DNA methylation profile: A composer-, conductor-, and player- orchestrated mammalian genome consisting of genes and transposable genetic elements

Journal of Reproduction and Development

Volumn 58, Issue 3, 2012, Pages 265-273

  Yagi, Shintaro ^a   Hirosawa, Mitsuko ^a   Shiota, Kunio ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

CpG island; DNA methylation profile; Methylome; Tissue dependent and differently methylated region (T DMR)

Indexed keywords

ANIMAL; BIOLOGICAL MODEL; BIOLOGY; CPG ISLAND; DNA METHYLATION; DNA SEQUENCE; EPIGENETICS; GENETIC ASSOCIATION; GENETIC TRANSCRIPTION; GENOME; GENOMICS; HUMAN; METHODOLOGY; MOUSE; REVIEW; TRANSPOSON;

ANIMALS; COMPUTATIONAL BIOLOGY; CPG ISLANDS; DNA METHYLATION; DNA TRANSPOSABLE ELEMENTS; EPIGENOMICS; GENOME; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; HUMANS; MICE; MODELS, BIOLOGICAL; MODELS, GENETIC; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION, GENETIC;

EUKARYOTA; MAMMALIA;

EID: 84863835904     PISSN: 09168818     EISSN: 13484400     Source Type: Journal    
DOI: 10.1262/jrd.2011-030     Document Type: Review

References (120)

1. Hattori N, Nishino K, Ko Y-G, Hattori N, Ohgane J, Tanaka S, Shiota K. Epigenetic control of mouse Oct-4 gene expression in embryonic stem cells and trophoblast stem cells. J Biol Chem 2004; 279: 17063-17069. [Medline] [CrossRef]
2. Nishino K, Hattori N, Tanaka S, Shiota K. DNA methylation-mediated control of Sry gene expression in mouse gonadal development. J Biol Chem 2004; 279: 22306-22313. [Medline] [CrossRef]
3. Bird A. DNA methylation patterns and epigenetic memory. Genes Dev 2002; 16: 6-21. [Medline] [CrossRef]
4. Chen T, Li E. Structure and function of eukaryotic DNA methyltransferases. Curr Top Dev Biol 2004; 60: 55-89. [Medline] [CrossRef]
5. Brideau CM, Eilertson KE, Hagarman JA, Bustamante CD, Soloway PD. Successful computational prediction of novel imprinted genes from epigenomic features. Mol Cell Biol 2010; 30: 3357-3370. [Medline] [CrossRef]
6. Yagi S, Hirabayashi K, Sato S, Li W, Takahashi Y, Hirakawa T, Wu G, Hattori N, Hattori N, Ohgane J, Tanaka S, Liu XS, Shiota K. DNA methylation profile of tissuedependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression. Genome Res 2008; 18: 1969-1978. [Medline] [CrossRef]
7. Sato S, Yagi S, Arai Y, Hirabayashi K, Hattori N, Iwatani M, Okita K, Ohgane J, Tanaka S, Wakayama T, Yamanaka S, Shiota K. Genome-wide DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) residing in mouse pluripotent stem cells. Genes Cells 2010; 15: 607-618. [Medline] [CrossRef]
8. Muramoto H, Yagi S, Hirabayashi K, Sato S, Ohgane J, Tanaka S, Shiota K. Enrichment of short interspersed transposable elements to embryonic stem cell-specific hypomethylated gene regions. Genes Cells 2010; 15: 855-865. [Medline]
9. Tan M, Luo H, Lee S, Jin F, Yang JS, Montellier E, Buchou T, Cheng Z, Rousseaux S, Rajagopal N, Lu Z, Ye Z, Zhu Q, Wysocka J, Ye Y, Khochbin S, Ren B, Zhao Y. Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 2011; 146: 1016-1028. [Medline] [CrossRef]
10. Shiota K. DNA methylation profiles of CpG islands for cellular differentiation and development in mammals. Cytogenet Genome Res 2004; 105: 325-334. [Medline] [CrossRef]
11. Ikegami K, Ohgane J, Tanaka S, Yagi S, Shiota K. Interplay between DNA methylation, histone modification and chromatin remodeling in stem cells and during development. Int J Dev Biol 2009; 53: 203-214. [Medline] [CrossRef]
12. Hattori N, Shiota K. Epigenetics: the study of embryonic stem cells by restriction landmark genomic scanning. FEBS J 2008; 275: 1624-1630. [Medline] [CrossRef]
13. Kremenskoy M, Kremenska Y, Ohgane J, Hattori N, Tanaka S, Hashizume K, Shiota K. Genome-wide analysis of DNA methylation status of CpG islands in embryoid bodies, teratomas, and fetuses. Biochem Biophys Res Commun 2003; 311: 884-890. [Medline] [CrossRef]
14. Sakamoto H, Kogo Y, Ohgane J, Hattori N, Yagi S, Tanaka S, Shiota K. Sequential changes in genome-wide DNA methylation status during adipocyte differentiation. Biochem Biophys Res Commun 2008; 366: 360-366. [Medline] [CrossRef]
15. Laird PW. Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet 2010; 11: 191-203. [Medline] [CrossRef]
16. Gu H, Smith ZD, Bock C, Boyle P, Gnirke A, Meissner A. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat Protoc 2011; 6: 468-481. [Medline] [CrossRef]
17. Schones DE, Zhao K. Genome-wide approaches to studying chromatin modifications. Nat Rev Genet 2008; 9: 179-191. [Medline] [CrossRef]
18. Lister R, Ecker JR. Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Res 2009; 19: 959-966. [Medline] [CrossRef]
19. Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol 2010; 28: 1097-1105. [Medline] [CrossRef]
20. Khulan B, Thompson RF, Ye K, Fazzari MJ, Suzuki M, Stasiek E, Figueroa ME, Glass JL, Chen Q, Montagna C, Hatchwell E, Selzer RR, Richmond TA, Green RD, Melnick A, Greally JM. Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res 2006; 16: 1046-1055. [Medline] [CrossRef]
21. Suzuki M, Jing Q, Lia D, Pascual M, McLellan A, Greally JM. Optimized design and data analysis of tag-based cytosine methylation assays. Genome Biol 2010; 11: R36. [Medline] [CrossRef]
22. Hatada I, Morita S, Kimura M, Horii T, Yamashita R, Nakai K. Genome-wide demethylation during neural differentiation of P19 embryonal carcinoma cells. J Hum Genet 2008; 53: 185-191. [Medline] [CrossRef]
23. Sved J, Bird A. The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model. Proc Natl Acad Sci USA 1990; 87: 4692-4696. [Medline] [CrossRef]
24. Krokan HE, Nilsen H, Skorpen F, Otterlei M, Slupphaug G. Base excision repair of DNA in mammalian cells. FEBS Lett 2000; 476: 73-77. [Medline] [CrossRef]
25. Bird A, Taggart M, Frommer M, Miller OJ, Macleod D. A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Cell 1985; 40: 91-99. [Medline] [CrossRef]
26. 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 USA 2006; 103: 1412-1417. [Medline] [CrossRef]
27. Fazzari MJ, Greally JM. Epigenomics: beyond CpG islands. Nat Rev Genet 2004; 5: 446-455. [Medline] [CrossRef]
28. Schrem H, Klempnauer J, Borlak J. Liver-enriched transcription factors in liver function and development. Part II: the C/EBPs and D site-binding protein in cell cycle control, carcinogenesis, circadian gene regulation, liver regeneration, apoptosis, and liver-specific gene regulation. Pharmacol Rev 2004; 56: 291-330. [Medline] [CrossRef]
29. Imai S, Kikuchi R, Kusuhara H, Yagi S, Shiota K, Sugiyama Y. Analysis of DNA methylation and histone modification profiles of liver-specific transporters. Mol Pharmacol 2009; 75: 568-576. [Medline] [CrossRef]
30. Kikuchi R, Yagi S, Kusuhara H, Imai S, Sugiyama Y, Shiota K. Genome-wide analysis of epigenetic signatures for kidney-specific transporters. Kidney Int 2010; 78: 569-577. [Medline] [CrossRef]
31. Odom DT, Zizlsperger N, Gordon DB, Bell GW, Rinaldi NJ, Murray HL, Volkert TL, Schreiber J, Rolfe PA, Gifford DK, Fraenkel E, Bell GI, Young RA. Control of pancreas and liver gene expression by HNF transcription factors. Science 2004; 303: 1378-1381. [Medline] [CrossRef]
32. Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, Loh YH, Yeo HC, Yeo ZX, Narang V, Govindarajan KR, Leong B, Shahab A, Ruan Y, Bourque G, Sung WK, Clarke ND, Wei CL, Ng HH. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008; 133: 1106-1117. [Medline] [CrossRef]
33. Yang J, Chai L, Fowles TC, Alipio Z, Xu D, Fink LM, Ward DC, Ma Y. Genomewide analysis reveals Sall4 to be a major regulator of pluripotency in murine-embryonic stem cells. Proc Natl Acad Sci USA 2008; 105: 19756-19761. [Medline] [CrossRef]
34. Lim CY, Tam W-L, Zhang J, Ang HS, Jia H, Lipovich L, Ng H-H, Wei C-L, Sung WK, Robson P, Yang H, Lim B. Sall4 regulates distinct transcription circuitries in different blastocyst-derived stem cell lineages. Cell Stem Cell 2008; 3: 543-554. [Medline] [CrossRef]
35. Larsen F, Gundersen G, Lopez R, Prydz H. Cpg islands as gene markers in the human genome. Genomics 1992; 13: 1095-1107. [Medline] [CrossRef]
36. Meléndez B, Malumbres M, Perez de Castro I, Santos J, Pellicer A, Fernandez-Piqueras J. Characterization of the murine p19(ARF) promoter CpG island and its methylation pattern in primary lymphomas. Carcinogenesis 2000; 21: 817-821. [Medline] [CrossRef]
37. Constância M, Pickard B, Kelsey G, Reik W. Imprinting mechanisms. Genome Res 1998; 8: 881-900. [Medline]
38. Jones PA. DNA methylation and cancer. Oncogene 2002; 21: 5358-5360. [Medline] [CrossRef]
39. Thompson RF, Atzmon G, Gheorghe C, Liang HQ, Lowes C, Greally JM, Barzilai N. Tissue-specific dysregulation of DNA methylation in aging. Aging Cell 2010; 9: 506-518. [Medline] [CrossRef]
40. Suzuki M, Sato S, Arai Y, Shinohara T, Tanaka S, Greally JM, Hattori N, Shiota K. A new class of tissue-specifically methylated regions involving entire CpG islands in the mouse. Genes Cells 2007; 12: 1305-1314. [Medline] [CrossRef]
41. Shen L, Kondo Y, Guo Y, Zhang J, Zhang L, Ahmed S, Shu J, Chen X, Waterland RA, Issa JP. G enome-wide p rofiling of D NA m ethylation r eveals a class of n ormally methylated CpG island promoters. PLoS Genet 2007; 3: e181. [Medline] [CrossRef]
42. Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, Rebhan M, Schubeler D. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 2007; 39: 457-466. [Medline] [CrossRef]
43. Imamura T, Miyauchi-Senda N, Tanaka S, Shiota K. Identification of genetic and epigenetic similarities of SPHK1/Sphk1 in mammals. J Vet Med Sci 2004; 66: 1387-1393. [Medline] [CrossRef]
44. Takasugi M, Yagi S, Hirabayashi K, Shiota K. DNA methylation status of nuclearencoded mitochondrial genes underlies the tissue-dependent mitochondrial functions. BMC Genomics 2010; 11: 481. [Medline] [CrossRef]
45. Irizarry RA, Ladd-Acosta C, Carvalho B, Wu H, Brandenburg SA, Wen B, Feinberg AP. Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res 2008; 18: 780-790. [Medline] [CrossRef]
46. Fouse SD, Shen Y, Pellegrini M, Cole S, Meissner A, Van Neste L, Jaenisch R, Fan G. Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and Histone H3 K4/K27 trimethylation. Cell Stem Cell 2008; 2: 160-169. [Medline] [CrossRef]
47. Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB, Gnirke A, Jaenisch R, Lander ES. Genomescale DNA methylation maps of pluripotent and differentiated cells. Nature 2008; 454: 766-770. [Medline]
48. Schilling E, Rehli M. Global, comparative analysis of tissue-specific promoter CpG methylation. Genomics 2007; 90: 314-323. [Medline] [CrossRef]
49. Kano H, Godoy I, Courtney C, Vetter MR, Gerton GL, Ostertag EM, Kazazian HH Jr. L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism. Genes Dev 2009; 23: 1303-1312. [Medline] [CrossRef]
50. Coufal NG, Garcia-Perez JL, Peng GE, Yeo GW, Mu Y, Lovci MT, Morell M, O'shea KS, Moran JV, Gage FH. L1 retrotransposition in human neural progenitor cells. Nature 2009; 460: 1127-1131. [Medline] [CrossRef]
51. Muotri AR, Zhao C, Marchetto MC, Gage FH. Environmental influence on L1 retrotransposons in the adult hippocampus. Hippocampus 2009; 19: 1002-1007. [Medline] [CrossRef]
52. Belancio VP, Roy-Engel AM, Pochampally RR, Deininger P. Somatic expression of LINE-1 elements in human tissues. Nucleic Acids Res 2010; 38: 3909-3922. [Medline] [CrossRef]
53. Baillie JK, Barnett MW, Upton KR, Gerhardt DJ, Richmond TA, De Sapio F, Brennan P, Rizzu P, Smith S, Fell M, Talbot RT, Gustincich S, Freeman TC, Mattick JS, Hume DA, Heutink P, Carninci P, Jeddeloh JA, Faulkner GJ. Somatic retrotransposition alters the genetic landscape of the human brain. Nature 2011; 479: 534-537. [Medline]
54. Consortium MGS. Initial sequencing and comparative analysis of the mouse genome. Nature 2002; 420: 520-562. [Medline] [CrossRef]
55. Greally JM. Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome. Proc Natl Acad Sci USA 2002; 99: 327-332. [Medline] [CrossRef]
56. Aravin AA, Bourc'his D. Small RNA guides for de novo DNA methylation in mammalian germ cells. Genes Dev 2008; 22: 970-975. [Medline] [CrossRef]
57. Aravin AA, Sachidanandam R, Bourc'his D, Schaefer C, Pezic D, Toth KF, Bestor T, Hannon GJ. A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol Cell 2008; 31: 785-799. [Medline] [CrossRef]
58. Siomi MC, Sato K, Pezic D, Aravin AA. PIWI-interacting small RNAs: the vanguard of genome defence. Nat Rev Mol Cell Biol 2011; 12: 246-258. [Medline] [CrossRef]
59. Michaud EJ, van Vugt MJ, Bultman SJ, Sweet HO, Davisson MT, Woychik RP. Differential expression of a new dominant agouti allele (Aiapy) is correlated with methylation state and is influenced by parental lineage. Genes Dev 1994; 8: 1463-1472. [Medline] [CrossRef]
60. Suzuki S, Ono R, Narita T, Pask AJ, Shaw G, Wang CS, Kohda T, Alsop AE, Graves JAM, Kohara Y, Ishino F, Renfree MB, Kaneko-Ishino T. Retrotransposon silencing by DNA methylation can drive mammalian genomic imprinting. PLoS Genet 2007; 3: e55. [Medline] [CrossRef]
61. Locke DP, Hillier L, Warren W, Worley K, Nazareth L, Muzny D, Yang S, Wang Z, Chinwalla A, Minx P. Comparative and demographic analysis of orang-utan genomes. Nature 2011; 469: 529-533. [Medline] [CrossRef]
62. Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang DL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SMJ, Sharpe T, et al. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 2007; 447: 167-177. [Medline] [CrossRef]
63. Pask AJ, Papenfuss AT, Ager EI, McColl KA, Speed TP, Renfree MB. Analysis of the platypus genome suggests a transposon origin for mammalian imprinting. Genome Biol 2009; 10: R1. [Medline] [CrossRef]
64. Hayakawa K, Nakanishi MO, Ohgane J, Tanaka S, Hirosawa M, Soares MJ, Yagi S, Shiota K. Bridging sequence diversity and tissue-specific expression by DNA methylation in genes of the mouse prolactin superfamily. Mamm Genome 2012; in press. [Medline]
65. Martin DI, Singer M, Dhahbi J, Mao G, Zhang L, Schroth G, Pachter L, Boffelli D. Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states. Genome Res 2011; 21: 2049-2057. [Medline] [CrossRef]
66. Molaro A, Hodges E, Fang F, Song Q, McCombie WR, Hannon GJ, Smith AD. Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates. Cell 2011; 146: 1029-1041. [Medline] [CrossRef]
67. 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. [Medline]
68. Chedin F, Lieber MR, Hsieh CL. The DNA methyltransferase-like protein DNMT3L stimulates de novo methylation by Dnmt3a. Proc Natl Acad Sci USA 2002; 99: 16916-16921. [Medline] [CrossRef]
69. Hattori N, Abe T, Hattori N, Suzuki M, Matsuyama T, Yoshida S, Li E, Shiota K. Preference of DNA methyltransferases for CpG islands in mouse embryonic stem cells. Genome Res 2004; 14: 1733-1740. [Medline] [CrossRef]
70. Gowher H, Jeltsch A. Enzymatic properties of recombinant Dnmt3a DNA methyltransferase from mouse: the enzyme modifies DNA in a non-processive manner and also methylates non-CpG [correction of non-CpA] sites. J Mol Biol 2001; 309: 1201-1208. [Medline] [CrossRef]
71. Lin IG, Han L, Taghva A, O'Brien LE, Hsieh C-L. Murine de novo methyltransferase Dnmt3a demonstrates strand asymmetry and site preference in the methylation of DNA in vitro. Mol Cell Biol 2002; 22: 704-723. [Medline] [CrossRef]
72. Lim HW, Iwatani M, Hattori N, Tanaka S, Yagi S, Shiota K. Resistance to 5-aza-2'-deoxycytidine in genic regions compared to non-genic repetitive sequences. J Reprod Dev 2010; 56: 86-93. [Medline] [CrossRef]
73. Okano M, Bell DW, Haber DA, Li E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 1999; 99: 247-257. [Medline] [CrossRef]
74. La Salle S, Mertineit C, Taketo T, Moens PB, Bestor TH, Trasler JM. Windows for sex-specific methylation marked by DNA methyltransferase expression profiles in mouse germ cells. Dev Biol 2004; 268: 403-415. [Medline] [CrossRef]
75. Iwatani M, Ikegami K, Kremenska Y, Hattori N, Tanaka S, Yagi S, Shiota K. Dimethyl sulfoxide has an impact on epigenetic profile in mouse embryoid body. Stem Cells 2006; 24: 2549-2556. [Medline] [CrossRef]
76. Rodríguez-Paredes M, Esteller M. Cancer epigenetics reaches mainstream oncology. Nat Med 2011; 17: 330-339. [Medline] [CrossRef]
77. Chuang LS, Ian HI, Koh TW, Ng H-H, Xu G, Li BF. Human DNA-(cytosine-5) methyltransferase-PCNA complex as a target for p21WAF1. Science (New York, NY) 1997; 277: 1996-2000. [Medline] [CrossRef]
78. Iida T, Suetake I, Tajima S, Morioka H, Ohta S, Obuse C, Tsurimoto T. PCNA clamp facilitates action of DNA cytosine methyltransferase 1 on hemimethylated DNA. Genes Cells 2002; 7: 997-1007. [Medline] [CrossRef]
79. Kimura H, Shiota K. Methyl-CpG-binding protein, MeCP2, is a target molecule for maintenance DNA methyltransferase, Dnmt1. J Biol Chem 2003; 278: 4806-4812. [Medline] [CrossRef]
80. Tatematsu KI, Yamazaki T, Ishikawa F. MBD2-MBD3 complex binds to hemimethylated DNA and forms a complex containing DNMT1 at the replication foci in late S phase. Genes Cells 2000; 5: 677-688. [Medline] [CrossRef]
81. 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. [Medline] [CrossRef]
82. 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. [Medline] [CrossRef]
83. Sharif J, Muto M, Takebayashi S, Suetake I, Iwamatsu A, Endo TA, Shinga J, Mizutani-Koseki Y, Toyoda T, Okamura K, Tajima S, Mitsuya K, Okano M, Koseki H. The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. Nature 2007; 450: 908-912. [Medline] [CrossRef]
84. Meilinger D, Fellinger K, Bultmann S, Rothbauer U, Bonapace IM, Klinkert WE, Spada F, Leonhardt H. Np95 interacts with de novo DNA methyltransferases, Dnmt3a and Dnmt3b, and mediates epigenetic silencing of the viral CMV promoter in embryonic stem cells. EMBO Rep 2009; 10: 1259-1264. [Medline] [CrossRef]
85. 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. Mol Cell 2010; 37: 457-468. [Medline] [CrossRef]
86. Hendrich B, Bird A. Identification and characterization of a family of mammalian methyl-CpG binding proteins. Mol Cell Biol 1998; 18: 6538-6547. [Medline]
87. Ono R, Taki T, Taketani T, Taniwaki M, Kobayashi H, Hayashi Y. LCX, leukemia-associated protein with a CXXC domain, is fused to MLL in acute myeloid leukemia with trilineage dysplasia having t(10;11)(q22;q23). Cancer Res 2002; 62: 4075-4080. [Medline]
88. Bestor TH. The DNA methyltransferases of mammals. Hum Mol Genet 2000; 9: 2395-2402. [Medline] [CrossRef]
89. Carlone DL, Skalnik DG. CpG binding protein is crucial for early embryonic development. Mol Cell Biol 2001; 21: 7601-7606. [Medline] [CrossRef]
90. Carlone DL, Lee J-H, Young SRL, Dobrota E, Butler JS, Ruiz J, Skalnik DG. Reduced genomic cytosine methylation and defective cellular differentiation in embryonic stem cells lacking CpG binding protein. Mol Cell Biol 2005; 25: 4881-4891. [Medline] [CrossRef]
91. Butler JS, Palam LR, Tate CM, Sanford JR, Wek RC, Skalnik DG. DNA Methyltransferase protein synthesis is reduced in CXXC finger protein 1-deficient embryonic stem cells. DNA Cell Biol 2009; 28: 223-231. [Medline] [CrossRef]
92. Tate CM, Lee JH, Skalnik DG. CXXC finger protein 1 restricts the Setd1A histone H3K4 methyltransferase complex to euchromatin. FEBS J 2010; 277: 210-223. [Medline] [CrossRef]
93. Thomson JP, Skene PJ, Selfridge J, Clouaire T, Guy J, Webb S, Kerr ARW, Deaton A, Andrews R, James KD, Turner DJ, Illingworth R, Bird A. CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Nature 2010; 464: 1082-1086. [Medline] [CrossRef]
94. Butler JS, Lee JH, Skalnik DG. C FP1 i nteracts w ith DNMT1 i ndependently of a ssociation with the Setd1 Histone H3K4 methyltransferase complexes. DNA Cell Biol 2008; 27: 533-543. [Medline] [CrossRef]
95. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, et al. The transcriptional landscape of the mammalian genome. Science 2005; 309: 1559-1563. [Medline] [CrossRef]
96. Birney E, Stamatoyannopoulos JA, Dutta A, Guig R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Stamatoyannopoulos JA, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007; 447: 799-816. [Medline] [CrossRef]
97. Lee JT, Davidow LS, Warshawsky D. Tsix, a gene antisense to Xist at the X-inactivation centre. Nat Genet 1999; 21: 400-404. [Medline] [CrossRef]
98. Rinn JL, Kertesz M, Wang J, Squazzo S, Xu X, Brugmann S, Goodnough L, Helms J, Farnham P, Segal E. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 2007; 129: 1311-1323. [Medline] [Cross-Ref]
99. Mohammad F, Pandey RR, Nagano T, Chakalova L, Mondal T, Fraser P, Kanduri C. Kcnq1ot1/Lit1 noncoding RNA mediates transcriptional silencing by targeting to the perinucleolar region. Mol Cell Biol 2008; 28: 3713-3728. [Medline] [CrossRef]
100. Pandey RR, Mondal T, Mohammad F, Enroth S, Redrup L, Komorowski J, Nagano T, Mancinidinardo D, Kanduri C. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell 2008; 32: 232-246. [Medline] [CrossRef]
101. Bertani S, Sauer S, Bolotin E, Sauer F. The noncoding RNA mistral activates Hoxa6 and Hoxa7 expression and stem cell differentiation by recruiting MLL1 to chromatin. Mol Cell 2011; 43: 1040-1046. [Medline] [CrossRef]
102. Nagano T, Fraser P. No-nonsense functions for long noncoding RNAs. Cell 2011; 145: 178-181. [Medline] [CrossRef]
103. Katayama S, Tomaru Y, Kasukawa T, Waki1 K, Nakanishi1 M, Nakamura1 M, Nishida1 H, Yap CC, Suzuki1 M, Kawai1 J, Suzuki1 H, Carninci1 P, Hayashizaki Y, Wells C, Frith M, et al. Antisense transcription in the mammalian transcriptome. Science 2005; 309: 1564-1566. [Medline] [CrossRef]
104. Imamura T, Yamamoto S, Ohgane J, Hattori N, Tanaka S, Shiota K. Non-coding RNA directed DNA demethylation of Sphk1 CpG island. Biochem Biophys Res Commun 2004; 322: 593-600. [Medline] [CrossRef]
105. Jones PA, Taylor SM. Hemimethylated duplex DNAs prepared f rom 5-azacytidinetreated cells. Nucleic Acids Res 1981; 9: 2933-2947. [Medline] [CrossRef]
106. Reik W, Dean W, Walter J. Epigenetic reprogramming in mammalian development. Science 2001; 293: 1089-1093. [Medline] [CrossRef]
107. Bhutani N, Burns DM, Blau HM. DNA demethylation dynamics. Cell 2011; 146: 866-872. [Medline] [CrossRef]
108. Wu H, D'Alessio A, Ito S, Xia K, Wang Z, Cui K, Zhao K, Sun Y, Zhang Y. Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells. Nature 2011; 473: 389-393. [Medline] [CrossRef]
109. Williams K, Christensen J, Pedersen MT, Johansen JV, Cloos PAC, Rappsilber J, Helin K. TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 2011; 473: 343-348. [Medline] [CrossRef]
110. Ko Y-G, Nishino K, Hattori N, Arai Y, Tanaka S, Shiota K. Stage-by-stage change in DNA methylation status of Dnmt1 locus during mouse early development. J Biol Chem 2005; 280: 9627-9634. [Medline] [CrossRef]
111. Waddington CH. The Epigenetics of Birds. Cambridge: University Press; 1952.
112. Ohgane J, Wakayama T, Kogo Y, Senda S, Hattori N, Tanaka S, Yanagimachi R, Shiota K. DNA methylation variation in cloned mice. Genesis 2001; 30: 45-50. [Medline] [CrossRef]
113. Chang G, Liu S, Wang F, Zhang Y, Kou Z, Chen D, Gao S. Differential methylation status of imprinted genes in nuclear transfer derived ES (NT-ES) cells. Genomics 2009; 93: 112-119. [Medline] [CrossRef]
114. Senda S, Wakayama T, Yamazaki Y, Ohgane J, Hattori N, Tanaka S, Yanagimachi R, Shiota K. Skewed X-inactivation in cloned mice. Biochem Biophys Res Commun 2004; 321: 38-44. [Medline] [CrossRef]
115. Kremenskoy M, Kremenska Y, Suzuki M, Imai K, Takahashi S, Hashizume K, Yagi S, Shiota K. DNA methylation profiles of donor nuclei cells and tissues of cloned bovine fetuses. J Reprod Dev 2006; 52: 259-266. [Medline] [CrossRef]
116. Doi A, Park IH, Wen B, Murakami P, Aryee MJ, Irizarry R, Herb B, Ladd-Acosta C, Rho J, Loewer S, Miller J, Schlaeger T, Daley GQ, Feinberg AP. Differential methylation of tissue-and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat Genet 2009; 41: 1350-1353. [Medline] [CrossRef]
117. Ji H, Ehrlich LIR, Seita J, Murakami P, Doi A, Lindau P, Lee H, Aryee MJ, Irizarry RA, Kim K, Rossi DJ, Inlay MA, Serwold T, Karsunky H, Ho L, Daley GQ, Weissman IL, Feinberg AP. Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature 2010; 467: 338-342. [Medline] [CrossRef]
118. Humpherys D, Eggan K, Akutsu H, Hochedlinger K, Rideout WM 3rd, Biniszkiewicz D, Yanagimachi R, Jaenisch R. Epigenetic instability in ES cells and cloned mice. Science 2001; 293: 95-97. [Medline] [CrossRef]
119. Shiota K, Yanagimachi R. Epigenetics by DNA methylation for development of normal and cloned animals. Differentiation 2002; 69: 162-166. [Medline] [CrossRef]
120. Okita K, Yamanaka S. Induction of pluripotency by defined factors. Exp Cell Res 2010; 316: 2565-2570. [Medline] [CrossRef]