Standardization and quality controls for the methylated DNA immunoprecipitation technique

References

• Illingworth R, Kerr A, Desousa D, Jørgensen H, Ellis P, Stalker J, et al. A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol 2008; 6:e22; http://dx.doi.org/10.1371/journal.pbio.0060022; PMID: 18232738
   PubMed Web of Science ®Google Scholar
• Wang Y, Leung FC. An evaluation of new criteria for CpG islands in the human genome as gene markers. Bioinformatics 2004; 20:1170 - 7; http://dx.doi.org/10.1093/bioinformatics/bth059; PMID: 14764558
   PubMed Web of Science ®Google Scholar
• Saxonov S, Berg P, Brutlag DL. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci U S A 2006; 103:1412 - 7; http://dx.doi.org/10.1073/pnas.0510310103; PMID: 16432200
   PubMed Web of Science ®Google Scholar
• Razin A, Cedar H. DNA methylation and gene expression. Microbiol Rev 1991; 55:451 - 8; PMID: 1943996
   PubMedGoogle Scholar
• Weber M, Hellmann I, Stadler MB, Ramos L, Pääbo S, Rebhan M, et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 2007; 39:457 - 66; http://dx.doi.org/10.1038/ng1990; PMID: 17334365
   PubMed Web of Science ®Google Scholar
• Reik W, Dean W, Walter J. Epigenetic reprogramming in mammalian development. Science 2001; 293:1089 - 93; http://dx.doi.org/10.1126/science.1063443; PMID: 11498579
   PubMed Web of Science ®Google Scholar
• Richardson B. Impact of aging on DNA methylation. Ageing Res Rev 2003; 2:245 - 61; http://dx.doi.org/10.1016/S1568-1637(03)00010-2; PMID: 12726774
   PubMed Web of Science ®Google Scholar
• Heard E, Disteche CM. Dosage compensation in mammals: fine-tuning the expression of the X chromosome. Genes Dev 2006; 20:1848 - 67; http://dx.doi.org/10.1101/gad.1422906; PMID: 16847345
   PubMed Web of Science ®Google Scholar
• Spahn L, Barlow DP. An ICE pattern crystallizes. Nat Genet 2003; 35:11 - 2; http://dx.doi.org/10.1038/ng0903-11; PMID: 12947402
   PubMed Web of Science ®Google Scholar
• Kim JK, Samaranayake M, Pradhan S. Epigenetic mechanisms in mammals. Cell Mol Life Sci 2009; 66:596 - 612; http://dx.doi.org/10.1007/s00018-008-8432-4; PMID: 18985277
   PubMed Web of Science ®Google Scholar
• Cooper DN, Youssoufian H. The CpG dinucleotide and human genetic disease. Hum Genet 1988; 78:151 - 5; http://dx.doi.org/10.1007/BF00278187; PMID: 3338800
   PubMed Web of Science ®Google Scholar
• Wilson AS, Power BE, Molloy PL. DNA hypomethylation and human diseases. Biochim Biophys Acta 2007; 1775:138-62.
   Google Scholar
• Taby R, Issa JP. Cancer epigenetics. CA Cancer J Clin 2010; 60:376 - 92; http://dx.doi.org/10.3322/caac.20085; PMID: 20959400
   PubMed Web of Science ®Google Scholar
• Esteller M. Epigenetic gene silencing in cancer: the DNA hypermethylome. Hum Mol Genet 2007; 16:Spec No 1 R50 - 9; http://dx.doi.org/10.1093/hmg/ddm018; PMID: 17613547
   PubMed Web of Science ®Google Scholar
• Mathers JC. Nutritional modulation of ageing: genomic and epigenetic approaches. Mech Ageing Dev 2006; 127:584 - 9; http://dx.doi.org/10.1016/j.mad.2006.01.018; PMID: 16513160
   PubMed Web of Science ®Google Scholar
• Bjornsson HT, Sigurdsson MI, Fallin MD, Irizarry RA, Aspelund T, Cui H, et al. Intra-individual change over time in DNA methylation with familial clustering. JAMA 2008; 299:2877 - 83; http://dx.doi.org/10.1001/jama.299.24.2877; PMID: 18577732
   PubMed Web of Science ®Google Scholar
• Maegawa S, Hinkal G, Kim HS, Shen L, Zhang L, Zhang J, et al. Widespread and tissue specific age-related DNA methylation changes in mice. Genome Res 2010; 20:332 - 40; http://dx.doi.org/10.1101/gr.096826.109; PMID: 20107151
   PubMed Web of Science ®Google Scholar
• Rakyan VK, Down TA, Maslau S, Andrew T, Yang TP, Beyan H, et al. Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. Genome Res 2010; 20:434 - 9; http://dx.doi.org/10.1101/gr.103101.109; PMID: 20219945
   PubMed Web of Science ®Google Scholar
• Teschendorff AE, Menon U, Gentry-Maharaj A, Ramus SJ, Weisenberger DJ, Shen H, et al. Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer. Genome Res 2010; 20:440 - 6; http://dx.doi.org/10.1101/gr.103606.109; PMID: 20219944
   PubMed Web of Science ®Google Scholar
• Esteller M. Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet 2007; 8:286 - 98; http://dx.doi.org/10.1038/nrg2005; PMID: 17339880
   PubMed Web of Science ®Google Scholar
• Kuo KC, McCune RA, Gehrke CW, Midgett R, Ehrlich M. Quantitative reversed-phase high performance liquid chromatographic determination of major and modified deoxyribonucleosides in DNA. Nucleic Acids Res 1980; 8:4763 - 76; http://dx.doi.org/10.1093/nar/8.20.4763; PMID: 7003544
   PubMed Web of Science ®Google Scholar
• Karimi M, Johansson S, Stach D, Corcoran M, Grandér D, Schalling M, et al. LUMA (LUminometric Methylation Assay)--a high throughput method to the analysis of genomic DNA methylation. Exp Cell Res 2006; 312:1989 - 95; http://dx.doi.org/10.1016/j.yexcr.2006.03.006; PMID: 16624287
   PubMed Web of Science ®Google Scholar
• Karimi M, Johansson S, Ekström TJ. Using LUMA: a Luminometric-based assay for global DNA-methylation. Epigenetics 2006; 1:45 - 8; http://dx.doi.org/10.4161/epi.1.1.2587; PMID: 17998810
   PubMed Web of Science ®Google Scholar
• Olek A, Oswald J, Walter J. A modified and improved method for bisulphite based cytosine methylation analysis. Nucleic Acids Res 1996; 24:5064 - 6; http://dx.doi.org/10.1093/nar/24.24.5064; PMID: 9016686
   PubMed Web of Science ®Google Scholar
• Xiong Z, Laird PW. COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res 1997; 25:2532 - 4; http://dx.doi.org/10.1093/nar/25.12.2532; PMID: 9171110
   PubMed Web of Science ®Google Scholar
• Herman JG, Graff JR, Myöhänen S, Nelkin BD, Baylin SB. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci U S A 1996; 93:9821 - 6; http://dx.doi.org/10.1073/pnas.93.18.9821; PMID: 8790415
   PubMed Web of Science ®Google Scholar
• Eads CA, Danenberg KD, Kawakami K, Saltz LB, Blake C, Shibata D, et al. MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res 2000; 28:E32; http://dx.doi.org/10.1093/nar/28.8.e32; PMID: 10734209
   PubMed Web of Science ®Google Scholar
• Uhlmann K, Brinckmann A, Toliat MR, Ritter H, Nürnberg P. Evaluation of a potential epigenetic biomarker by quantitative methyl-single nucleotide polymorphism analysis. Electrophoresis 2002; 23:4072 - 9; http://dx.doi.org/10.1002/elps.200290023; PMID: 12481262
   PubMed Web of Science ®Google Scholar
• Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL, et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 2005; 37:853 - 62; http://dx.doi.org/10.1038/ng1598; PMID: 16007088
   PubMed Web of Science ®Google Scholar
• Klagsbrun M. An evolutionary study of the methylation of transfer and ribosomal ribonucleic acid in prokaryote and eukaryote organisms. J Biol Chem 1973; 248:2612 - 20; PMID: 4633356
   PubMed Web of Science ®Google Scholar
• Karijolich J, Kantartzis A, Yu YT. Quantitative analysis of RNA modifications. Methods Mol Biol 2010; 629:21 - 32; http://dx.doi.org/10.1007/978-1-60761-657-3_2; PMID: 20387140
   PubMedGoogle Scholar
• Motorin Y, Lyko F, Helm M. 5-methylcytosine in RNA: detection, enzymatic formation and biological functions. Nucleic Acids Res 2010; 38:1415 - 30; http://dx.doi.org/10.1093/nar/gkp1117; PMID: 20007150
   PubMed Web of Science ®Google Scholar
• Cantara WA, Crain PF, Rozenski J, McCloskey JA, Harris KA, Zhang X, et al. The RNA Modification Database, RNAMDB: 2011 update. Nucleic Acids Res; 39:D195-201.
   Google Scholar
• Butcher LM, Beck S. AutoMeDIP-seq: a high-throughput, whole genome, DNA methylation assay. Methods 2010; 52:223 - 31; http://dx.doi.org/10.1016/j.ymeth.2010.04.003; PMID: 20385236
   PubMed Web of Science ®Google Scholar
• Pfaffl MW. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 2001; 29:e45; http://dx.doi.org/10.1093/nar/29.9.e45; PMID: 11328886
   PubMed Web of Science ®Google Scholar
• Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol 2008; 26:779 - 85; http://dx.doi.org/10.1038/nbt1414; PMID: 18612301
   PubMed Web of Science ®Google Scholar
• Feber A, Wilson GA, Zhang L, Presneau N, Idowu B, Down TA, et al. Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors. Genome Res 2011; 21:515 - 24; http://dx.doi.org/10.1101/gr.109678.110; PMID: 21324880
   PubMed Web of Science ®Google Scholar
• Lasken RS, Egholm M. Whole genome amplification: abundant supplies of DNA from precious samples or clinical specimens. Trends Biotechnol 2003; 21:531 - 5; http://dx.doi.org/10.1016/j.tibtech.2003.09.010; PMID: 14624861
   PubMed Web of Science ®Google Scholar
• Choi YC, Chae CB. DNA hypomethylation and germ cell-specific expression of testis-specific H2B histone gene. J Biol Chem 1991; 266:20504 - 11; PMID: 1718964
   PubMed Web of Science ®Google Scholar
• Choi YC, Gu W, Hecht NB, Feinberg AP, Chae CB. Molecular cloning of mouse somatic and testis-specific H2B histone genes containing a methylated CpG island. DNA Cell Biol 1996; 15:495 - 504; http://dx.doi.org/10.1089/dna.1996.15.495; PMID: 8672246
   PubMed Web of Science ®Google Scholar
• Tremblay KD, Duran KL, Bartolomei MS. A 5′ 2-kilobase-pair region of the imprinted mouse H19 gene exhibits exclusive paternal methylation throughout development. Mol Cell Biol 1997; 17:4322 - 9; PMID: 9234689
   PubMed Web of Science ®Google Scholar
• Weber M, Milligan L, Delalbre A, Antoine E, Brunel C, Cathala G, et al. Extensive tissue-specific variation of allelic methylation in the Igf2 gene during mouse fetal development: relation to expression and imprinting. Mech Dev 2001; 101:133 - 41; http://dx.doi.org/10.1016/S0925-4773(00)00573-6; PMID: 11231066
   PubMed Web of Science ®Google Scholar
• Gao ZH, Suppola S, Liu J, Heikkilä P, Jänne J, Voutilainen R. Association of H19 promoter methylation with the expression of H19 and IGF-II genes in adrenocortical tumors. J Clin Endocrinol Metab 2002; 87:1170 - 6; http://dx.doi.org/10.1210/jc.87.3.1170; PMID: 11889182
   PubMed Web of Science ®Google Scholar
• Li LC, Dahiya R. MethPrimer: designing primers for methylation PCRs. Bioinformatics 2002; 18:1427 - 31; http://dx.doi.org/10.1093/bioinformatics/18.11.1427; PMID: 12424112
   PubMed Web of Science ®Google Scholar
• Rowlatt C, Chesterman FC, Sheriff MU. Lifespan, age changes and tumour incidence in an ageing C57BL mouse colony. Lab Anim 1976; 10:419 - 42; http://dx.doi.org/10.1258/002367776780956917; PMID: 979138
   PubMedGoogle Scholar
• Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 2009; 55:611 - 22; http://dx.doi.org/10.1373/clinchem.2008.112797; PMID: 19246619
   PubMed Web of Science ®Google Scholar
• Jiang M, Zhang Y, Fei J, Chang X, Fan W, Qian X, et al. Rapid quantification of DNA methylation by measuring relative peak heights in direct bisulfite-PCR sequencing traces. Lab Invest 2010; 90:282 - 90; http://dx.doi.org/10.1038/labinvest.2009.132; PMID: 20010852
   PubMed Web of Science ®Google Scholar
• Bock C, Reither S, Mikeska T, Paulsen M, Walter J, Lengauer T. BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics 2005; 21:4067 - 8; http://dx.doi.org/10.1093/bioinformatics/bti652; PMID: 16141249
   PubMed Web of Science ®Google Scholar