References
1 Singal R, Ginder GD. DNA methylation
Blood 1999 93:4059-4070
2 Duncan BK, Miller JH. Mutagenic deamination of cytosine residues in DNA
Nature 1980 287:560-561
3 Fazzari MJ, Greally JM. Epigenomics: beyond CpG islands
Nat Rev Genet 2004 5:446-455
4 Cross SH, Bird AP. CpG islands and genes
Curr Opin Genet Dev 1995 5:309-314
5 Li E, Bestor TH, Jaenisch R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality
Cell 1992 69:915-926
6 Shukla V, Vaissiere T, Herceg Z. Histone acetylation and chromatin signature in stem cell identity and cancer
Mutat Res 2008 637:1-15
7 van Holde K.
Chromatin. New York: Springer-Verlag;
1989.Chromatin 1989
8 Malik HS, Henikoff S. Phylogenomics of the nucleosome
Nat Struct Biol 2003 10:882-891
9 Jenuwein T, Allis CD. Translating the histone code
Science 2001 293:1074-1080
10 Strahl BD, Allis CD. The language of covalent histone modifications
Nature 2000 403:41-45
11 Kouzarides T. Histone methylation in transcriptional control
Curr Opin Genet Dev 2002 12:198-209
12 Zhang Y, Reinberg D. Transcription regulation by histone methylation: interplay between different covalent modifications of the core histone tails
Genes Dev 2001 15:2343-2360
13 Fischle W, Wang Y, Allis CD. Histone and chromatin cross-talk
Curr Opin Cell Biol 2003 15:172-183
14 Shukla A, Chaurasia P, Bhaumik SR. Histone methylation and ubiquitination with their cross-talk and roles in gene expression and stability
Cell Mol Life Sci 2008 66:1419-1433
15 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
16 Ooi SK, Qiu C, Bernstein E,
et al. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA
Nature 2007 448:714-717
17 Cedar H, Bergman Y. Linking DNA methylation and histone modification: patterns and paradigms
Nat Rev Genet 2009 10:295-304
18 Eden S, Hashimshony T, Keshet I, Cedar H, Thorne AW. DNA methylation models histone acetylation
Nature 1998 394:842
19 Nan X, Campoy FJ, Bird A. MeCP2 is a transcriptional repressor with abundant binding sites in genomic chromatin
Cell 1997 88:471-481
20 Ballestar E, Paz MF, Valle L,
et al. Methyl-CpG binding proteins identify novel sites of epigenetic inactivation in human cancer
EMBO J 2003 22:6335-6345
21 Schlesinger Y, Straussman R, Keshet I,
et al. Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer
Nat Genet 2007 39:232-236
22 Jones PA, Baylin SB. The epigenomics of cancer
Cell 2007 128:683-692
23 He L, Hannon GJ. MicroRNAs: small RNAs with a big role in gene regulation
Nat Rev Genet 2004 5:522-531
24 Rouhi A, Mager DL, Humphries RK, Kuchenbauer F. MiRNAs, epigenetics, and cancer
Mamm Genome 2008 19:517-525
25 Hwang HW, Mendell JT. MicroRNAs in cell proliferation, cell death, and tumorigenesis
Br J Cancer 2006 94:776-780
26 Bartel DP. MicroRNAs: target recognition and regulatory functions
Cell 2009 136:215-233
27 Calin GA, Dumitru CD, Shimizu M,
et al. Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia
Proc Natl Acad Sci U S A 2002 99:15524-15529
28 Calin GA, Sevignani C, Dumitru CD,
et al. Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers
Proc Natl Acad Sci U S A 2004 101:2999-3004
29 Croce CM, Calin GA. miRNAs, cancer, and stem cell division
Cell 2005 122:6-7
30 Lujambio A, Ropero S, Ballestar E,
et al. Genetic unmasking of an epigenetically silenced microRNA in human cancer cells
Cancer Res 2007 67:1424-1429
31 Lu J, Getz G, Miska EA,
et al. MicroRNA expression profiles classify human cancers
Nature 2005 435:834-838
32 Katayama S, Tomaru Y, Kasukawa T,
et al. Antisense transcription in the mammalian transcriptome
Science 2005 309:1564-1566
33 Yu W, Gius D, Onyango P,
et al. Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA
Nature 2008 451:202-206
34 Tufarelli C, Stanley JA, Garrick D,
et al. Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease
Nat Genet 2003 34:157-165
35 Espada J, Ballestar E, Fraga MF,
et al. Human DNA methyltransferase 1 is required for maintenance of the histone H3 modification pattern
J Biol Chem 2004 279:37175-37184
36 Feinberg AP, Vogelstein B. Hypomethylation distinguishes genes of some human cancers from their normal counterparts
Nature 1983 301:89-92
37 Warnecke PM, Bestor TH. Cytosine methylation and human cancer
Curr Opin Oncol 2000 12:68-73
38 Feinberg AP, Tycko B. The history of cancer epigenetics
Nat Rev Cancer 2004 4:143-153
39 Ng MH, Wong IH, Lo KW. DNA methylation changes and multiple myeloma
Leuk Lymphoma 1999 34:463-472
40 Eden A, Gaudet F, Waghmare A, Jaenisch R. Chromosomal instability and tumors promoted by DNA hypomethylation
Science 2003 300:455
41 Bestor TH. Transposons reanimated in mice
Cell 2005 122:322-325
42 Esteller M. Epigenetics in cancer
N Engl J Med 2008 358:1148-1159
43 Lohrum M, Stunnenberg HG, Logie C. The new frontier in cancer research: deciphering cancer epigenetics
Int J Biochem Cell Biol 2007 39:1450-1461
44 Greger V, Passarge E, Hopping W, Messmer E, Horsthemke B. Epigenetic changes may contribute to the formation and spontaneous regression of retinoblastoma
Hum Genet 1989 83:155-158
45 Kastrinakis NG, Gorgoulis VG, Foukas PG, Dimopoulos MA, Kittas C. Molecular aspects of multiple myeloma
Ann Oncol 2000 11:1217-1228
46 Alexander DD, Mink PJ, Adami HO,
et al. Multiple myeloma: a review of the epidemiologic literature
Int J Cancer 2007 120:40-61
47 Seidl S, Ackermann J, Kaufmann H,
et al. DNA-methylation analysis identifies the E-cadherin gene as a potential marker of disease progression in patients with monoclonal gammopathies
Cancer 2004 100:2598-2606
48 Chim CS, Fung TK, Liang R. Disruption of INK4/CDK/Rb cell cycle pathway by gene hypermethylation in multiple myeloma and MGUS
Leukemia 2003 17:2533-2535
49 Chim CS, Kwong YL, Fung TK, Liang R. Methylation profiling in multiple myeloma
Leuk Res 2004 28:379-385
50 Uchida T, Kinoshita T, Ohno T, Ohashi H, Nagai H,
et al. Hypermethylation of p16INK4A gene promoter during the progression of plasma cell dyscrasia
Leukemia 2001 15:157-165
51 Guillerm G, Depil S, Wolowiec D, Quesnel B. Different prognostic values of p15(INK4b) and p16(INK4a) gene methylations in multiple myeloma
Haematologica 2003 88:476-478
52 Guillerm G, Gyan E, Wolowiec D,
et al. p16(INK4a) and p15(INK4b) gene methylations in plasma cells from monoclonal gammopathy of undetermined significance
Blood 2001 98:244-246
53 Galm O, Wilop S, Reichelt J,
et al. DNA methylation changes in multiple myeloma
Leukemia 2004 18:1687-1692
54 Chiusolo P, Farina G, Putzulu R,
et al. Analysis of MTHFR polymorphisms and P16 methylation and their correlation with clinical-biological features of multiple myeloma
Ann Hematol 2006 85:474-477
55 Gonzalez-Paz N, Chng WJ, McClure RF,
et al. Tumor suppressor p16 methylation in multiple myeloma: biological and clinical implications
Blood 2007 109:1228-1232
56 Ribas C, Colleoni GW, Felix RS,
et al. p16 gene methylation lacks correlation with angiogenesis and prognosis in multiple myeloma
Cancer Lett 2005 222:247-254
57 Mateos MV, Garcia-Sanz R, Lopez-Perez R,
et al. Methylation is an inactivating mechanism of the p16 gene in multiple myeloma associated with high plasma cell proliferation and short survival
Br J Haematol 2002 118:1034-1040
58 Dib A, Barlogie B, Shaughnessy JD, Kuehl WM,
Jr. Methylation and expression of the p16INK4A tumor suppressor gene in multiple myeloma
Blood 2007 109:1337-1338
59 Chim CS, Liang R, Leung MH, Kwong YL. Aberrant gene methylation implicated in the progression of monoclonal gammopathy of undetermined significance to multiple myeloma
J Clin Pathol 2007 60:104-106
60 Deligezer U, Erten N, Akisik EE, Dalay N. Methylation of the INK4A/ARF locus in blood mononuclear cells
Ann Hematol 2006 85:102-107
61 Lavelle D, DeSimone J, Hankewych M, Kousnetzova T, Chen YH. Decitabine induces cell cycle arrest at the G1 phase via p21(WAF1) and the G2/M phase via the p38 MAP kinase pathway
Leuk Res 2003 27:999-1007
62 Ng MH, To KW, Lo KW,
et al. Frequent death-associated protein kinase promoter hypermethylation in multiple myeloma
Clin Cancer Res 2001 7:1724-1729
63 Chim CS, Liang R, Fung TK, Choi CL, Kwong YL. Epigenetic dysregulation of the death-associated protein kinase/p14/HDM2/p53/Apaf-1 apoptosis pathway in multiple myeloma
J Clin Pathol 2007 60:664-669
64 Chim CS, Fung TK, Cheung WC, Liang R, Kwong YL. SOCS1 and SHP1 hypermethylation in multiple myeloma: implications for epigenetic activation of the Jak/STAT pathway
Blood 2004 103:4630-4635
65 Galm O, Yoshikawa H, Esteller M, Osieka R, Herman JG. SOCS-1, a negative regulator of cytokine signaling, is frequently silenced by methylation in multiple myeloma
Blood 2003 101:2784-2788
66 Depil S, Saudemont A, Quesnel B. SOCS-1 gene methylation is frequent but does not appear to have prognostic value in patients with multiple myeloma
Leukemia 2003 17:1678-1679
67 Reddy J, Shivapurkar N, Takahashi T,
et al. Differential methylation of genes that regulate cytokine signaling in lymphoid and hematopoietic tumors
Oncogene 2005 24:732-736
68 Chim CS, Liang R, Fung TK, Kwong YL. Infrequent epigenetic dysregulation of CIP/KIP family of cyclin-dependent kinase inhibitors in multiple myeloma
Leukemia 2005 19:2352-2355
69 Song YF, Xu R, Zhang XH,
et al. High-frequency promoter hypermethylation of the deleted in liver cancer-1 gene in multiple myeloma
J Clin Pathol 2006 59:947-951
70 Hurt EM, Thomas SB, Peng B, Farrar WL. Reversal of p53 epigenetic silencing in multiple myeloma permits apoptosis by a p53 activator
Cancer Biol Ther 2006 5:1154-1160
71 Takada S, Morita K, Hayashi K,
et al. Methylation status of fragile histidine triad (FHIT) gene and its clinical impact on prognosis of patients with multiple myeloma
Eur J Haematol 2005 75:505-510
72 Tatetsu H, Ueno S, Hata H,
et al. Down-regulation of PU.1 by methylation of distal regulatory elements and the promoter is required for myeloma cell growth
Cancer Res 2007 67:5328-5336
73 Turner JG, Gump JL, Zhang C,
et al. ABCG2 expression, function, and promoter methylation in human multiple myeloma
Blood 2006 108:3881-3889
74 Murai M, Toyota M, Satoh A.
et al. Aberrant DNA methylation associated with silencing BNIP3 gene expression in haematopoietic tumours
Br J Cancer 2005 92:1165-1172
75 Wang Z, Zhang Y, Ramsahoye B, Bowen D, Lim SH. Sp17 gene expression in myeloma cells is regulated by promoter methylation
Br J Cancer 2004 91:1597-1603
76 Wang Z, Zhang J, Zhang Y, Lim SH. SPAN-Xb expression in myeloma cells is dependent on promoter hypomethylation and can be upregulated pharmacologically
Int J Cancer 2006 118:1436-1444
77 Peng B, Hodge DR, Thomas SB,
et al. Epigenetic silencing of the human nucleotide excision repair gene, hHR23B, in interleukin-6-responsive multiple myeloma KAS-6/1 cells
J Biol Chem 2005 280:4182-4187
78 Peng B, Hurt EM, Hodge DR, Thomas SB, Farrar WL. DNA hypermethylation and partial gene silencing of human thymine- DNA glycosylase in multiple myeloma cell lines
Epigenetics 2006 1:138-145
79 Martin P, Santon A, Garcia-Cosio M, Bellas C. hMLH1 and MGMT inactivation as a mechanism of tumorigenesis in monoclonal gammopathies
Mod Pathol 2006 19:914-921
80 Chim CS, Pang R, Fung TK, Choi CL, Liang R. Epigenetic dysregulation of Wnt signaling pathway in multiple myeloma
Leukemia 2007 21:2527-2536
81 Hodge DR, Peng B, Pompeia C,
et al. Epigenetic silencing of manganese superoxide dismutase (SOD-2) in KAS 6/1 human multiple myeloma cells increases cell proliferation
Cancer Biol Ther 2005 4:585-592
82 Drucker L, Tohami T, Tartakover-Matalon S,
et al. Promoter hypermethylation of tetraspanin members contributes to their silencing in myeloma cell lines
Carcinogenesis 2006 27:197-204
83 Houde C, Li Y, Song L,
et al. Overexpression of the NOTCH ligand JAG2 in malignant plasma cells from multiple myeloma patients and cell lines
Blood 2004 104:3697-3704
84 Bacolla A, Pradhan S, Larson JE, Roberts RJ, Wells RD. Recombinant human DNA (cytosine-5) methyltransferase. III. Allosteric control, reaction order, and influence of plasmid topology and triplet repeat length on methylation of the fragile X CGG.CCG sequence
J Biol Chem 2001 276:18605-18613
85 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
86 Hodge DR, Peng B, Cherry JC,
et al. Interleukin 6 supports the maintenance of p53 tumor suppressor gene promoter methylation
Cancer Res 2005 65:4673-4682
87 Kiziltepe T, Hideshima T, Catley L,
et al. 5-Azacytidine, a DNA methyltransferase inhibitor, induces ATR-mediated DNA double-strand break responses, apoptosis, and synergistic cytotoxicity with doxorubicin and bortezomib against multiple myeloma cells
Mol Cancer Ther 2007 6:1718-1727
88 Heller G, Schmidt WM, Ziegler B,
et al. Genome-wide transcriptional response to 5-aza-2′-deoxycytidine and trichostatin a in multiple myeloma cells
Cancer Res 2008 68:44-54
89 Issa JP, Garcia-Manero G, Giles FJ,
et al. Phase 1 study of low-dose prolonged exposure schedules of the hypomethylating agent 5-aza-2′-deoxycytidine (decitabine) in hematopoietic malignancies
Blood 2004 103:1635-1640
90 Figueroa ME, Reimers M, Thompson RF,
et al. An integrative genomic and epigenomic approach for the study of transcriptional regulation
PLoS One 2008 3:e1882
91 Figueroa ME, Skrabanek L, Li Y,
et al. MDS and secondary AML display unique patterns and abundance of aberrant DNA methylation
Blood 2009 114:3448-3458
92 Pompeia C, Hodge DR, Plass C,
et al. Microarray analysis of epigenetic silencing of gene expression in the KAS-6/1 multiple myeloma cell line
Cancer Res 2004 64:3465-3473
93 Hodges E, Smith AD, Kendall J,
et al. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing
Genome Res 2009 19:1593-1605
94 Weber M, Davies JJ, Wittig D
et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells
Nat Genet 2005 37:853-862
95 Irizarry RA, Ladd-Acosta C, Carvalho B,
et al. Comprehensive high-throughput arrays for relative methylation (CHARM)
Genome Res 2008 18:780-790
96 Khulan B, Thompson RF, Ye K,
et al. Comparative isoschizomer profiling of cytosine methylation: the HELP assay
Genome Res 2006 16:1046-1055
97 Figueroa ME, Wouters BJ, Skrabanek L,
et al. Genome-wide epigenetic analysis delineates a biologically distinct immature acute leukemia with myeloid/T-lymphoid features
Blood 2009 113:2795-2804
98 Ball MP, Li JB, Gao Y,
et al. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells
Nat Biotechnol 2009 27:361-368
99 Sohal D, Yeatts A, Ye K,
et al. Meta-analysis of microarray studies reveals a novel hematopoietic progenitor cell signature and demonstrates feasibility of inter-platform data integration
PLoS One 2008 3:e2965