Mediators and dynamics of DNA methylation

Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Volumn 3, Issue 3, 2011, Pages 281-298

  Shoemaker, Robert ^a   Wang, Wei ^a   Zhang, Kun ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTIDINE DEAMINASE; DNA; TRANSCRIPTION FACTOR; TUMOR PROTEIN;

ALLELE; ANIMAL; DNA METHYLATION; GENETIC ASSOCIATION; GENETIC EPIGENESIS; GENETICS; HUMAN; METABOLISM; NEOPLASM; REVIEW;

ALLELES; ANIMALS; CYTIDINE DEAMINASE; DNA METHYLATION; DNA, NEOPLASM; EPIGENESIS, GENETIC; GENOME-WIDE ASSOCIATION STUDY; HUMANS; NEOPLASM PROTEINS; NEOPLASMS; TRANSCRIPTION FACTORS;

EUKARYOTA;

EID: 79960338874     PISSN: 19395094     EISSN: 1939005X     Source Type: Journal    
DOI: 10.1002/wsbm.124     Document Type: Review

References (185)

1. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-filippini J, Nery JR, Lee L, Ye Z, Ngo QM, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009, 462:315-322.
2. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 2008, 133:523-536.
3. Cokus SJ. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 2008, 452:215-219.
4. Sasai N, Nakao M, Defossez PA. Sequence-specific recognition of methylated DNA by human zinc-finger proteins. Nucleic Acids Res 2010, 38:5015-5022.
5. Bostick M, Kim JK, Esteve PO, Clark A, Pradhan S, Jacobsen SE. UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science 2007, 317:1760-1764.
6. Johnson LM, Bostick M, Zhang X, Kraft E, Henderson I, Callis J, Jacobsen SE. The SRA methyl-cytosinebinding domain links DNA and histone methylation. Curr Biol 2007, 17:379-384.
7. Filion GJ, Zhenilo S, Salozhin S, Yamada D, Prokhortchouk E, Defossez PA. A family of human zinc finger proteins that bind methylated DNA and repress transcription.Mol Cell Biol 2006, 26:169-181.
8. Daniel JM, Spring CM, Crawford HC, Reynolds AB, Baig A. The p120(ctn)-binding partner Kaiso is a bimodal DNA-binding protein that recognizes both a sequence-specific consensus and methylated CpG dinucleotides. Nucleic Acids Res 2002, 30:2911-2919.
9. Defossez PA, Kelly KF, Filion GJ, Perez-Torrado R, Magdinier F, Menoni H, Nordgaard CL, Daniel JM, Gilson E. The human enhancer blocker CTC-binding factor interacts with the transcription factor Kaiso. J Biol Chem 2005, 280:43017-43023.
10. Margot JB, Ehrenhofer-Murray AE, Leonhardt H. Interactions within the mammalian DNA methyltransferase family. BMC Mol Biol 2003, 4.7.
11. Li E. Chromatin modification and epigenetic reprogramming in mammalian development. Nat Rev Genet 2002, 3:662-673.
12. Lan J, Hua S, He X, Zhang Y. DNA methyltransferases and methyl-binding proteins of mammals. Acta Biochim Biophys Sin (Shanghai) 2010, 42:243-252.
13. Bestor TH. The DNA methyltransferases of mammals. Hum Mol Genet 2000, 9:2395-2402.
14. Goll MG, Kirpekar F, Maggert KA, Yoder JA, Hsieh CL, Zhang X, Golic KG, Jacobsen SE, Bestor TH. Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2. Science 2006, 311:395-398.
15. Liang G, Chan MF, Tomigahara Y, Tsai YC, Gonzales FA, Li E, Laird PW, Jones PA. Cooperativity between DNA methyltransferases in the maintenance methylation of repetitive elements.Mol Cell Biol 2002, 22:480-491.
16. Chen T, Hevi S, Gay F, Tsujimoto N, He T, Zhang B, Ueda Y, Li E. Complete inactivation of DNMT1 leads to mitotic catastrophe in human cancer cells. Nat Genet 2007, 39:391-396.
17. Dong A, Yoder JA, Zhang X, Zhou L, Bestor TH, Cheng X. Structure of human DNMT2, an enigmatic DNA methyltransferase homolog that displays denaturant-resistant binding to DNA. Nucleic Acids Res 2001, 29:439-448.
18. Yoder JA, Bestor TH. A candidate mammalian DNA methyltransferase related to pmt1p of fission yeast. Hum Mol Genet 1998, 7:279-284.
19. Li E, Bestor TH, Jaenisch R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 1992, 69:915-926.
20. Gowher H, Liebert K, Hermann A, Xu G, Jeltsch A. Mechanism of stimulation of catalytic activity of Dnmt3A and Dnmt3B DNA-(cytosine-C5)-methyltransferases by Dnmt3L. J Biol Chem 2005, 280: 13341-13348.
21. Chen ZX, Mann JR, Hsieh CL, Riggs AD, Chedin F. Physical and functional interactions between the human DNMT3L protein and members of the de novo methyltransferase family. J Cell Biochem 2005, 95:902-917.
22. Hata K, Okano M, Lei H, Li E. Dnmt3L cooperates with the Dnmt3 family of de novo DNA methyltransferases to establish maternal imprints in mice. Development 2002, 129:1983-1993.
23. Chedin F, Lieber MR, Hsieh CL. The DNA methyltransferase-like protein DNMT3L stimulates de novo methylation by Dnmt3a. Proc Natl Acad Sci U S A 2002, 99:16916-16921.
24. Holz-Schietinger C, Reich NO. The inherent processivity of the human de novo DNA methyltransferase 3A (DNMT3A) is enhanced by DNMT3L. J Biol Chem 2010.
25. Glass JL, Fazzari MJ, Ferguson-Smith AC, Greally JM. CG dinucleotide periodicities recognized by the Dnmt3a-Dnmt3L complex are distinctive at retroelements and imprinted domains. Mamm Genome 2009, 20:633-643.
26. Jurkowska RZ, Anspach N, Urbanke C, Jia D, Reinhardt R, Nellen W, Cheng X, Jeltsch A. Formation of nucleoprotein filaments by mammalian DNA methyltransferase Dnmt3a in complex with regulator Dnmt3L. Nucleic Acids Res 2008, 36:6656-6663.
27. Feng S, Cokus SJ, Zhang X, Chen PY, Bostick M, Goll MG, Hetzel J, Jain J, Strauss SH, Halpern ME, et al. Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci U S A 2010, 107:8689-8694.
28. Zemach A, McDaniel IE, Silva P, Zilberman D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 2010, 328:916-919.
29. Field LM, Lyko F, Mandrioli M, Prantera G. DNA methylation in insects. Insect Mol Biol 2004, 13:109-115.
30. Gold M, Gefter M, Hausmann R, Hurwitz J. Methylation of DNA. J Gen Physiol 1966, 49:5-28.
31. Doerfler W. Patterns of DNA methylation-evolutionary vestiges of foreign DNA inactivation as a host defense mechanism. A proposal. Biol Chem Hoppe Seyler 1991, 372:557-564.
32. Matzke MA, Mette MF, Aufsatz W, Jakowitsch J, Matzke AJ. Host defenses to parasitic sequences and the evolution of epigenetic controlmechanisms. Genetica 1999, 107:271-287.
33. Wolffe AP, Matzke MA. Epigenetics: regulation through repression. Science 1999, 286:481-486.
34. Zilberman D. The evolving functions of DNA methylation. Curr Opin Plant Biol 2008, 11:554-559.
35. Hughes T, Webb R, Fei Y, Wren JD, Sawalha AH. DNA methylome in human CD4+ T cells identifies transcriptionally repressive and non-repressive methylation peaks. Genes Immun 2010.
36. Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong CT, Low HM, Kin Sung KW, Rigoutsos I, Loring J, et al. Dynamic changes in the human methylome during differentiation. Genome Res 2010, 20:320-331.
37. Xiang H, Zhu J, Chen Q, Dai F, Li X, Li M, Zhang H, Zhang G, Li D, Dong Y, et al. Single base-resolution methylome of the silkworm reveals a sparse epigenomic map. Nat Biotechnol 2010, 28:516-520.
38. Deng J, Shoemaker R, Xie B, Gore A, LeProust EM, Antosiewicz-Bourget J, Egli D, Maherali N, Park IH, Yu J, et al. Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotechnol 2009, 27:353-360.
39. Shoemaker R, Deng J, Wang W, Zhang K. Allelespecific methylation is prevalent and is contributed by CpG-SNPs in the human genome. Genome Res 2010, 20:883-889.
40. Irizarry Ra, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M, et al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nature Genetics 2009, 41:178-186.
41. Doi A, Park I-H, Wen B, Murakami P, Aryee MJ, Irizarry R, Herb B, Ladd-Acosta C, Rho J, Loewer S, et al. Differential methylation of tissue- and cancerspecific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts.Nature Genetics 2009, 41:1350-1353.
42. Figueroa ME, Lugthart S, LiY, Erpelinck-Verschueren C, Deng X, Christos PJ, Schifano E, Booth J, van Putten W, Skrabanek L, et al. DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia. Cancer Cell 2010, 17:13-27.
43. International Agency for Research in Cancer. WHO Classification of Tumours of Haematopoietic and Lymphoid Tissue. 4th ed. Geneva: World Health Organization, 2008, 441.
44. Flanagan JM, Cocciardi S, Waddell N, Johnstone CN, Marsh A, Henderson S, Simpson P, da Silva L, Khanna K, Lakhani S, et al. DNA methylome of familial breast cancer identifies distinct profiles defined by mutation status. American Journal of Human Genetics 2010, 86:420-433.
45. Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A 2001, 98:10869-10874.
46. Teschendorff AE, Menon U, Gentry-Maharaj A, Ramus SJ, Gayther SA, Apostolidou S, Jones A, Lechner M, Beck S, Jacobs IJ, et al. An epigenetic signature in peripheral blood predicts active ovarian cancer. PLoS One 2009, 4.e8274.
47. Grutzmann R, Molnar B, Pilarsky C, Habermann JK, Schlag PM, Saeger HD, Miehlke S, Stolz T, Model F, Roblick UJ, et al. Sensitive detection of colorectal cancer in peripheral blood by septin 9 DNA methylation assay. PLoS One 2008, 3.e3759.
48. deVos T, Tetzner R, Model F, Weiss G, Schuster M, Distler J, Steiger KV, Grutzmann R, Pilarsky C, Habermann JK, et al. Circulating methylated SEPT9 DNA in plasma is a biomarker for colorectal cancer. Clin Chem 2009, 55:1337-1346.
49. Muller HM, Fiegl H, Widschwendter A, Widschwendter M. Prognostic DNA methylation marker in serum of cancer patients. Ann N Y Acad Sci 2004, 1022:44-49.
50. Muller HM, Widschwendter A, Fiegl H, Ivarsson L, Goebel G, Perkmann E, Marth C, Widschwendter M. DNA methylation in serum of breast cancer patients: an independent prognostic marker. Cancer Res 2003, 63:7641-7645.
51. Widschwendter M, Apostolidou S, Raum E, Rothenbacher D, Fiegl H, Menon U, Stegmaier C, Jacobs IJ, Brenner H. Epigenotyping in peripheral blood cell DNA and breast cancer risk: a proof of principle study. PLoS One 2008, 3.e2656.
52. Luedi PP, Dietrich FS, Weidman JR, Bosko JM, Jirtle RL, Hartemink AJ. Computational and experimental identification of novel human imprinted genes. Genome Res 2007, 17:1723-1730.
53. Frost JM, Moore GE. The importance of imprinting in the human placenta. Plos Genet 2010, 6.e1001015.
54. Hudson QJ, Kulinski TM, Huetter SP, Barlow DP. Genomic imprinting mechanisms in embryonic and extraembryonic mouse tissues. Heredity 2010, 105:45-56.
55. Gregg C, Zhang J, Weissbourd B, Luo S, Schroth GP, Haig D, Dulac C. High-resolution analysis of parentof-origin allelic expression in the mouse brain. Science 2010, 329:643-648.
56. Kerkel K, Spadola A, Yuan E, Kosek J, Jiang L, Hod E, Li K, Murty VV, Schupf N, Vilain E. Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation. Nat Genet 2008, 40:904-908.
57. Brown CJ, Ballabio A, Rupert JL, Lafreniere RG, Grompe M, Tonlorenzi R, Willard HF. A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome. Nature 1991, 349:38-44.
58. Brown CJ, Lafreniere RG, Powers VE, Sebastio G, Ballabio A, Pettigrew AL, Ledbetter DH, Levy E,Craig IW, Willard HF. Localization of the X inactivation centre on the human X chromosome in Xq13. Nature 1991, 349:82-84.
59. Chureau C, Prissette M, Bourdet A, Barbe V, Cattolico L, Jones L, EggenA, Avner P, Duret L. Comparative sequence analysis of the X-inactivation center region in mouse, human, and bovine. Genome Res 2002, 12:894-908.
60. Willard HF. X chromosome inactivation, XIST, and pursuit of the X-inactivation center. Cell 1996, 86:5-7.
61. Lee JT, Davidow LS, Warshawsky D. Tsix, a gene antisense to Xist at the X-inactivation centre. Nat Genet 1999, 21:400-404.
62. Lee JT. Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome. Genes & Development 2009, 23:1831-1842.
63. Donohoe ME, Silva SS, Pinter SF, Xu N, Lee JT. The pluripotency factor Oct4 interacts with Ctcf and also controls X-chromosome pairing and counting. Nature 2009, 460:128-132.
64. Anguera MC, Sun BK, Xu N, Lee JT. X-chromosome kiss and tell: how the Xs go their separate ways. Cold Spring Harb Symp Quant Biol 2006, 71:429-437.
65. Xu N, Tsai CL, Lee JT. Transient homologous chromosome pairing marks the onset of X inactivation. Science 2006, 311:1149-1152.
66. Lee JT. Molecular links between X-inactivation and autosomal imprinting: X-inactivation as a driving force for the evolution of imprinting? Curr Biol 2003, 13:R242-254.
67. Xu N, Donohoe ME, Silva SS, Lee JT. Evidence that homologous X-chromosome pairing requires transcription and Ctcf protein. Nat Genet 2007, 39: 1390-1396.
68. Barakat TS, Jonkers I, Monkhorst K, Gribnau J. Xchanging information on X inactivation. Exp Cell Res 2010, 316:679-687.
69. Jonkers I, Barakat TS, Achame EM, Monkhorst K, Kenter A, Rentmeester E, Grosveld F, Grootegoed JA, Gribnau J. RNF12 is an X-Encoded dose-dependent activator of X chromosome inactivation. Cell 2009, 139:999-1011.
70. Sun BK, Deaton AM, Lee JT. A transient heterochromatic state in Xist preempts X inactivation choice without RNA stabilization. Mol Cell 2006, 21: 617-628.
71. Zhao J, Sun BK, Erwin JA, Song JJ, Lee JT. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 2008, 322:750-756.
72. Maenner S, Blaud M, Fouillen L, Savoye A, Marchand V, Dubois A, Sanglier-Cianferani S,x Van Dorsselaer A, Clerc P, Avner P, et al. 2-D structure of the A region of Xist RNA and its implication for PRC2 association. PLoS Biol 2010, 8.e1000276.
73. Wutz A, Rasmussen TP, Jaenisch R. Chromosomal silencing and localization are mediated by different domains of Xist RNA. Nat Genet 2002, 30:167-174.
74. Vire E, Brenner C, Deplus R, Blanchon L, Fraga M, Didelot C, Morey L, Van Eynde A, Bernard D, Vanderwinden JM, et al. The Polycomb group protein EZH2 directly controls DNA methylation. Nature 2006, 439:871-874.
75. Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Curr Biol 2004, 14:1214-1220.
76. Qi Y, He X, Wang XJ, Kohany O, Jurka J, Hannon GJ. Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature 2006, 443:1008-1012.
77. Gao Z, Liu HL,Daxinger L, Pontes O, He X, Qian W, Lin H, Xie M, Lorkovic ZJ, Zhang S, et al. An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature 2010, 465:106-109.
78. He XJ, Hsu YF, Zhu S, Wierzbicki AT, Pontes O, Pikaard CS, Liu HL, Wang CS, Jin H, Zhu JK. An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein. Cell 2009, 137:498-508.
79. Lucifero D, Mertineit C, Clarke HJ, Bestor TH, TraslerJM. Methylation dynamics of imprinted genes in mouse germ cells. Genomics 2002, 79:530-538.
80. Li JY, Lees-Murdock DJ, Xu GL, Walsh CP. Timing of establishment of paternal methylation imprints in the mouse. Genomics 2004, 84:952-960.
81. Davis TL, Trasler JM, Moss SB, Yang GJ, Bartolomei MS. Acquisition of the H19 methylation imprint occurs differentially on the parental alleles during spermatogenesis. Genomics 1999, 58:18-28.
82. Bourc'his D, Proudhon C. Sexual dimorphism in parental imprint ontogeny and contribution to embryonic development. Mol Cell Endocrinol 2008, 282:87-94.
83. Hirasawa R, Chiba H, Kaneda M, Tajima S, Li E, Jaenisch R, Sasaki H. Maternal and zygotic Dnmt1 are necessary and sufficient for the maintenance of DNA methylation imprints during preimplantation development. Genes Dev 2008, 22:1607-1616.
84. Zhao Q, Rank G, Tan YT, Li H, Moritz RL, Simpson RJ, Cerruti L, Curtis DJ, Patel DJ, Allis CD, et al. PRMT5-mediated methylation of histone H4R3 recruits DNMT3A, coupling histone and DNA methylation in gene silencing. Nat Struct Mol Biol 2009, 16:304-311.
85. Jia D, Jurkowska RZ, Zhang X, Jeltsch A, Cheng X. Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature 2007, 449:248-251.
86. Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 2007, 130:77-88.
87. Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 2007, 39:311-318.
88. Koerner MV, Pauler FM, Huang R, Barlow DP. The function of non-coding RNAs in genomic imprinting. Development 2009, 136:1771-1783.
89. Mancini-Dinardo D, Steele SJ, Levorse JM, Ingram RS, Tilghman SM. Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes. Genes Dev 2006, 20:1268-1282.
90. Shin JY, Fitzpatrick GV, Higgins MJ. Two distinct mechanisms of silencing by the KvDMR1 imprinting control region. EMBO J 2008, 27:168-178.
91. Sahoo T, del Gaudio D,German JR, ShinawiM, Peters SU, Person RE, Garnica A, Cheung SW, Beaudet AL. Prader-Willi phenotype caused by paternal deficiency for the HBII-85 C/D box small nucleolar RNA cluster. Nat Genet 2008, 40:719-721.
92. Bastepe M, Pincus JE, Sugimoto T, Tojo K, Kanatani M, Azuma Y, Kruse K, Rosenbloom aL, Koshiyama H, Jüppner H. Positional dissociation between the genetic mutation responsible for pseudohypoparathyroidism type Ib and the associated methylation defect at exon A/B: evidence for a long-range regulatory element within the imprinted GNAS1 locus. Human Molecular Genetics 2001, 10:1231-1241.
93. Lecumberri B, Ferńandez-Rebollo E, Sentchordi L, Saavedra P, Bernal-ChicoA, Pallardo LF, Bustos JMJn, Castaño L, de Santiago M, Hiort O, et al. Coexistence of two different pseudohypoparathyroidism subtypes (Ia and Ib) in the same kindred with independent Gs{alpha} coding mutations and GNAS imprinting defects. Journal of Medical Genetics 2010, 47:276-280.
94. Cerrato F, Sparago A, Verde G, Crescenzo AD, Citro V, Cubellis MV, Rinaldi MM, Boccuto L, Neri G, Magnani C, et al. Differentmechanisms cause imprinting defects at the IGF2/H19 locus in Beckwith-Wiedemann syndrome and Wilms, Äô tumour. Hum. Mol Genet 2008, 17:1427-1435.
95. Skene PJ, Illingworth RS, Webb S, Kerr ARW, James KD, Turner DJ, Andrews R, Bird AP. Neuronal MeCP2 is expressed at near histone-octamer levels and globally alters the chromatin state. Molecular Cell 2010, 37:457-468.
96. Schilling E, El Chartouni C, Rehli M. Allele-specific DNA methylation in mouse strains is mainly determined by cis-acting sequences. Genome Res 2009, 19:2028-2035.
97. Murrell A, Heeson S, Cooper WN, Douglas E, Apostolidou S, Moore GE, Maher ER, Reik W. An association between variants in the IGF2 gene and Beckwith-Wiedemann syndrome: interaction between genotype and epigenotype. Hum Mol Genet 2004, 13:247-255.
98. Flanagan JM, Popendikyte V, Pozdniakovaite N, Sobolev M, Assadzadeh A, Schumacher A, Zangeneh M, Lau L, Virtanen C, Wang SC, et al. Intra- and interindividual epigenetic variation in human germ cells. Am J Hum Genet 2006, 79:67-84.
99. Heijmans BT, Kremer D, Tobi EW, Boomsma DI, Slagboom PE. Heritable rather than age-related environmental and stochastic factors dominate variation in DNA methylation of the human IGF2/H19 locus. Hum Mol Genet 2007, 16:547-554.
100. Schalkwyk LC, Meaburn EL, Smith R, Dempster EL, Jeffries AR, Davies MN, Plomin R, Mill J. Allelic skewing of DNA methylation is widespread across the genome. Am J Hum Genet 2010, 86:196-212.
101. Plagnol V, Uz E, Wallace C, Stevens H, Clayton D, Ozcelik T, Todd JA. Extreme clonality in lymphoblastoid cell lines with implications for allele specific expression analyses. PLoS One 2008, 3.e2966.
102. Choy E, Yelensky R, Bonakdar S, Plenge RM, Saxena R, De Jager PL, Shaw SY, Wolfish CS, Slavik JM, Cotsapas C, et al. Genetic analysis of human traits in vitro: drug response and gene expression in lymphoblastoid cell lines. Plos Genet 2008, 4.e1000287.
103. Lee JH, Park IH, Gao Y, Li JB, Li Z, Daley GQ, Zhang K, Church GM. A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells. Plos Genet 2009, 5.e1000718.
104. Gimelbrant A, Hutchinson JN, Thompson BR, Chess A. Widespread monoallelic expression on human autosomes. Science 2007, 318:1136-1140.
105. Takahashi K, Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 2006, 126:663-676.
106. Yu J, Vodyanik MA, Smuga-Otto K, Antosiewicz-Bourget J, Frane JL, Tian S, Nie J, Jonsdottir GA, Ruotti V, Stewart R, et al. Induced pluripotent stem cell lines derived from human somatic cells. Science 2007, 318:1917-1920.
107. Yu J, Vodyanik MA, He P, Slukvin, II, Thomson JA. Human embryonic stem cells reprogram myeloid precursors following cell-cell fusion. Stem Cells 2006, 24:168-176.
108. Yu J, Hu K, Smuga-Otto K, Tian S, Stewart R, Slukvin, II, Thomson JA. Human induced pluripotent stem cells free of vector and transgene sequences. Science 2009, 324:797-801.
109. Okita K, Ichisaka T, Yamanaka S. Generation of germline-competent induced pluripotent stem cells. Nature 2007, 448:313-317.
110. Banito A, Gil J. Induced pluripotent stem cells and senescence: learning the biology to improve the technology. EMBO Rep 2010, 11:353-359.
111. Kaji K, Norrby K, Paca A, Mileikovsky M, Mohseni P, Woltjen K. Virus-free induction of pluripotency and subsequent excision of reprogramming factors. Nature 2009, 458:771-775.
112. Kawamura T, Suzuki J, Wang YV, Menendez S, Morera LB, Raya A, Wahl GM, Belmonte JC. Linking the p53 tumour suppressor pathway to somatic cell reprogramming. Nature 2009, 460:1140-1144.
113. Woltjen K, Michael IP, Mohseni P, Desai R, Mileikovsky M, Hamalainen R, Cowling R, Wang W, Liu P, Gertsenstein M, et al. piggyBac transposition reprograms fibroblasts to induced pluripotent stem cells. Nature 2009, 458:766-770.
114. Okita K, Nakagawa M, Hyenjong H, Ichisaka T, Yamanaka S. Generation of mouse induced pluripotent stem cells without viral vectors. Science 2008, 322:949-953.
115. Jia F,Wilson KD, Sun N, Gupta DM, Huang M, Li Z, Panetta NJ, Chen ZY, Robbins RC, Kay MA, et al. A nonviral minicircle vector for deriving human iPS cells. Nat Methods 2010, 7:197-199.
116. Longacre A, Storb U. A novel cytidine deaminase affects antibody diversity. Cell 2000, 102:541-544.
117. Muramatsu M, Kinoshita K, Fagarasan S, Yamada S, Shinkai Y, Honjo T. Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme. Cell 2000, 102:553-563.
118. Revy P, Muto T, Levy Y, Geissmann F, Plebani A, Sanal O, Catalan N, Forveille M, Dufourcq-Labelouse R, Gennery A, et al. Activation-induced cytidine deaminase (AID) deficiency causes the autosomal recessive form of the Hyper-IgM syndrome (HIGM2). Cell 2000, 102:565-575.
119. Morgan HD, Dean W, Coker HA, Reik W, Petersen-Mahrt SK. Activation-induced cytidine deaminase deaminates 5-methylcytosine in DNA and is expressed in pluripotent tissues: implications for epigenetic reprogramming. J Biol Chem 2004, 279:52353-52360.
120. Conticello SG, Langlois MA, Yang Z, Neuberger MS. DNA deamination in immunity: AID in the context of its APOBEC relatives. Adv Immunol 2007, 94:37-73.
121. Macduff DA, Harris RS. Directed DNA deamination by AID/APOBEC3 in immunity. Curr Biol 2006, 16:R186-189.
122. Rai K, Huggins IJ, James SR, Karpf AR, Jones DA, Cairns BR. DNA demethylation in zebrafish involves the coupling of a deaminase, a glycosylase, and gadd45. Cell 2008, 135:1201-1212.
123. Hendrich B, Hardeland U, Ng HH, Jiricny J, Bird A. The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites. Nature 1999, 401:301-304.
124. Bhutani N, Brady JJ, Damian M, Sacco A, Corbel SpY, Blau HM. Reprogramming towards pluripotency requires AID-dependent DNA demethylation. Nature 2010, 463:1042-1047.
125. Sasaki H, Matsui Y. Epigenetic events in mammalian germ-cell development: reprogramming and beyond. Nat Rev Genet 2008, 9:129-140.
126. Hajkova P, Ancelin K, Waldmann T, Lacoste N, Lange UC, Cesari F, Lee C, Almouzni G, Schneider R, Surani MA. Chromatin dynamics during epigenetic reprogramming in the mouse germ line. Nature 2008, 452:877-881.
127. Reik W, Dean W, Walter J. Epigenetic reprogramming in mammalian development. Science 2001, 293:1089-1093.
128. Mayer W, Niveleau A, Walter J, Fundele R, Haaf T. Demethylation of the zygotic paternal genome. Nature 2000, 403:501-502.
129. Hajkova P, Erhardt S, Lane N, Haaf T, El-Maarri O, Reik W, Walter J, Surani MA. Epigenetic reprogramming in mouse primordial germ cells. Mech Dev 2002, 117:15-23.
130. Popp C, Dean W, Feng S, Cokus SJ, Andrews S, Pellegrini M, Jacobsen SE, Reik W. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature 2010, 463:1101-1105.
131. Seki Y, Yamaji M, Yabuta Y, Sano M, Shigeta M, Matsui Y, Saga Y, Tachibana M, Shinkai Y, Saitou M. Cellular dynamics associated with the genomewide epigenetic reprogramming in migrating primordial germ cells in mice. Development 2007, 134:2627-2638.
132. Daujat S, Weiss T, Mohn F, Lange UC, Ziegler-Birling C, Zeissler U, Lappe M, Schubeler D, Torres-Padilla ME, Schneider R. H3K64 trimethylation marks heterochromatin and is dynamically remodeled during developmental reprogramming. Nat Struct Mol Biol 2009, 16:777-781.
133. Chuva de Sousa Lopes SM, Hayashi K, Shovlin TC, Mifsud W, Surani MA, McLaren A. X chromosome activity inmouse XXprimordial germcells. Plos Genet 2008, 4.e30.
134. Thomson JP, Skene PJ, Selfridge J, Clouaire T, Guy J, Webb S, Kerr ARW, Deaton Ae, Andrews R, James KD, et al. CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Nature 2010, 464:1082-1086.
135. Lee JH, Tate CM, You JS, Skalnik DG. Identification and characterization of the human Set1B histone H3-Lys4 methyltransferase complex. J Biol Chem 2007, 282:13419-13428.
136. Lee JH, Skalnik DG. CpG-binding protein (CXXC finger protein 1) is a component of the mammalian Set1histone H3-Lys4 methyltransferase complex, the analogue of the yeast Set1/COMPASS complex. J Biol Chem 2005, 280:41725-41731.
137. Xie X,Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M, Lander ES. Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites. Proc Natl Acad Sci U S A 2007, 104:7145-7150.
138. Li T, Hu JF, Qiu X, Ling J, Chen H, Wang S, Hou A, Vu TH, Hoffman AR. CTCF regulates allelic expression of Igf2 by orchestrating a promoter-polycomb repressive complex 2 intrachromosomal loop. Mol Cell Biol 2008, 28:6473-6482.
139. Cuddapah S, Jothi R, Schones DE, Roh TY, Cui K, Zhao K. Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Res 2009, 19:24-32.
140. Gombert WM, Krumm A. Targeted deletion of multiple CTCF-binding elements in the human C-MYC gene reveals a requirement for CTCF in C-MYC expression. PloS One 2009, 4.e6109.
141. Ishihara K, Oshimura M, Nakao M. CTCF-dependent chromatin insulator is linked to epigenetic remodeling. Mol Cell 2006, 23:733-742.
142. Chahrour M, Jung SY, Shaw C, Zhou X, Wong ST, Qin J, Zoghbi HY. MeCP2, a key contributor to neurological disease, activates and represses transcription. Science 2008, 320:1224-1229.
143. Boumber Ya, Kondo Y, Chen X, Shen L, Guo Y, Tellez C, Estécio MRH, Ahmed S, Issa J-PJ. An Sp1/Sp3 binding polymorphism confers methylation protection. Plos Genet 2008, 4:e1000162-e1000162.
144. Brandeis M, Frank D, Keshet I, Siegfried Z, Mendelsohn M, Nemes A, Temper V, Razin A, Cedar H. Sp1 elements protect a CpG island from de novo methylation. Nature 1994, 371:435-438.
145. Ohlsson R, Renkawitz R, Lobanenkov V. CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease. Trends Genet 2001, 17:520-527.
146. Phillips JE, Corces VG. CTCF: master weaver of the genome. Cell 2009, 137:1194-1211.
147. Baniahmad A, Steiner C, Kohne AC, Renkawitz R. Modular structure of a chicken lysozyme silencer: involvement of an unusual thyroid hormone receptor binding site. Cell 1990, 61:505-514.
148. Klenova EM, Nicolas RH, Paterson HF, Carne AF, Heath CM, Goodwin GH, Neiman PE, Lobanenkov VV. CTCF, a conserved nuclear factor required for optimal transcriptional activity of the chicken c-myc gene, is an 11-Zn-finger protein differentially expressed in multiple forms. Mol Cell Biol 1993, 13:7612-7624.
149. Lobanenkov VV, Nicolas RH, Adler VV, Paterson H, Klenova EM, Polotskaja AV, Goodwin GH. A novel sequence-specific DNA binding protein which interacts with three regularly spaced direct repeats of the CCCTC-motif in the 5'-flanking sequence of the chicken c-myc gene. Oncogene 1990, 5:1743-1753.
150. Vostrov AA, Quitschke WW. The zinc finger protein CTCF binds to the APBbeta domain of the amyloid beta-protein precursor promoter. Evidence for a role in transcriptional activation. J Biol Chem 1997, 272:33353-33359.
151. Bell AC, Felsenfeld G. Methylation of a CTCFdependent boundary controls imprinted expression of the Igf2 gene. Nature 2000, 405:482-485.
152. Hark AT, Schoenherr CJ, Katz DJ, Ingram RS, Levorse JM, Tilghman SM. CTCF mediates methylationsensitive enhancer-blocking activity at the H19/Igf2 locus. Nature 2000, 405:486-489.
153. Szabo P, Tang SH, Rentsendorj A, Pfeifer GP, Mann JR. Maternal-specific footprints at putative CTCF sites in the H19 imprinting control region give evidence for insulator function. Curr Biol 2000, 10:607-610.
154. Yoon YS, Jeong S, Rong Q, Park KY, Chung JH, Pfeifer K. Analysis of the H19ICR insulator. Mol Cell Biol 2007, 27:3499-3510.
155. De La Rosa-Velazquez IA, Rincon-Arano H, Benitez-Bribiesca L, Recillas-Targa F. Epigenetic regulation of the human retinoblastoma tumor suppressor gene promoter by CTCF. Cancer Res 2007, 67:2577-2585.
156. Voo KS, Carlone DL, Jacobsen BM, Flodin A, Skalnik DG. Cloning of a mammalian transcriptional activator that binds unmethylated CpG motifs and shares a CXXC domain with DNA methyltransferase, human trithorax, and methyl-CpG binding domain protein 1.Mol Cell Biol 2000, 20:2108-2121.
157. Lee JH, Voo KS, Skalnik DG. Identification and characterization of the DNA binding domain of CpG-binding protein. J Biol Chem 2001, 276:44669-44676.
158. Shi X, Kachirskaia I, Walter KL, Kuo JH, Lake A, Davrazou F, Chan SM, Martin DG, Fingerman IM, Briggs SD, et al. Proteome-wide analysis in Saccharomyces cerevisiae identifies several PHD fingers as novel direct and selective binding modules of histone H3 methylated at either lysine 4 or lysine 36. J Biol Chem 2007, 282:2450-2455.
159. Mikkelsen TS, Hanna J, Zhang X, Ku M, Wernig M, Schorderet P, Bernstein BE, Jaenisch R, Lander ES, Meissner A. Dissecting direct reprogramming through integrative genomic analysis. Nature 2008, 454: 49-55.
160. Meehan RR, Lewis JD, McKay S, Kleiner EL, Bird AP. Identification of a mammalian protein that binds specifically to DNA containing methylated CpGs. Cell 1989, 58:499-507.
161. Nan X, Campoy FJ, Bird A. MeCP2 is a transcriptional repressor with abundant binding sites in genomic chromatin. Cell 1997, 88:471-481.
162. Bogdanovic O, Veenstra GJ. DNA methylation and methyl-CpG binding proteins: developmental requirements and function. Chromosoma 2009, 118: 549-565.
163. Clouaire T, Stancheva I. Methyl-CpG binding proteins: specialized transcriptional repressors or structural components of chromatin? Cell Mol Life Sci 2008, 65:1509-1522.
164. Hendrich B, Tweedie S. The methyl-CpG binding domain and the evolving role of DNA methylation in animals. Trends Genet 2003, 19:269-277.
165. Zhang Y, Ng HH, Erdjument-Bromage H, Tempst P, Bird A, Reinberg D. Analysis of the NuRD subunits reveals a histone deacetylase core complex and a connection with DNA methylation. Genes Dev 1999, 13:1924-1935.
166. Fuks F, Hurd PJ, Wolf D, Nan X, Bird AP, Kouzarides T. The methyl-CpG-binding protein MeCP2 links DNA methylation to histone methylation. J Biol Chem 2003, 278:4035-4040.
167. Nan X, Ng HH, Johnson CA, Laherty CD, Turner BM, Eisenman RN, Bird A. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 1998, 393:386-389.
168. Jones PL, Veenstra GJ, Wade PA, Vermaak D, Kass SU, Landsberger N, Strouboulis J, Wolffe AP. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat Genet 1998, 19:187-191.
169. Balmer D, Goldstine J, Rao YM, LaSalle JM. Elevated methyl-CpG-binding protein 2 expression is acquired during postnatal human brain development and is correlated with alternative polyadenylation. J Mol Med 2003, 81:61-68.
170. Gonzales ML, LaSalle JM. The role of MeCP2 in brain development and neurodevelopmental disorders. Curr Psychiatry Rep 2010, 12:127-134.
171. Guy J, Hendrich B, Holmes M, Martin JE, Bird A. A mouse Mecp2-null mutation causes neurological symptoms that mimic Rett syndrome. NatGenet 2001, 27:322-326.
172. Collins AL, Levenson JM, Vilaythong AP, Richman R, Armstrong DL, Noebels JL, David Sweatt J, Zoghbi HY. Mild overexpression of MeCP2 causes a progressive neurological disorder in mice. Hum Mol Genet 2004, 13:2679-2689.
173. Gebhard C, Benner C, Ehrich M, Schwarzfischer L, Schilling E, Klug M, Dietmaier W, Thiede C, Holler E, Andreesen R, et al. General transcription factor binding at CpG islands in normal cells correlates with resistance to de novo DNA methylation in cancer cells. Cancer Res 2010, 70:1398-1407.
174. Caretti G, Di Padova M, Micales B, Lyons GE, Sartorelli V. The Polycomb Ezh2 methyltransferase regulates muscle gene expression and skeletal muscle differentiation. Genes Dev 2004, 18:2627-2638.
175. Lindroth AM, Park YJ, McLean CM, Dokshin GA, Persson JM, Herman H, Pasini D, Miro X, Donohoe ME, Lee JT, et al. Antagonism between DNA and H3K27 methylation at the imprinted Rasgrf1 locus. Plos Genet 2008, 4.e1000145.
176. Kriaucionis S, Heintz N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science (New York, NY) 2009, 324:929-930.
177. Tahiliani M, Koh KP, Shen Y, Pastor Wa, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu DR, Aravind L, et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science (New York, NY) 2009, 324:930-935.
178. Cliffe LJ, Kieft R, Southern T, Birkeland SR, Marshall M, Sweeney K, Sabatini R. JBP1 and JBP2 are two distinct thymidine hydroxylases involved in J biosynthesis in genomic DNA of African trypanosomes. Nucleic Acids Res 2009, 37:1452-1462.
179. Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL, Schubeler D. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 2005, 37:853-862.
180. Wilson IM, Davies JJ, Weber M, Brown CJ, Alvarez CE, MacAulay C, Schubeler D, Lam WL. Epigenomics: mapping the methylome. Cell Cycle 2006, 5:155-158.
181. Jacinto FV, Ballestar E, Esteller M. Methyl-DNA immunoprecipitation (MeDIP): hunting down the DNA methylome. Biotechniques 2008, 44.35, 37, 39 passim.
182. Fraga MF, Ballestar E, Montoya G, Taysavang P, Wade PA, Esteller M. The affinity of different MBD proteins for a specific methylated locus depends on their intrinsic binding properties. Nucleic Acids Res 2003, 31:1765-1774.
183. Fatemi M, Wade PA. MBD family proteins: reading the epigenetic code. J Cell Sci 2006, 119:3033-3037.
184. Sasai N, Defossez PA. Many paths to one goal? The proteins that recognize methylated DNA in eukaryotes. Int J Dev Biol 2009, 53:323-334.
185. Flusberg BA, Webster DR, Lee JH, Travers KJ, Olivares EC, Clark TA, Korlach J, Turner SW. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods 2010, 7:461-465.