Experimental approaches to the study of epigenomic dysregulation in ageing

Experimental Gerontology

Volumn 45, Issue 4, 2010, Pages 255-268

  Thompson, Reid F ^a   Fazzari, Melissa J ^a   Greally, John M ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

Aging; Chromatin; DNA methylation; Epigenetic; Microarray

Indexed keywords

ADENOSINE TRIPHOSPHATE; BISULFITE; HISTONE; METHYL CPG BINDING PROTEIN;

AGING; CELL AGING; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN IMMUNOPRECIPITATION; DNA BINDING; DNA METHYLATION; EPIGENETICS; EXPERIMENTAL STUDY; GENE MUTATION; GENETIC ANALYSIS; GENETIC REGULATION; GENETIC VARIABILITY; HUMAN; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN PROCESSING; SHORT SURVEY; TWO DIMENSIONAL GEL ELECTROPHORESIS;

AGING; AMINO ACID SEQUENCE; ANIMALS; DNA METHYLATION; EPIGENESIS, GENETIC; HISTONES; HUMANS; MOLECULAR SEQUENCE DATA; MUTATION;

EID: 77649337965     PISSN: 05315565     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.exger.2009.12.013     Document Type: Short Survey

References (225)

1. Agarwal N., Hardt T., Brero A., Nowak D., Rothbauer U., Becker A., Leonhardt H., and Cardoso M.C. MeCP2 interacts with HP1 and modulates its heterochromatin association during myogenic differentiation. Nucleic Acids Res. 35 (2007) 5402-5408
2. Akintola A.D., Crislip Z.L., Catania J.M., Chen G., Zimmer W.E., Burghardt R.C., and Parrish A.R. Promoter methylation is associated with the age-dependent loss of N-cadherin in the rat kidney. Am. J. Physiol. Renal. Physiol. 294 (2008) F170-F176
3. Amir R.E., Van den Veyver I.B., Wan M., Tran C.Q., Francke U., and Zoghbi H.Y. Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2. Nat. Genet. 23 (1999) 185-188
4. Ammerpohl O., Martin-Subero J.I., Richter J., Vater I., and Siebert R. Hunting for the 5th base: Techniques for analyzing DNA-methylation. Biochim. Biophys. Acta. 1790 (2009) 847-862
5. Anderson J.D., Lowary P.T., and Widom J. Effects of histone acetylation on the equilibrium accessibility of nucleosomal DNA target sites. J. Mol. Biol. 307 (2001) 977-985
6. Ball M.P., Li J.B., Gao Y., Lee J.H., LeProust E.M., Park I.H., Xie B., Daley G.Q., and Church G.M. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat. Biotechnol. 27 (2009) 361-368
7. Barboro P., D'Arrigo C., Mormino M., Coradeghini R., Parodi S., Patrone E., and Balbi C. An intranuclear frame for chromatin compartmentalization and higher-order folding. J. Cell. Biochem. 88 (2003) 113-120
8. Barr H., Hermann A., Berger J., Tsai H.H., Adie K., Prokhortchouk A., Hendrich B., and Bird A. Mbd2 contributes to DNA methylation-directed repression of the Xist gene. Mol. Cell. Biol. 27 (2007) 3750-3757
9. Barski A., Cuddapah S., Cui K., Roh T.Y., Schones D.E., Wang Z., Wei G., Chepelev I., and Zhao K. High-resolution profiling of histone methylations in the human genome. Cell 129 (2007) 823-837
10. Bell A.C., and Felsenfeld G. Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature 405 (2000) 482-485
11. Berdyshev G.D., Korotaev G.K., Boiarskikh G.V., and Vaniushin B.F. Nucleotide composition of DNA and RNA from somatic tissues of humpback and its changes during spawning. Biokhimiia 32 (1967) 988-993
12. Bernstein B.E., Humphrey E.L., Erlich R.L., Schneider R., Bouman P., Liu J.S., Kouzarides T., and Schreiber S.L. Methylation of histone H3 Lys 4 in coding regions of active genes. Proc. Natl. Acad. Sci. USA 99 (2002) 8695-8700
13. Bernstein B.E., Mikkelsen T.S., Xie X., Kamal M., Huebert D.J., Cuff J., Fry B., Meissner A., Wernig M., Plath K., Jaenisch R., Wagschal A., Feil R., Schreiber S.L., and Lander E.S. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125 (2006) 315-326
14. Bibikova M., and Fan J.B. GoldenGate assay for DNA methylation profiling. Methods Mol. Biol. 507 (2009) 149-163
15. Bibikova M., Lin Z., Zhou L., Chudin E., Garcia E.W., Wu B., Doucet D., Thomas N.J., Wang Y., Vollmer E., Goldmann T., Seifart C., Jiang W., Barker D.L., Chee M.S., Floros J., and Fan J.B. High-throughput DNA methylation profiling using universal bead arrays. Genome Res. 16 (2006) 383-393
16. Bird A.P. CpG-rich islands and the function of DNA methylation. Nature 321 (1986) 209-213
17. Bjornsson H.T., Sigurdsson M.I., Fallin M.D., Irizarry R.A., Aspelund T., Cui H., Yu W., Rongione M.A., Ekstrom T.J., Harris T.B., Launer L.J., Eiriksdottir G., Leppert M.F., Sapienza C., Gudnason V., and Feinberg A.P. Intra-individual change over time in DNA methylation with familial clustering. JAMA 299 (2008) 2877-2883
18. Boeger H., Griesenbeck J., Strattan J.S., and Kornberg R.D. Removal of promoter nucleosomes by disassembly rather than sliding in vivo. Mol. Cell 14 (2004) 667-673
19. Bollati V., Schwartz J., Wright R., Litonjua A., Tarantini L., Suh H., Sparrow D., Vokonas P., and Baccarelli A. Decline in genomic DNA methylation through aging in a cohort of elderly subjects. Mech. Ageing Dev. 130 (2009) 234-239
20. Boyes J., and Bird A. Repression of genes by DNA methylation depends on CpG density and promoter strength: evidence for involvement of a methyl-CpG binding protein. EMBO J. 11 (1992) 327-333
21. Brena R.M., Auer H., Kornacker K., Hackanson B., Raval A., Byrd J.C., and Plass C. Accurate quantification of DNA methylation using combined bisulfite restriction analysis coupled with the Agilent 2100 Bioanalyzer platform. Nucleic Acids Res. 34 (2006) e17
22. Bruno M., Flaus A., Stockdale C., Rencurel C., Ferreira H., and Owen-Hughes T. Histone H2A/H2B dimer exchange by ATP-dependent chromatin remodeling activities. Mol. Cell 12 (2003) 1599-1606
23. Burns L.G., and Peterson C.L. The yeast SWI-SNF complex facilitates binding of a transcriptional activator to nucleosomal sites in vivo. Mol. Cell. Biol. 17 (1997) 4811-4819
24. Butler J.S., Palam L.R., Tate C.M., Sanford J.R., Wek R.C., and Skalnik D.G. DNA Methyltransferase protein synthesis is reduced in CXXC finger protein 1-deficient embryonic stem cells. DNA Cell Biol. 28 (2009) 223-231
25. Cairns B.R. Chromatin remodeling: insights and intrigue from single-molecule studies. Nat. Struct. Mol. Biol. 14 (2007) 989-996
26. Calvanese V., Lara E., Kahn A., and Fraga M.F. The role of epigenetics in aging and age-related diseases. Ageing Res. Rev. 8 (2009) 268-276
27. Carrozza M.J., Li B., Florens L., Suganuma T., Swanson S.K., Lee K.K., Shia W.J., Anderson S., Yates J., Washburn M.P., and Workman J.L. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123 (2005) 581-592
28. Chen T., Ueda Y., Xie S., and Li E. A novel Dnmt3a isoform produced from an alternative promoter localizes to euchromatin and its expression correlates with active de novo methylation. J. Biol. Chem. 277 (2002) 38746-38754
29. Chen C.M., Chen H.L., Hsiau T.H., Hsiau A.H., Shi H., Brock G.J., Wei S.H., Caldwell C.W., Yan P.S., and Huang T.H. Methylation target array for rapid analysis of CpG island hypermethylation in multiple tissue genomes. Am. J. Pathol. 163 (2003) 37-45
30. Cheung V.G., Conlin L.K., Weber T.M., Arcaro M., Jen K.Y., Morley M., and Spielman R.S. Natural variation in human gene expression assessed in lymphoblastoid cells. Nat. Genet. 33 (2003) 422-425
31. Choi J.K., Grimes D.E., Rowe K.M., and Howe L.J. Acetylation of Rsc4p by Gcn5p is essential in the absence of histone H3 acetylation. Mol. Cell. Biol. 28 (2008) 6967-6972
32. Clark S.J., Harrison J., Paul C.L., and Frommer M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res. 22 (1994) 2990-2997
33. Clements A., Poux A.N., Lo W.S., Pillus L., Berger S.L., and Marmorstein R. Structural basis for histone and phosphohistone binding by the GCN5 histone acetyltransferase. Mol. Cell 12 (2003) 461-473
34. Cote J., Quinn J., Workman J.L., and Peterson C.L. Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex. Science 265 (1994) 53-60
35. Crawford G.E., Davis S., Scacheri P.C., Renaud G., Halawi M.J., Erdos M.R., Green R., Meltzer P.S., Wolfsberg T.G., and Collins F.S. DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat. Methods 3 (2006) 503-509
36. Crawford G.E., Holt I.E., Whittle J., Webb B.D., Tai D., Davis S., Margulies E.H., Chen Y., Bernat J.A., Ginsburg D., Zhou D., Luo S., Vasicek T.J., Daly M.J., Wolfsberg T.G., and Collins F.S. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res. 16 (2006) 123-131
37. Dacwag C.S., Ohkawa Y., Pal S., Sif S., and Imbalzano A.N. The protein arginine methyltransferase Prmt5 is required for myogenesis because it facilitates ATP-dependent chromatin remodeling. Mol. Cell. Biol. 27 (2007) 384-394
38. Dacwag C.S., Bedford M.T., Sif S., and Imbalzano A.N. Distinct protein arginine methyltransferases promote ATP-dependent chromatin remodeling function at different stages of skeletal muscle differentiation. Mol. Cell. Biol. 29 (2009) 1909-1921
39. Dekker J., Rippe K., Dekker M., and Kleckner N. Capturing chromosome conformation. Science 295 (2002) 1306-1311
40. DeLange R.J., Hooper J.A., and Smith E.L. Complete amino-acid sequence of calf-thymus histone 3. Proc. Natl. Acad. Sci. USA 69 (1972) 882-884
41. Dikow N., Nygren A.O., Schouten J.P., Hartmann C., Kramer N., Janssen B., and Zschocke J. Quantification of the methylation status of the PWS/AS imprinted region: comparison of two approaches based on bisulfite sequencing and methylation-sensitive MLPA. Mol. Cell. Probes. 21 (2007) 208-215
42. DiRenzo J., Shang Y., Phelan M., Sif S., Myers M., Kingston R., and Brown M. BRG-1 is recruited to estrogen-responsive promoters and cooperates with factors involved in histone acetylation. Mol. Cell. Biol. 20 (2000) 7541-7549
43. Dorigo B., Schalch T., Kulangara A., Duda S., Schroeder R.R., and Richmond T.J. Nucleosome arrays reveal the two-start organization of the chromatin fiber. Science 306 (2004) 1571-1573
44. Dostie J., Richmond T.A., Arnaout R.A., Selzer R.R., Lee W.L., Honan T.A., Rubio E.D., Krumm A., Lamb J., Nusbaum C., Green R.D., and Dekker J. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 16 (2006) 1299-1309
45. Down T.A., Rakyan V.K., Turner D.J., Flicek P., Li H., Kulesha E., Graf S., Johnson N., Herrero J., Tomazou E.M., Thorne N.P., Backdahl L., Herberth M., Howe K.L., Jackson D.K., Miretti M.M., Marioni J.C., Birney E., Hubbard T.J., Durbin R., Tavare S., and Beck S. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat. Biotechnol. 26 (2008) 779-785
46. Dupont J.M., Tost J., Jammes H., and Gut I.G. De novo quantitative bisulfite sequencing using the pyrosequencing technology. Anal. Biochem. 333 (2004) 119-127
47. Eads C.A., Danenberg K.D., Kawakami K., Saltz L.B., Blake C., Shibata D., Danenberg P.V., and Laird P.W. MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res. 28 (2000) E32
48. Ehrich M., Nelson M.R., Stanssens P., Zabeau M., Liloglou T., Xinarianos G., Cantor C.R., Field J.K., and van den Boom D. Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc. Natl. Acad. Sci. USA 102 (2005) 15785-15790
49. Esteve P.O., Chin H.G., Benner J., Feehery G.R., Samaranayake M., Horwitz G.A., Jacobsen S.E., and Pradhan S. Regulation of DNMT1 stability through SET7-mediated lysine methylation in mammalian cells. Proc. Natl. Acad. Sci. USA 106 (2009) 5076-5081
50. Fabbrizio E., El Messaoudi S., Polanowska J., Paul C., Cook J.R., Lee J.H., Negre V., Rousset M., Pestka S., Le Cam A., and Sardet C. Negative regulation of transcription by the type II arginine methyltransferase PRMT5. EMBO Rep. 3 (2002) 641-645
51. Fairweather D.S., Fox M., and Margison G.P. The in vitro lifespan of MRC-5 cells is shortened by 5-azacytidine-induced demethylation. Exp. Cell Res. 168 (1987) 153-159
52. Feng Q., and Zhang Y. The MeCP1 complex represses transcription through preferential binding, remodeling, and deacetylating methylated nucleosomes. Genes Dev. 15 (2001) 827-832
53. Filion G.J., Zhenilo S., Salozhin S., Yamada D., Prokhortchouk E., and Defossez P.A. A family of human zinc finger proteins that bind methylated DNA and repress transcription. Mol. Cell Biol. 26 (2006) 169-181
54. Fischle W., Wang Y., Jacobs S.A., Kim Y., Allis C.D., and Khorasanizadeh S. Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. Genes Dev. 17 (2003) 1870-1881
55. Fischle W., Tseng B.S., Dormann H.L., Ueberheide B.M., Garcia B.A., Shabanowitz J., Hunt D.F., Funabiki H., and Allis C.D. Regulation of HP1-chromatin binding by histone H3 methylation and phosphorylation. Nature 438 (2005) 1116-1122
56. Fraga M.F., Ballestar E., Paz M.F., Ropero S., Setien F., Ballestar M.L., Heine-Suner D., Cigudosa J.C., Urioste M., Benitez J., Boix-Chornet M., Sanchez-Aguilera A., Ling C., Carlsson E., Poulsen P., Vaag A., Stephan Z., Spector T.D., Wu Y.Z., Plass C., and Esteller M. Epigenetic differences arise during the lifetime of monozygotic twins. Proc. Natl. Acad. Sci. USA 102 (2005) 10604-10609
57. Frigola J., Ribas M., Risques R.A., and Peinado M.A. Methylome profiling of cancer cells by amplification of inter-methylated sites (AIMS). Nucleic Acids Res. 30 (2002) e28
58. Friso S., Choi S.W., Dolnikowski G.G., and Selhub J. A method to assess genomic DNA methylation using high-performance liquid chromatography/electrospray ionization mass spectrometry. Anal. Chem. 74 (2002) 4526-4531
59. Frommer M., McDonald L.E., Millar D.S., Collis C.M., Watt F., Grigg G.W., Molloy P.L., and Paul C.L. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl. Acad. Sci. USA 89 (1992) 1827-1831
60. Fujita N., Shimotake N., Ohki I., Chiba T., Saya H., Shirakawa M., and Nakao M. Mechanism of transcriptional regulation by methyl-CpG binding protein MBD1. Mol. Cell Biol. 20 (2000) 5107-5118
61. Fujita N., Watanabe S., Ichimura T., Tsuruzoe S., Shinkai Y., Tachibana M., Chiba T., and Nakao M. Methyl-CpG binding domain 1 (MBD1) interacts with the Suv39h1-HP1 heterochromatic complex for DNA methylation-based transcriptional repression. J. Biol. Chem. 278 (2003) 24132-24138
62. Fuke C., Shimabukuro M., Petronis A., Sugimoto J., Oda T., Miura K., Miyazaki T., Ogura C., Okazaki Y., and Jinno Y. Age related changes in 5-methylcytosine content in human peripheral leukocytes and placentas: an HPLC-based study. Ann. Hum. Genet. 68 (2004) 196-204
63. Fuks F., Hurd P.J., Wolf D., Nan X., Bird A.P., and Kouzarides T. The methyl-CpG-binding protein MeCP2 links DNA methylation to histone methylation. J. Biol. Chem. 278 (2003) 4035-4040
64. Fuks F., Hurd P.J., Deplus R., and Kouzarides T. The DNA methyltransferases associate with HP1 and the SUV39H1 histone methyltransferase. Nucleic Acids Res. 31 (2003) 2305-2312
65. Galetzka D., Tralau T., Stein R., and Haaf T. Expression of DNMT3A transcripts and nucleolar localization of DNMT3A protein in human testicular and fibroblast cells suggest a role for de novo DNA methylation in nucleolar inactivation. J. Cell. Biochem. 98 (2006) 885-894
66. Garcia B.A., Pesavento J.J., Mizzen C.A., and Kelleher N.L. Pervasive combinatorial modification of histone H3 in human cells. Nat. Methods 4 (2007) 487-489
67. Gartner K. A third component causing random variability beside environment and genotype. A reason for the limited success of a 30 year long effort to standardize laboratory animals?. Lab. Anim. 24 (1990) 71-77
68. Geng F., and Laurent B.C. Roles of SWI/SNF and HATs throughout the dynamic transcription of a yeast glucose-repressible gene. EMBO J. 23 (2004) 127-137
69. Giresi P.G., Kim J., McDaniell R.M., Iyer V.R., and Lieb J.D. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res. 17 (2007) 877-885
70. Gissot M., Choi S.W., Thompson R.F., Greally J.M., and Kim K. Toxoplasma gondii and Cryptosporidium parvum lack detectable DNA cytosine methylation. Eukaryot. Cell 7 (2008) 537-540
71. Goldmark J.P., Fazzio T.G., Estep P.W., Church G.M., and Tsukiyama T. The Isw2 chromatin remodeling complex represses early meiotic genes upon recruitment by Ume6p. Cell 103 (2000) 423-433
72. Gonzalgo M.L., and Jones P.A. Quantitative methylation analysis using methylation-sensitive single-nucleotide primer extension (Ms-SNuPE). Methods 27 (2002) 128-133
73. Gopalakrishnan S., Sullivan B.A., Trazzi S., Della Valle G., and Robertson K.D. DNMT3B interacts with constitutive centromere protein CENP-C to modulate DNA methylation and the histone code at centromeric regions. Hum. Mol. Genet. 18 (2009) 3178-3193
74. Gurland B.J., Page W.F., and Plassman B.L. A twin study of the genetic contribution to age-related functional impairment. J. Gerontol. A Biol. Sci. Med. Sci. 59 (2004) 859-863
75. Guschin D., Wade P.A., Kikyo N., and Wolffe A.P. ATP-Dependent histone octamer mobilization and histone deacetylation mediated by the Mi-2 chromatin remodeling complex. Biochemistry 39 (2000) 5238-5245
76. Hamiche A., Sandaltzopoulos R., Gdula D.A., and Wu C. ATP-dependent histone octamer sliding mediated by the chromatin remodeling complex NURF. Cell 97 (1999) 833-842
77. Hark A.T., Schoenherr C.J., Katz D.J., Ingram R.S., Levorse J.M., and Tilghman S.M. CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus. Nature 405 (2000) 486-489
78. Hassan A.H., Neely K.E., Vignali M., Reese J.C., and Workman J.L. Promoter targeting of chromatin-modifying complexes. Front. Biosci. 6 (2001) D1054-D1064
79. Hata K., Okano M., Lei H., and Li E. Dnmt3L cooperates with the Dnmt3 family of de novo DNA methyltransferases to establish maternal imprints in mice. Development 129 (2002) 1983-1993
80. Hayakawa T., Haraguchi T., Masumoto H., and Hiraoka Y. Cell cycle behavior of human HP1 subtypes: distinct molecular domains of HP1 are required for their centromeric localization during interphase and metaphase. J. Cell Sci. 116 (2003) 3327-3338
81. Hayatsu H. Bisulfite modification of nucleic acids and their constituents. Prog. Nucleic Acid Res. Mol. Biol. 16 (1976) 75-124
82. Hebbes T.R., Thorne A.W., and Crane-Robinson C. A direct link between core histone acetylation and transcriptionally active chromatin. EMBO J. 7 (1988) 1395-1402
83. Heijmans B.T., Tobi E.W., Stein A.D., Putter H., Blauw G.J., Susser E.S., Slagboom P.E., and Lumey L.H. Persistent epigenetic differences associated with prenatal exposure to famine in humans. Proc. Natl. Acad. Sci. USA 105 (2008) 17046-17049
84. Hendrich B., and Bird A. Identification and characterization of a family of mammalian methyl-CpG binding proteins. Mol. Cell. Biol. 18 (1998) 6538-6547
85. Hendrich B., Guy J., Ramsahoye B., Wilson V.A., and Bird A. Closely related proteins MBD2 and MBD3 play distinctive but interacting roles in mouse development. Genes Dev. 15 (2001) 710-723
86. Herman J.G., Graff J.R., Myohanen S., Nelkin B.D., and Baylin S.B. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc. Natl. Acad. Sci. USA 93 (1996) 9821-9826
87. Hermann A., Goyal R., and Jeltsch A. The Dnmt1 DNA-(cytosine-C5)-methyltransferase methylates DNA processively with high preference for hemimethylated target sites. J. Biol. Chem. 279 (2004) 48350-48359
88. Hinshelwood R.A., Melki J.R., Huschtscha L.I., Paul C., Song J.Z., Stirzaker C., Reddel R.R., and Clark S.J. Aberrant de novo methylation of the p16INK4A CpG island is initiated post gene silencing in association with chromatin remodeling and mimics nucleosome positioning. Hum. Mol. Genet. 18 (2009) 3098-3109
89. Holstege F.C., Jennings E.G., Wyrick J.J., Lee T.I., Hengartner C.J., Green M.R., Golub T.R., Lander E.S., and Young R.A. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95 (1998) 717-728
90. Howard B.H. Replicative senescence: considerations relating to the stability of heterochromatin domains. Exp. Gerontol. 31 (1996) 281-293
91. Huang T.H., Perry M.R., and Laux D.E. Methylation profiling of CpG islands in human breast cancer cells. Hum. Mol. Genet. 8 (1999) 459-470
92. Ibrahim A.E., Thorne N.P., Baird K., Barbosa-Morais N.L., Tavare S., Collins V.P., Wyllie A.H., Arends M.J., and Brenton J.D. MMASS: an optimized array-based method for assessing CpG island methylation. Nucleic Acids Res. 34 (2006) e136
93. Imbalzano A.N., Kwon H., Green M.R., and Kingston R.E. Facilitated binding of TATA-binding protein to nucleosomal DNA. Nature 370 (1994) 481-485
94. Impey S., McCorkle S.R., Cha-Molstad H., Dwyer J.M., Yochum G.S., Boss J.M., McWeeney S., Dunn J.J., Mandel G., and Goodman R.H. Defining the CREB regulon: a genome-wide analysis of transcription factor regulatory regions. Cell 119 (2004) 1041-1054
95. Irizarry R.A., Ladd-Acosta C., Carvalho B., Wu H., Brandenburg S.A., Jeddeloh J.A., Wen B., and Feinberg A.P. Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res. 18 (2008) 780-790
96. Ito T., Bulger M., Pazin M.J., Kobayashi R., and Kadonaga J.T. ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor. Cell 90 (1997) 145-155
97. Jacinto, F.V., Ballestar, E., Esteller, M., 2008. Methyl-DNA immunoprecipitation (MeDIP): hunting down the DNA methylome. Biotechniques 44, 35, 37, 39 passim
98. Jeddeloh J.A., Greally J.M., and Rando O.J. Reduced-representation methylation mapping. Genome Biol. 9 (2008) 231
99. Jeppesen P., and Turner B.M. The inactive X chromosome in female mammals is distinguished by a lack of histone H4 acetylation, a cytogenetic marker for gene expression. Cell 74 (1993) 281-289
100. Jia D., Jurkowska R.Z., Zhang X., Jeltsch A., and Cheng X. Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature 449 (2007) 248-251
101. Jiang M.H., Fei J., Lan M.S., Lu Z.P., Liu M., Fan W.W., Gao X., and Lu D.R. Hypermethylation of hepatic Gck promoter in ageing rats contributes to diabetogenic potential. Diabetologia 51 (2008) 1525-1533
102. Johnson D.S., Mortazavi A., Myers R.M., and Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science 316 (2007) 1497-1502
103. Jones P.L., Veenstra G.J., Wade P.A., Vermaak D., Kass S.U., Landsberger N., Strouboulis J., and Wolffe A.P. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat. Genet. 19 (1998) 187-191
104. Jorgensen H.F., and Bird A. MeCP2 and other methyl-CpG binding proteins. Ment. Retard. Dev. Disabil. Res. Rev. 8 (2002) 87-93
105. Jorgensen H.F., Ben-Porath I., and Bird A.P. Mbd1 is recruited to both methylated and nonmethylated CpGs via distinct DNA binding domains. Mol. Cell Biol. 24 (2004) 3387-3395
106. Joshi A.A., and Struhl K. Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to Pol II elongation. Mol. Cell 20 (2005) 971-978
107. Kaminsky Z.A., Tang T., Wang S.C., Ptak C., Oh G.H., Wong A.H., Feldcamp L.A., Virtanen C., Halfvarson J., Tysk C., McRae A.F., Visscher P.M., Montgomery G.W., Gottesman I.I., Martin N.G., and Petronis A. DNA methylation profiles in monozygotic and dizygotic twins. Nat. Genet. 41 (2009) 240-245
108. Kanduri C., Whitehead J., and Mohammad F. The long and the short of it: RNA-directed chromatin asymmetry in mammalian X-chromosome inactivation. FEBS Lett. 583 (2009) 857-864
109. Karasik D., Hannan M.T., Cupples L.A., Felson D.T., and Kiel D.P. Genetic contribution to biological aging: the Framingham Study. J. Gerontol. A Biol. Sci. Med. Sci. 59 (2004) 218-226
110. Karimi M., Johansson S., and Ekstrom T.J. Using LUMA: a Luminometric-based assay for global DNA-methylation. Epigenetics 1 (2006) 45-48
111. Karimi M., Johansson S., Stach D., Corcoran M., Grander D., Schalling M., Bakalkin G., Lyko F., Larsson C., and Ekstrom T.J. LUMA (LUminometric Methylation Assay)-a high throughput method to the analysis of genomic DNA methylation. Exp. Cell Res. 312 (2006) 1989-1995
112. Kawai J., Hirotsune S., Hirose K., Fushiki S., Watanabe S., and Hayashizaki Y. Methylation profiles of genomic DNA of mouse developmental brain detected by restriction landmark genomic scanning (RLGS) method. Nucleic Acids Res. 21 (1993) 5604-5608
113. Kerjean A., Vieillefond A., Thiounn N., Sibony M., Jeanpierre M., and Jouannet P. Bisulfite genomic sequencing of microdissected cells. Nucleic Acids Res. 29 (2001) E106-E116
114. Khulan B., Thompson R.F., Ye K., Fazzari M.J., Suzuki M., Stasiek E., Figueroa M.E., Glass J.L., Chen Q., Montagna C., Hatchwell E., Selzer R.R., Richmond T.A., Green R.D., Melnick A., and Greally J.M. Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res. 16 (2006) 1046-1055
115. Kim S.K., Jang H.R., Kim J.H., Kim M., Noh S.M., Song K.S., Kang G.H., Kim H.J., Kim S.Y., Yoo H.S., and Kim Y.S. CpG methylation in exon 1 of transcription factor 4 increases with age in normal gastric mucosa and is associated with gene silencing in intestinal-type gastric cancers. Carcinogenesis 29 (2008) 1623-1631
116. Kim E.K., Kang J.Y., Rho Y.H., Kim Y.S., Kim D.S., and Bae Y.S. Silencing of the CKII alpha and CKII alpha' genes during cellular senescence is mediated by DNA methylation. Gene 431 (2009) 55-60
117. Klose R.J., and Bird A.P. MeCP2 behaves as an elongated monomer that does not stably associate with the Sin3a chromatin remodeling complex. J. Biol. Chem. 279 (2004) 46490-46496
118. Kouzarides T. Chromatin modifications and their function. Cell 128 (2007) 693-705
119. Krebs J.E., Fry C.J., Samuels M.L., and Peterson C.L. Global role for chromatin remodeling enzymes in mitotic gene expression. Cell 102 (2000) 587-598
120. Kundu S., Horn P.J., and Peterson C.L. SWI/SNF is required for transcriptional memory at the yeast GAL gene cluster. Genes Dev. 21 (2007) 997-1004
121. Lachner M., O'Carroll D., Rea S., Mechtler K., and Jenuwein T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410 (2001) 116-120
122. Laird C.D., Pleasant N.D., Clark A.D., Sneeden J.L., Hassan K.M., Manley N.C., Vary Jr. J.C., Morgan T., Hansen R.S., and Stoger R. Hairpin-bisulfite PCR: assessing epigenetic methylation patterns on complementary strands of individual DNA molecules. Proc. Natl. Acad. Sci. USA 101 (2004) 204-209
123. Lanctot C., Cheutin T., Cremer M., Cavalli G., and Cremer T. Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nat. Rev. Genet. 8 (2007) 104-115
124. Langst G., Bonte E.J., Corona D.F., and Becker P.B. Nucleosome movement by CHRAC and ISWI without disruption or trans-displacement of the histone octamer. Cell 97 (1999) 843-852
125. Le Guezennec X., Vermeulen M., Brinkman A.B., Hoeijmakers W.A., Cohen A., Lasonder E., and Stunnenberg H.G. MBD2/NuRD and MBD3/NuRD, two distinct complexes with different biochemical and functional properties. Mol. Cell. Biol. 26 (2006) 843-851
126. Lehnertz B., Ueda Y., Derijck A.A., Braunschweig U., Perez-Burgos L., Kubicek S., Chen T., Li E., Jenuwein T., and Peters A.H. Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr. Biol. 13 (2003) 1192-1200
127. Lemon B., Inouye C., King D.S., and Tjian R. Selectivity of chromatin-remodelling cofactors for ligand-activated transcription. Nature 414 (2001) 924-928
128. Lippman Z., Gendrel A.V., Colot V., and Martienssen R. Profiling DNA methylation patterns using genomic tiling microarrays. Nat. Methods 2 (2005) 219-224
129. Liu C.L., Kaplan T., Kim M., Buratowski S., Schreiber S.L., Friedman N., and Rando O.J. Single-nucleosome mapping of histone modifications in S. Cerevisiae. PLoS Biol. 3 (2005) e328
130. Lopez-Serra L., Ballestar E., Fraga M.F., Alaminos M., Setien F., and Esteller M. A profile of methyl-CpG binding domain protein occupancy of hypermethylated promoter CpG islands of tumor suppressor genes in human cancer. Cancer Res. 66 (2006) 8342-8346
131. Lopez-Serra L., Ballestar E., Ropero S., Setien F., Billard L.M., Fraga M.F., Lopez-Nieva P., Alaminos M., Guerrero D., Dante R., and Esteller M. Unmasking of epigenetically silenced candidate tumor suppressor genes by removal of methyl-CpG-binding domain proteins. Oncogene 27 (2008) 3556-3566
132. Lorch Y., Zhang M., and Kornberg R.D. Histone octamer transfer by a chromatin-remodeling complex. Cell 96 (1999) 389-392
133. Lorch Y., Maier-Davis B., and Kornberg R.D. Chromatin remodeling by nucleosome disassembly in vitro. Proc. Natl. Acad. Sci. USA 103 (2006) 3090-3093
134. Luger K., Mader A.W., Richmond R.K., Sargent D.F., and Richmond T.J. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389 (1997) 251-260
135. Lujambio A., Ropero S., Ballestar E., Fraga M.F., Cerrato C., Setien F., Casado S., Suarez-Gauthier A., Sanchez-Cespedes M., Git A., Spiteri I., Das P.P., Caldas C., Miska E., and Esteller M. Genetic unmasking of an epigenetically silenced microRNA in human cancer cells. Cancer Res. 67 (2007) 1424-1429
136. Maeda T., Guan J.Z., Oyama J.I., Higuchi Y., and Makino N. Aging-associated alteration of subtelomeric methylation in Parkinson's disease. J. Gerontol. A Biol. Sci. Med. Sci. 64 (2009) 949-955
137. Meissner A., Mikkelsen T.S., Gu H., Wernig M., Hanna J., Sivachenko A., Zhang X., Bernstein B.E., Nusbaum C., Jaffe D.B., Gnirke A., Jaenisch R., and Lander E.S. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454 (2008) 766-770
138. Melnikov A.A., Gartenhaus R.B., Levenson A.S., Motchoulskaia N.A., and Levenson Chernokhvostov V.V. MSRE-PCR for analysis of gene-specific DNA methylation. Nucleic Acids Res. 33 (2005) e93
139. Metivier R., Penot G., Hubner M.R., Reid G., Brand H., Kos M., and Gannon F. Estrogen receptor-alpha directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell 115 (2003) 751-763
140. Mikkelsen T.S., Ku M., Jaffe D.B., Issac B., Lieberman E., Giannoukos G., Alvarez P., Brockman W., Kim T.K., Koche R.P., Lee W., Mendenhall E., O'Donovan A., Presser A., Russ C., Xie X., Meissner A., Wernig M., Jaenisch R., Nusbaum C., Lander E.S., and Bernstein B.E. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448 (2007) 553-560
141. Mizuguchi G., Shen X., Landry J., Wu W.H., Sen S., and Wu C. ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science 303 (2004) 343-348
142. Mozziconacci J., and Victor J.M. Nucleosome gaping supports a functional structure for the 30nm chromatin fiber. J. Struct. Biol. 143 (2003) 72-76
143. Nagano T., Mitchell J.A., Sanz L.A., Pauler F.M., Ferguson-Smith A.C., Feil R., and Fraser P. The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 322 (2008) 1717-1720
144. Nan X., Campoy F.J., and Bird A. MeCP2 is a transcriptional repressor with abundant binding sites in genomic chromatin. Cell 88 (1997) 471-481
145. Nan X., Ng H.H., Johnson C.A., Laherty C.D., Turner B.M., Eisenman R.N., and Bird A. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393 (1998) 386-389
146. Narlikar G.J., Fan H.Y., and Kingston R.E. Cooperation between complexes that regulate chromatin structure and transcription. Cell 108 (2002) 475-487
147. Neely K.E., Hassan A.H., Wallberg A.E., Steger D.J., Cairns B.R., Wright A.P., and Workman J.L. Activation domain-mediated targeting of the SWI/SNF complex to promoters stimulates transcription from nucleosome arrays. Mol. Cell 4 (1999) 649-655
148. Nelson C.J., Santos-Rosa H., and Kouzarides T. Proline isomerization of histone H3 regulates lysine methylation and gene expression. Cell 126 (2006) 905-916
149. Nimura K., Ishida C., Koriyama H., Hata K., Yamanaka S., Li E., Ura K., and Kaneda Y. Dnmt3a2 targets endogenous Dnmt3L to ES cell chromatin and induces regional DNA methylation. Genes Cells 11 (2006) 1225-1237
150. Noll M., and Kornberg R.D. Action of micrococcal nuclease on chromatin and the location of histone H1. J. Mol. Biol. 109 (1977) 393-404
151. Oakes C.C., Smiraglia D.J., Plass C., Trasler J.M., and Robaire B. Aging results in hypermethylation of ribosomal DNA in sperm and liver of male rats. Proc. Natl. Acad. Sci. USA 100 (2003) 1775-1780
152. Okano M., Xie S., and Li E. Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases. Nat. Genet. 19 (1998) 219-220
153. Okano M., Bell D.W., Haber D.A., and Li E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99 (1999) 247-257
154. Olins A.L., and Olins D.E. Spheroid chromatin units (v bodies). Science 183 (1974) 330-332
155. Ooi S.K., Qiu C., Bernstein E., Li K., Jia D., Yang Z., Erdjument-Bromage H., Tempst P., Lin S.P., Allis C.D., Cheng X., and Bestor T.H. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448 (2007) 714-717
156. Ordway J.M., Budiman M.A., Korshunova Y., Maloney R.K., Bedell J.A., Citek R.W., Bacher B., Peterson S., Rohlfing T., Hall J., Brown R., Lakey N., Doerge R.W., Martienssen R.A., Leon J., McPherson J.D., and Jeddeloh J.A. Identification of novel high-frequency DNA methylation changes in breast cancer. PLoS ONE 2 (2007) e1314
157. Orlando V., and Paro R. Mapping Polycomb-repressed domains in the bithorax complex using in vivo formaldehyde cross-linked chromatin. Cell 75 (1993) 1187-1198
158. Oudet P., Gross-Bellard M., and Chambon P. Electron microscopic and biochemical evidence that chromatin structure is a repeating unit. Cell 4 (1975) 281-300
159. Owen-Hughes T., Utley R.T., Cote J., Peterson C.L., and Workman J.L. Persistent site-specific remodeling of a nucleosome array by transient action of the SWI/SNF complex. Science 273 (1996) 513-516
160. Papamichos-Chronakis M., Krebs J.E., and Peterson C.L. Interplay between Ino80 and Swr1 chromatin remodeling enzymes regulates cell cycle checkpoint adaptation in response to DNA damage. Genes Dev. 20 (2006) 2437-2449
161. Pfister S., Schlaeger C., Mendrzyk F., Wittmann A., Benner A., Kulozik A., Scheurlen W., Radlwimmer B., and Lichter P. Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma. Nucleic Acids Res. 35 (2007) e51
162. Pokholok D.K., Harbison C.T., Levine S., Cole M., Hannett N.M., Lee T.I., Bell G.W., Walker K., Rolfe P.A., Herbolsheimer E., Zeitlinger J., Lewitter F., Gifford D.K., and Young R.A. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122 (2005) 517-527
163. Pollard K.J., and Peterson C.L. Role for ADA/GCN5 products in antagonizing chromatin-mediated transcriptional repression. Mol. Cell. Biol. 17 (1997) 6212-6222
164. Pomraning K.R., Smith K.M., and Freitag M. Genome-wide high throughput analysis of DNA methylation in eukaryotes. Methods 47 (2009) 142-150
165. Prokhortchouk A., Hendrich B., Jorgensen H., Ruzov A., Wilm M., Georgiev G., Bird A., and Prokhortchouk E. The p120 catenin partner Kaiso is a DNA methylation-dependent transcriptional repressor. Genes Dev. 15 (2001) 1613-1618
166. Rauch T., and Pfeifer G.P. Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated-CpG islands in cancer. Lab. Invest. 85 (2005) 1172-1180
167. Richmond T.J., and Davey C.A. The structure of DNA in the nucleosome core. Nature 423 (2003) 145-150
168. Roberts S.M., and Winston F. Essential functional interactions of SAGA, a Saccharomyces cerevisiae complex of Spt, Ada, and Gcn5 proteins, with the Snf/Swi and Srb/mediator complexes. Genetics 147 (1997) 451-465
169. Robertson K.D., Ait-Si-Ali S., Yokochi T., Wade P.A., Jones P.L., and Wolffe A.P. DNMT1 forms a complex with Rb, E2F1 and HDAC1 and represses transcription from E2F-responsive promoters. Nat. Genet. 25 (2000) 338-342
170. Robertson G., Hirst M., Bainbridge M., Bilenky M., Zhao Y., Zeng T., Euskirchen G., Bernier B., Varhol R., Delaney A., Thiessen N., Griffith O.L., He A., Marra M., Snyder M., and Jones S. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods. 4 (2007) 651-657
171. Robyr D., Suka Y., Xenarios I., Kurdistani S.K., Wang A., Suka N., and Grunstein M. Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell 109 (2002) 437-446
172. Roh T.Y., Ngau W.C., Cui K., Landsman D., and Zhao K. High-resolution genome-wide mapping of histone modifications. Nat. Biotechnol. 22 (2004) 1013-1016
173. Ronn T., Poulsen P., Hansson O., Holmkvist J., Almgren P., Nilsson P., Tuomi T., Isomaa B., Groop L., Vaag A., and Ling C. Age influences DNA methylation and gene expression of COX7A1 in human skeletal muscle. Diabetologia 51 (2008) 1159-1168
174. Rountree M.R., Bachman K.E., and Baylin S.B. DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci. Nat. Genet. 25 (2000) 269-277
175. Russanova V.R., Hirai T.H., and Howard B.H. Semirandom sampling to detect differentiation-related and age-related epigenome remodeling. J. Gerontol. A Biol. Sci. Med. Sci. 59 (2004) 1221-1233
176. Russanova V.R., Hirai T.H., Tchernov A.V., and Howard B.H. Mapping development-related and age-related chromatin remodeling by a high throughput ChIP-HPLC approach. J. Gerontol. A Biol. Sci. Med. Sci. 59 (2004) 1234-1243
177. Sanders S.L., Portoso M., Mata J., Bahler J., Allshire R.C., and Kouzarides T. Methylation of histone H4 lysine 20 controls recruitment of Crb2 to sites of DNA damage. Cell 119 (2004) 603-614
178. Sansom O.J., Maddison K., and Clarke A.R. Mechanisms of disease: methyl-binding domain proteins as potential therapeutic targets in cancer. Nat. Clin. Pract. Oncol. 4 (2007) 305-315
179. Sarraf S.A., and Stancheva I. Methyl-CpG binding protein MBD1 couples histone H3 methylation at lysine 9 by SETDB1 to DNA replication and chromatin assembly. Mol. Cell 15 (2004) 595-605
180. Schalch T., Duda S., Sargent D.F., and Richmond T.J. X-ray structure of a tetranucleosome and its implications for the chromatin fibre. Nature 436 (2005) 138-141
181. Schilling E., and Rehli M. Global, comparative analysis of tissue-specific promoter CpG methylation. Genomics 90 (2007) 314-323
182. Schmitz A., Short M., Ammerpohl O., Asbrand C., Nickel J., and Renkawitz R. Cis-elements required for the demethylation of the mouse M-lysozyme downstream enhancer. J. Biol. Chem. 272 (1997) 20850-20856
183. Selker E.U. Trichostatin A causes selective loss of DNA methylation in Neurospora. Proc. Natl. Acad. Sci. USA 95 (1998) 9430-9435
184. Sharma A., Sharma V.K., Horn-Saban S., Lancet D., Ramachandran S., and Brahmachari S.K. Assessing natural variations in gene expression in humans by comparing with monozygotic twins using microarrays. Physiol. Genomics 21 (2005) 117-123
185. Shi Y., Lan F., Matson C., Mulligan P., Whetstine J.R., Cole P.A., and Casero R.A. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119 (2004) 941-953
186. Shogren-Knaak M., Ishii H., Sun J.M., Pazin M.J., Davie J.R., and Peterson C.L. Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science 311 (2006) 844-847
187. Simonis M., Klous P., Splinter E., Moshkin Y., Willemsen R., de Wit E., van Steensel B., and de Laat W. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat. Genet. 38 (2006) 1348-1354
188. Smallwood A., Esteve P.O., Pradhan S., and Carey M. Functional cooperation between HP1 and DNMT1 mediates gene silencing. Genes Dev. 21 (2007) 1169-1178
189. So K., Tamura G., Honda T., Homma N., Endoh M., Togawa N., Nishizuka S., and Motoyama T. Quantitative assessment of RUNX3 methylation in neoplastic and non-neoplastic gastric epithelia using a DNA microarray. Pathol. Int. 56 (2006) 571-575
190. Strahl B.D., and Allis C.D. The language of covalent histone modifications. Nature 403 (2000) 41-45
191. Sudarsanam P., Iyer V.R., Brown P.O., and Winston F. Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 97 (2000) 3364-3369
192. Suetake I., Shinozaki F., Miyagawa J., Takeshima H., and Tajima S. DNMT3L stimulates the DNA methylation activity of Dnmt3a and Dnmt3b through a direct interaction. J. Biol. Chem. 279 (2004) 27816-27823
193. Sun Z.W., and Allis C.D. Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast. Nature 418 (2002) 104-108
194. Sutherland E., Coe L., and Raleigh E.A. McrBC: a multisubunit GTP-dependent restriction endonuclease. J. Mol. Biol. 225 (1992) 327-348
195. Tate C.M., Lee J.H., and Skalnik D.G. CXXC finger protein 1 contains redundant functional domains that support embryonic stem cell cytosine methylation, histone methylation, and differentiation. Mol. Cell. Biol. 29 (2009) 3817-3831
196. Thoma F., and Koller T. Influence of histone H1 on chromatin structure. Cell 12 (1977) 101-107
197. Toyota M., Ho C., Ahuja N., Jair K.W., Li Q., Ohe-Toyota M., Baylin S.B., and Issa J.P. Identification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification. Cancer Res. 59 (1999) 2307-2312
198. Ushijima T. Detection and interpretation of altered methylation patterns in cancer cells. Nat. Rev. Cancer 5 (2005) 223-231
199. Ushijima T., Watanabe N., Okochi E., Kaneda A., Sugimura T., and Miyamoto K. Fidelity of the methylation pattern and its variation in the genome. Genome Res. 13 (2003) 868-874
200. Vakoc C.R., Mandat S.A., Olenchock B.A., and Blobel G.A. Histone H3 lysine 9 methylation and HP1gamma are associated with transcription elongation through mammalian chromatin. Mol. Cell 19 (2005) 381-391
201. Vogt G., Huber M., Thiemann M., van den Boogaart G., Schmitz O.J., and Schubart C.D. Production of different phenotypes from the same genotype in the same environment by developmental variation. J. Exp. Biol. 211 (2008) 510-523
202. Waalwijk C., and Flavell R.A. MspI, an isoschizomer of hpaII which cleaves both unmethylated and methylated hpaII sites. Nucleic Acids Res. 5 (1978) 3231-3236
203. Wang J., Hevi S., Kurash J.K., Lei H., Gay F., Bajko J., Su H., Sun W., Chang H., Xu G., Gaudet F., Li E., and Chen T. The lysine demethylase LSD1 (KDM1) is required for maintenance of global DNA methylation. Nat. Genet. 41 (2009) 125-129
204. Weber M., Davies J.J., Wittig D., Oakeley E.J., Haase M., Lam W.L., and Schubeler D. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet. 37 (2005) 853-862
205. Wei C.L., Wu Q., Vega V.B., Chiu K.P., Ng P., Zhang T., Shahab A., Yong H.C., Fu Y., Weng Z., Liu J., Zhao X.D., Chew J.L., Lee Y.L., Kuznetsov V.A., Sung W.K., Miller L.D., Lim B., Liu E.T., Yu Q., Ng H.H., and Ruan Y. A global map of p53 transcription-factor binding sites in the human genome. Cell 124 (2006) 207-219
206. Whitehouse I., Flaus A., Cairns B.R., White M.F., Workman J.L., and Owen-Hughes T. Nucleosome mobilization catalysed by the yeast SWI/SNF complex. Nature 400 (1999) 784-787
207. Whitlock Jr. J.P., and Simpson R.T. Removal of histone H1 exposes a fifty base pair DNA segment between nucleosomes. Biochemistry 15 (1976) 3307-3314
208. Whitlock Jr. J.P., and Simpson R.T. Localization of the sites along nucleosome DNA which interact with NH2-terminal histone regions. J. Biol. Chem. 252 (1977) 6516-6520
209. Wilson V.L., and Jones P.A. DNA methylation decreases in aging but not in immortal cells. Science 220 (1983) 1055-1057
210. Wimmer K., Zhu Xx X.X., Rouillard J.M., Ambros P.F., Lamb B.J., Kuick R., Eckart M., Weinhausl A., Fonatsch C., and Hanash S.M. Combined restriction landmark genomic scanning and virtual genome scans identify a novel human homeobox gene, ALX3, that is hypermethylated in neuroblastoma. Genes Chromosomes Cancer 33 (2002) 285-294
211. Xiong Z., and Laird P.W. COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res. 25 (1997) 2532-2534
212. Yamada T., Mizuno K., Hirota K., Kon N., Wahls W.P., Hartsuiker E., Murofushi H., Shibata T., and Ohta K. Roles of histone acetylation and chromatin remodeling factor in a meiotic recombination hotspot. EMBO J. 23 (2004) 1792-1803
213. Yan P.S., Chen C.M., Shi H., Rahmatpanah F., Wei S.H., and Huang T.H. Applications of CpG island microarrays for high-throughput analysis of DNA methylation. J. Nutr. 132 (2002) 2430S-2434S
214. Yang X., Zaurin R., Beato M., and Peterson C.L. Swi3p controls SWI/SNF assembly and ATP-dependent H2A-H2B displacement. Nat. Struct. Mol. Biol. 14 (2007) 540-547
215. Yegnasubramanian S., Lin X., Haffner M.C., DeMarzo A.M., and Nelson W.G. Combination of methylated-DNA precipitation and methylation-sensitive restriction enzymes (COMPARE-MS) for the rapid, sensitive and quantitative detection of DNA methylation. Nucleic Acids Res. 34 (2006) e19
216. Yoon H.G., Chan D.W., Reynolds A.B., Qin J., and Wong J. N-CoR mediates DNA methylation-dependent repression through a methyl CpG binding protein Kaiso. Mol. Cell 12 (2003) 723-734
217. Yuan E., Haghighi F., White S., Costa R., McMinn J., Chun K., Minden M., and Tycko B. A single nucleotide polymorphism chip-based method for combined genetic and epigenetic profiling: validation in decitabine therapy and tumor/normal comparisons. Cancer Res. 66 (2006) 3443-3451
218. Zeggini E., Weedon M.N., Lindgren C.M., Frayling T.M., Elliott K.S., Lango H., Timpson N.J., Perry J.R., Rayner N.W., Freathy R.M., Barrett J.C., Shields B., Morris A.P., Ellard S., Groves C.J., Harries L.W., Marchini J.L., Owen K.R., Knight B., Cardon L.R., Walker M., Hitman G.A., Morris A.D., Doney A.S., McCarthy M.I., and Hattersley A.T. Replication of genome-wide association signals in U.K. samples reveals risk loci for type 2 diabetes. Science 316 (2007) 1336-1341
219. Zhang Y., Ng H.H., Erdjument-Bromage H., Tempst P., Bird A., and Reinberg D. Analysis of the NuRD subunits reveals a histone deacetylase core complex and a connection with DNA methylation. Genes Dev. 13 (1999) 1924-1935
220. Zhang F., Wang L., Wu P.P., Yan Z.W., Zheng L., Yu Y.Y., and Jiang X.C. In situ analysis of p16/INK4 promoter hypermethylation in esophageal carcinoma and gastric carcinoma. Chin. J. Dig. Dis. 5 (2004) 149-155
221. Zhang X., Yazaki J., Sundaresan A., Cokus S., Chan S.W., Chen H., Henderson I.R., Shinn P., Pellegrini M., Jacobsen S.E., and Ecker J.R. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell 126 (2006) 1189-1201
222. Zhang W., Ji W., Yang J., Yang L., Chen W., and Zhuang Z. Comparison of global DNA methylation profiles in replicative versus premature senescence. Life Sci. 83 (2008) 475-480
223. Zhao Z., Tavoosidana G., Sjolinder M., Gondor A., Mariano P., Wang S., Kanduri C., Lezcano M., Sandhu K.S., Singh U., Pant V., Tiwari V., Kurukuti S., and Ohlsson R. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat. Genet. 38 (2006) 1341-1347
224. Zhao Q., Rank G., Tan Y.T., Li H., Moritz R.L., Simpson R.J., Cerruti L., Curtis D.J., Patel D.J., Allis C.D., Cunningham J.M., and Jane S.M. PRMT5-mediated methylation of histone H4R3 recruits DNMT3A, coupling histone and DNA methylation in gene silencing. Nat. Struct. Mol. Biol. 16 (2009) 304-311
225. Zilberman D., Gehring M., Tran R.K., Ballinger T., and Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat. Genet. 39 (2007) 61-69