903 911 (Pubitemid 47041882)
21. Z. Liu, S. Liu, Z. Xie, W. Blum, D. Perrotti, P. Paschka, R. Klisovic, J. Byrd, K.K. Chan, and G. Marcucci Characterization of in vitro and in vivo hypomethylating effects of decitabine in acute myeloid leukemia by a rapid, specific, and sensitive LC-MS/MS method Nucleic Acids Res. 35 2007 e31
22. Z. Liu, J. Wu, Z. Xie, S. Liu, P. Fan-Havard, T.H. Huang, C. Plass, G. Marcucci, and K.K. Chan Quantification of regional DNA methylation by liquid chromatography/tandem mass spectrometry Anal. Biochem. 391 2009 106 113
23. 15N]methyldeoxycytidine internal standards Nucleic Acids Res. 36 2008 e119
24. L. Song, S.R. James, L. Kazim, and A.R. Karpf Specific method for the determination of genomic DNA methylation by liquid chromatography-electrospray ionization tandem mass spectrometry Anal. Chem. 77 2005 504 510 (Pubitemid 40116829)
25. I. Yang, S.K. Kim, D.G. Burke, K. Griffiths, Z. Kassir, K.R. Emslie, Y. Gao, J. Wang, C.A. Foy, A.C. Pardos-Pardos, S. Ellison, P.J. Domann, S. Fujii, and S.R. Park An international comparability study on quantification of total methyl cytosine content Anal. Biochem. 384 2009 288 295
26. K. Takahashi, K. Tanabe, M. Ohnuki, M. Narita, T. Ichisaka, K. Tomoda, and S. Yamanaka Induction of pluripotent stem cells from adult human fibroblasts by defined factors Cell 131 2007 861 872 (Pubitemid 350138099)
27. M. Jackson, A. Krassowska, N. Gilbert, T. Chevassut, L. Forrester, J. Ansell, and B. Ramsahoye Severe global DNA hypomethylation blocks differentiation and induces histone hyperacetylation in embryonic stem cells Mol. Cell. Biol. 24 2004 8862 8871 (Pubitemid 39313892)
28. C. Popp, W. Dean, S. Feng, S.J. Cokus, S. Andrews, M. Pellegrini, S.E. Jacobsen, and W. Reik Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency Nature 463 2010 1101 1105
29. J. Deng, R. Shoemaker, B. Xie, A. Gore, E.M. LeProust, J. Antosiewicz-Bourget, D. Egli, N. Maherali, I.H. Park, J. Yu, G.Q. Daley, K. Eggan, K. Hochedlinger, J. Thomson, W. Wang, Y. Gao, and K. Zhang Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming Nat. Biotechnol. 27 2009 353 360
30. A. Doi, I.H. Park, B. Wen, P. Murakami, M.J. Aryee, R. Irizarry, B. Herb, C. Ladd-Acosta, J. Rho, S. Loewer, J. Miller, T. Schlaeger, G.Q. Daley, and A.P. Feinberg Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells, and fibroblasts Nat. Genet. 41 2009 1350 1353
31. K. Kim, A. Doi, B. Wen, K. Ng, R. Zhao, P. Cahan, J. Kim, M.J. Aryee, H. Ji, L.I. Ehrlich, A. Yabuuchi, A. Takeuchi, K.C. Cunniff, H. Hongguang, S. McKinney-Freeman, O. Naveiras, T.J. Yoon, R.A. Irizarry, N. Jung, J. Seita, J. Hanna, P. Murakami, R. Jaenisch, R. Weissleder, S.H. Orkin, I.L. Weissman, A.P. Feinberg, and G.Q. Daley Epigenetic memory in induced pluripotent stem cells Nature 467 2010 285 290
32. M. Pick, Y. Stelzer, O. Bar-Nur, Y. Mayshar, A. Eden, and N. Benvenisty Clone- and gene-specific aberrations of parental imprinting in human induced pluripotent stem cells Stem cells 27 2009 2686 2690
33. M. Stadtfeld, E. Apostolou, H. Akutsu, A. Fukuda, P. Follett, S. Natesan, T. Kono, T. Shioda, and K. Hochedlinger Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells Nature 465 2010 175 181
34. T.S. Mikkelsen, J. Hanna, X. Zhang, M. Ku, M. Wernig, P. Schorderet, B.E. Bernstein, R. Jaenisch, E.S. Lander, and A. Meissner Dissecting direct reprogramming through integrative genomic analysis Nature 454 2008 49 55 (Pubitemid 351931978)