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

Analytical Biochemistry - Tập 412 - Trang 203-209 - 2011
Thuc Le1,2, Kee-Pyo Kim1, Guoping Fan1, Kym F. Faull2
1Department of Human Genetics, Broad Stem Cell Research Center, David Geffen School of Medicine, University of California – Los Angeles, Los Angeles, CA 90095, USA
2Pasarow Mass Spectrometry Laboratory, Department of Psychiatry and Biobehavioral Sciences and Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA

Tài liệu tham khảo

Cross, 1997, A component of the transcriptional repressor MeCP1 shares a motif with DNA methyltransferase and HRX proteins, Nat. Genet., 16, 256, 10.1038/ng0797-256 Nan, 1997, MeCP2 is a transcriptional repressor with abundant binding sites in genomic chromatin, Cell, 88, 471, 10.1016/S0092-8674(00)81887-5 Jones, 1998, Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription, Nat. Genet., 19, 187, 10.1038/561 Nan, 1998, Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex, Nature, 393, 386, 10.1038/30764 Martinowich, 2003, DNA methylation-related chromatin remodeling in activity-dependent BDNF gene regulation, Science, 302, 890, 10.1126/science.1090842 Fan, 2005, DNA methylation controls the timing of astrogliogenesis through regulation of JAK–STAT signaling, Development, 132, 3345, 10.1242/dev.01912 Fan, 2001, DNA hypomethylation perturbs the function and survival of CNS neurons in postnatal animals, J. Neurosci., 21, 788, 10.1523/JNEUROSCI.21-03-00788.2001 Hutnick, 2009, DNA hypomethylation restricted to the murine forebrain induces cortical degeneration and impairs postnatal neuronal maturation, Hum. Mol. Genet., 18, 2875, 10.1093/hmg/ddp222 Feng, 2010, Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons, Nat. Neurosci., 13, 423, 10.1038/nn.2514 Tahiliani, 2009, Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1, Science, 324, 930, 10.1126/science.1170116 Penn, 1972, The presence of 5-hydroxymethylcytosine in animal deoxyribonucleic acid, Biochem. J., 126, 781, 10.1042/bj1260781 Kriaucionis, 2009, The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain, Science, 324, 929, 10.1126/science.1169786 Ito, 2010, Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal, and inner cell mass specification, Nature, 466, 1129, 10.1038/nature09303 Privat, 1996, Photochemical deamination and demethylation of 5-methylcytosine, Chem. Res. Toxicol., 9, 745, 10.1021/tx950182o Liutkeviciute, 2009, Cytosine-5-methyltransferases add aldehydes to DNA, Nat. Chem. Biol., 5, 400, 10.1038/nchembio.172 Huang, 2010, The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing, PLoS ONE, 5, e8888, 10.1371/journal.pone.0008888 Szwagierczak, 2010, Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA, Nucleic Acids Res., 38, e181, 10.1093/nar/gkq684 Flusberg, 2010, Direct detection of DNA methylation during single-molecule, real-time sequencing, Nat. Methods, 7, 461, 10.1038/nmeth.1459 Burke, 2009, Accurate measurement of DNA methylation that is traceable to the international system of units, Anal. Chem., 81, 7294, 10.1021/ac901116f Kok, 2007, Global DNA methylation measured by liquid chromatography–tandem mass spectrometry: analytical technique, reference values, and determinants in healthy subjects, Clin. Chem. Lab. Med., 45, 903, 10.1515/CCLM.2007.137 Liu, 2007, 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, e31, 10.1093/nar/gkl1156 Liu, 2009, Quantification of regional DNA methylation by liquid chromatography/tandem mass spectrometry, Anal. Biochem., 391, 106, 10.1016/j.ab.2009.05.012 Quinlivan, 2008, DNA methylation determination by liquid chromatography–tandem mass spectrometry using novel biosynthetic [U-15N]deoxycytidine and [U-15N]methyldeoxycytidine internal standards, Nucleic Acids Res., 36, e119, 10.1093/nar/gkn534 Song, 2005, Specific method for the determination of genomic DNA methylation by liquid chromatography–electrospray ionization tandem mass spectrometry, Anal. Chem., 77, 504, 10.1021/ac0489420 Yang, 2009, An international comparability study on quantification of total methyl cytosine content, Anal. Biochem., 384, 288, 10.1016/j.ab.2008.09.036 Takahashi, 2007, Induction of pluripotent stem cells from adult human fibroblasts by defined factors, Cell, 131, 861, 10.1016/j.cell.2007.11.019 Jackson, 2004, Severe global DNA hypomethylation blocks differentiation and induces histone hyperacetylation in embryonic stem cells, Mol. Cell. Biol., 24, 8862, 10.1128/MCB.24.20.8862-8871.2004 Popp, 2010, Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency, Nature, 463, 1101, 10.1038/nature08829 Deng, 2009, Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming, Nat. Biotechnol., 27, 353, 10.1038/nbt.1530 Doi, 2009, Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells, and fibroblasts, Nat. Genet., 41, 1350, 10.1038/ng.471 Kim, 2010, Epigenetic memory in induced pluripotent stem cells, Nature, 467, 285, 10.1038/nature09342 Pick, 2009, Clone- and gene-specific aberrations of parental imprinting in human induced pluripotent stem cells, Stem cells, 27, 2686, 10.1002/stem.205 Stadtfeld, 2010, Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells, Nature, 465, 175, 10.1038/nature09017 Mikkelsen, 2008, Dissecting direct reprogramming through integrative genomic analysis, Nature, 454, 49, 10.1038/nature07056