Epigenetics

Kelley's Textbook of Rheumatology: Volume 1-2, Ninth Edition

Volumn 1, Issue , 2012, Pages 316-324

  Ospelt, Caroline ^a   Gay, Steffen ^a  

^a Life Science Zurich   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84898049185     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-1-4377-1738-9.00022-0     Document Type: Chapter

References (100)

1. CH Waddington (1957) The strategy of the genes. London: Allen & Unwin
2. A Bird (2007) Perceptions of epigenetics. Nature 447 396-398
3. R Lister, M Pelizzola, RH Dowen, et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462 315-322
4. RA Irizarry, C Ladd-Acosta, B Wen, et al. (2009) The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 41 178-186
5. J Oswald, S Engemann, N Lane, et al. (2008) Active demethylation of the paternal genome in the mouse zygote. Curr Biol 10 475-478
6. S Kangaspeska, B Stride, R Metivier, et al. (2008) Transient cyclical methylation of promoter DNA. Nature 452 112-115
7. R Metivier, R Gallais, C Tiffoche, et al. (2008) Cyclical DNA methylation of a transcriptionally active promoter. Nature 452 45-50
8. SC Wu and Y Zhang (2010) Active DNA demethylation: many roads lead to Rome. Nat Rev Mol Cell Biol 11 607-620
9. SD Taverna, H Li, AJ Ruthenburg, et al. (2007) How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat Struct Mol Biol 14 1025-1040
10. S Chambeyron and WA Bickmore (2004) Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. Genes Dev 18 1119-1130
11. L Hong, GP Schroth, HR Matthews, et al. (1993) Studies of the DNA binding properties of histone H4 amino terminus: thermal denaturation studies reveal that acetylation markedly reduces the binding constant of the H4 “tail” to DNA. J Biol Chem 268 305-314
12. C Dhalluin, JE Carlson, L Zeng, et al. (1999) Structure and ligand of a histone acetyltransferase bromodomain. Nature 399 491-496
13. BR Keppler and TK Archer (2008) Chromatin-modifying enzymes as therapeutic targets—Part 1. Expert Opin Ther Targets 12 1301-1312
14. H Vaziri, SK Dessain, E Ng Eaton, et al. (2001) hSIR2(SIRT1) functions as an NAD-dependent p53 deacetylase. Cell 107 149-159
15. V Azuara, P Perry, S Sauer, et al. (2006) Chromatin signatures of pluripotent cell lines. Nat Cell Biol 8 532-538
16. BE Bernstein, M Kamal, K Lindblad-Toh, et al. (2005) Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120 169-181
17. CR Vakoc, SA Mandat, BA Olenchock and GA Blobel (2005) Histone H3 lysine 9 methylation and HP1gamma are associated with transcription elongation through mammalian chromatin. Mol Cell 19 381-391
18. Y Wang, J Wysocka, J Sayegh, et al. (2004) Human PAD4 regulates histone arginine methylation levels via demethylimination. Science 306 279-283
19. S Thomson, AL Clayton, CA Hazzalin, et al. (1999) The nucleosomal response associated with immediate-early gene induction is mediated via alternative MAP kinase cascades: MSK1 as a potential histone H3/HMG-14 kinase. EMBO J 18 4779-4793
20. P Cheung, KG Tanner, WL Cheung, et al. (2000) Synergistic coupling of histone H3 phosphorylation and acetylation in response to epidermal growth factor stimulation. Mol Cell 5 905-915
21. Y Zhang and D Reinberg (2001) Transcription regulation by histone methylation: interplay between different covalent modifications of the core histone tails. Genes Dev 15 2343-2360
22. SJ Nowak and VG Corces (2004) Phosphorylation of histone H3: a balancing act between chromosome condensation and transcriptional activation. Trends Genet 20 214-220
23. VG Wilson and PR Heaton (2008) Ubiquitin proteolytic system: focus on SUMO. Expert Rev Proteomics 5 121-135
24. Y Shiio and RN Eisenman (2003) Histone sumoylation is associated with transcriptional repression. Proc Natl Acad Sci U S A 100 13225-13230
25. SJ Nielsen, R Schneider, UM Bauer, et al. (2001) Rb targets histone H3 methylation and HP1 to promoters. Nature 412 561-565
26. Y Zhang (2003) Transcriptional regulation by histone ubiquitination and deubiquitination. Genes Dev 17 2733-2740
27. SD Briggs, T Xiao, ZW Sun, et al. (2002) Gene silencing: trans-histone regulatory pathway in chromatin. Nature 418 498
28. PO Hassa, SS Haenni, M Elser and MO Hottiger (2006) Nuclear ADP-ribosylation reactions in mammalian cells: where are we today and where are we going? Microbiol Mol Biol Rev 70 789-829
29. N Malik and M Smulson (1984) A relationship between nuclear poly(adenosine diphosphate ribosylation) and acetylation posttranslational modifications. 1. Nucleosome studies. Biochemistry 23 3721-3725
30. A Wutz and J Gribnau (2007) X inactivation Xplained. Curr Opin Genet Dev 17 387-393
31. T Nagano, JA Mitchell, LA Sanz, et al. (2008) The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 322 1717-1720
32. ES Chen, K Zhang, E Nicolas, et al. (2008) Cell cycle control of centromeric repeat transcription and heterochromatin assembly. Nature 451 734-737
33. M El-Shami, D Pontier, S Lahmy, et al. (2007) Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components. Genes Dev 21 2539-2544
34. Z Lippman and R Martienssen (2004) The role of RNA interference in heterochromatic silencing. Nature 431 364-370
35. A Rodriguez, S Griffiths-Jones, JL Ashurst and A Bradley (2004) Identification of mammalian microRNA host genes and transcription units. Genome Res 14 1902-1910
36. AS O’Toole, S Miller, N Haines, et al. (2006) Comprehensive thermodynamic analysis of 3′ double-nucleotide overhangs neighboring Watson-Crick terminal base pairs. Nucleic Acids Res 34 3338-3344
37. DP Bartel (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116 281-297
38. A Grimson, KK Farh, WK Johnston, et al. (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27 91-105
39. BP Lewis, CB Burge and DP Bartel (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120 15-20
40. B Weber, C Stresemann, B Brueckner and F Lyko (2007) Methylation of human microRNA genes in normal and neoplastic cells. Cell Cycle 6 1001-1005
41. F Eckhardt, J Lewin, R Cortese, et al. (2006) DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 38 1378-1385
42. L Zhang, J Huang, N Yang, et al. (2006) MicroRNAs exhibit high frequency genomic alterations in human cancer. Proc Natl Acad Sci USA 103 9136-9141
43. C Braconi, N Huang and T Patel (2010) MicroRNA-dependent regulation of DNA methyltransferase-1 and tumor suppressor gene expression by interleukin-6 in human malignant cholangiocytes. Hepatology 51 881-890
44. EJ Noonan, RF Place, D Pookot, et al. (2009) MiR-449a targets HDAC-1 and induces growth arrest in prostate cancer. Oncogene 28 1714-1724
45. JF Chen, EM Mandel, JM Thomson, et al. (2006) The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nat Genet 38 228-233
46. L Greco, R Romino, I Coto, et al. (2002) The first large population based twin study of coeliac disease. Gut 50 624-628
47. L Nistico, C Fagnani, I Coto, et al. (2006) Concordance, disease progression, and heritability of coeliac disease in Italian twins. Gut 55 803-808
48. AJ MacGregor, H Snieder, AS Rigby, et al. (2000) Characterizing the quantitative genetic contribution to rheumatoid arthritis using data from twins. Arthritis Rheum 43 30-37
49. MF Fraga, E Ballestar, MF Paz, et al. (2005) Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci U S A 102 10604-10609
50. T Ushijima, N Watanabe, E Okochi, et al. (2003) Fidelity of the methylation pattern and its variation in the genome. Genome Res 13 868-874
51. M Esteller (2007) Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet 8 286-298
52. R Mechelli, V Annibali, G Ristori, et al. (2010) Multiple sclerosis etiology: beyond genes and environment. Expert Rev Clin Immunol 6 481-490
53. J Mill, T Tang, Z Kaminsky, et al. (2008) Epigenomic profiling reveals DNA-methylation changes associated with major psychosis. Am J Hum Genet 82 696-711
54. KD Robertson (2005) DNA methylation and human disease. Nat Rev Genet 6 597-610
55. DH Lim and ER Maher (2010) Genomic imprinting syndromes and cancer. Adv Genet 70 145-175
56. MP Lee, MR DeBaun, K Mitsuya, et al. (1999) Loss of imprinting of a paternally expressed transcript, with antisense orientation to KVLQT1, occurs frequently in Beckwith-Wiedemann syndrome and is independent of insulin-like growth factor II imprinting. Proc Natl Acad Sci U S A 96 5203-5208
57. C Kanduri, G Fitzpatrick, R Mukhopadhyay, et al. (2002) A differentially methylated imprinting control region within the Kcnq1 locus harbors a methylation-sensitive chromatin insulator. J Biol Chem 277 18106-18110
58. S Sharma, TK Kelly and PA Jones (2010) Epigenetics in cancer. Carcinogenesis 31 27-36
59. MF Fraga, E Ballestar, A Villar-Garea, et al. (2005) Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer. Nat Genet 37 391-400
60. VP Tryndyak, O Kovalchuk and IP Pogribny (2006) Loss of DNA methylation and histone H4 lysine 20 trimethylation in human breast cancer cells is associated with aberrant expression of DNA methyltransferase 1, Suv4-20h2 histone methyltransferase and methyl-binding proteins. Cancer Biol Ther 5 65-70
61. IP Pogribny, SA Ross, VP Tryndyak, et al. (2006) Histone H3 lysine 9 and H4 lysine 20 trimethylation and the expression of Suv4-20h2 and Suv-39h1 histone methyltransferases in hepatocarcinogenesis induced by methyl deficiency in rats. Carcinogenesis 27 1180-1186
62. AS Wilkins (2010) The enemy within: an epigenetic role of retrotransposons in cancer initiation. Bioessays 32 856-865
63. BM Javierre, AF Fernandez, J Richter, et al. (2010) Changes in the pattern of DNA methylation associated with twin discordance in systemic lupus erythematosus. Genome Res 20 170-179
64. B Richardson, L Scheinbart, J Strahler, et al. (1990) Evidence for impaired T cell DNA methylation in systemic lupus erythematosus and rheumatoid arthritis. Arthritis Rheum 33 1665-1673
65. W Pan, S Zhu, M Yuan, et al. (2010) MicroRNA-21 and microRNA-148a contribute to DNA hypomethylation in lupus CD4+ T cells by directly and indirectly targeting DNA methyltransferase 1. J Immunol 184 6773-6781
66. C Deng, MJ Kaplan, J Yang, et al. (2001) Decreased Ras-mitogen-activated protein kinase signaling may cause DNA hypomethylation in T lymphocytes from lupus patients. Arthritis Rheum 44 397-407
67. J Quddus, KJ Johnson, J Gavalchin, et al. (1993) Treating activated CD4+ T cells with either of two distinct DNA methyltransferase inhibitors, 5-azacytidine or procainamide, is sufficient to cause a lupus-like disease in syngeneic mice. J Clin Invest 92 38-53
68. MJ Kaplan, Q Lu, A Wu, et al. (2004) Demethylation of promoter regulatory elements contributes to perforin overexpression in CD4+ lupus T cells. J Immunol 172 3652-3661
69. Q Lu, A Wu and BC Richardson (2005) Demethylation of the same promoter sequence increases CD70 expression in lupus T cells and T cells treated with lupus-inducing drugs. J Immunol 174 6212-6219
70. Q Lu, M Kaplan, D Ray, et al. (2002) Demethylation of ITGAL (CD11a) regulatory sequences in systemic lupus erythematosus. Arthritis Rheum 46 1282-1291
71. M Zhao, Y Sun, F Gao, et al. (2010) Epigenetics and SLE: RFX1 downregulation causes CD11a and CD70 overexpression by altering epigenetic modifications in lupus CD4+ T cells. J Autoimmun 35 58-69
72. A Perl and K Banki (1993) Human endogenous retroviral elements and autoimmunity: data and concepts. Trends Microbiol 1 153-156
73. M Okada, H Ogasawara, H Kaneko, et al. (2002) Role of DNA methylation in transcription of human endogenous retrovirus in the pathogenesis of systemic lupus erythematosus. J Rheumatol 29 1678-1682
74. PC Piotrowski, S Duriagin and PP Jagodzinski (2005) Expression of human endogenous retrovirus clone 4-1 may correlate with blood plasma concentration of anti-U1 RNP and anti-Sm nuclear antibodies. Clin Rheumatol 24 620-624
75. N Hu, X Qiu, Y Luo, et al. (2008) Abnormal histone modification patterns in lupus CD4+ T cells. J Rheumatol 35 804-810
76. Y Dai, L Zhang, C Hu and Y Zhang (2010) Genome-wide analysis of histone H3 lysine 4 trimethylation by ChIP-chip in peripheral blood mononuclear cells of systemic lupus erythematosus patients. Clin Exp Rheumatol 28 158-168
77. C Ospelt and S Gay (2008) The role of resident synovial cells in destructive arthritis. Best Pract Res Clin Rheumatol 22 239-252
78. E Karouzakis, RE Gay, BA Michel, et al. (2009) DNA hypomethylation in rheumatoid arthritis synovial fibroblasts. Arthritis Rheum 60 3613-3622
79. M Neidhart, J Rethage, S Kuchen, et al. (2000) Retrotransposable L1 elements expressed in rheumatoid arthritis synovial tissue: association with genomic DNA hypomethylation and influence on gene expression. Arthritis Rheum 43 2634-2647
80. N Takami, K Osawa, Y Miura, et al. (2006) Hypermethylated promoter region of DR3, the death receptor 3 gene, in rheumatoid arthritis synovial cells. Arthritis Rheum 54 779-787
81. Y Chen, GJ Gorelik, FM Strickland and BC Richardson (2010) Decreased ERK and JNK signaling contribute to gene overexpression in “senescent” CD4+CD28- T cells through epigenetic mechanisms. J Leukoc Biol 87 137-145
82. CJ Nile, RC Read, M Akil, et al. (2008) Methylation status of a single CpG site in the IL6 promoter is related to IL6 messenger RNA levels and rheumatoid arthritis. Arthritis Rheum 58 2686-2693
83. T Kitamura, Y Kabuyama, A Kamataki, et al. (2008) Enhancement of lymphocyte migration and cytokine production by ephrinB1 system in rheumatoid arthritis. Am J Physiol Cell Physiol 294 C189-C196
84. J Stanczyk, C Ospelt, E Karouzakis, et al. (2011) Altered expression of miR-203 in rheumatoid arthritis synovial fibroblasts and its role in fibroblast activation. Arthritis Rheum 63 373-381
85. K Murata, H Yoshitomi, S Tanida, et al. (2010) Plasma and synovial fluid microRNAs as potential biomarkers of rheumatoid arthritis and osteoarthritis. Arthritis Res Ther 12 R86
86. Y Nakamachi, S Kawano, M Takenokuchi, et al. (2009) MicroRNA-124a is a key regulator of proliferation and monocyte chemoattractant protein 1 secretion in fibroblast-like synoviocytes from patients with rheumatoid arthritis. Arthritis Rheum 60 1294-1304
87. T Nakasa, S Miyaki, A Okubo, et al. (2008) Expression of microRNA-146 in rheumatoid arthritis synovial tissue. Arthritis Rheum 58 1284-1292
88. KM Pauley, M Satoh, AL Chan, et al. (2008) Upregulated miR-146a expression in peripheral blood mononuclear cells from rheumatoid arthritis patients. Arthritis Res Ther 10 R101
89. J Stanczyk, DM Pedrioli, F Brentano, et al. (2008) Altered expression of microRNA in synovial fibroblasts and synovial tissue in rheumatoid arthritis. Arthritis Rheum 58 1001-1009
90. LC Huber, M Brock, H Hemmatazad, et al. (2007) Histone deacetylase/acetylase activity in total synovial tissue derived from rheumatoid arthritis and osteoarthritis patients. Arthritis Rheum 56 1087-1093
91. T Kawabata, K Nishida, K Takasugi, et al. (2010) Increased activity and expression of histone deacetylase 1 in relation to tumor necrosis factor-alpha in synovial tissue of rheumatoid arthritis. Arthritis Res Ther 12 R133
92. YL Chung, MY Lee, AJ Wang and LF Yao (2003) A therapeutic strategy uses histone deacetylase inhibitors to modulate the expression of genes involved in the pathogenesis of rheumatoid arthritis. Mol Ther 8 707-717
93. HS Lin, CY Hu, HY Chan, et al. (2007) Anti-rheumatic activities of histone deacetylase (HDAC) inhibitors in vivo in collagen-induced arthritis in rodents. Br J Pharmacol 150 862-872
94. T Nakamura, T Kukita, T Shobuike, et al. (2005) Inhibition of histone deacetylase suppresses osteoclastogenesis and bone destruction by inducing IFN-beta production. J Immunol 175 5809-5816
95. K Nishida, T Komiyama, S Miyazawa, et al. (2004) Histone deacetylase inhibitor suppression of autoantibody-mediated arthritis in mice via regulation of p16INK4a and p21(WAF1/Cip1) expression. Arthritis Rheum 50 3365-3376
96. H Maciejewska-Rodrigues, E Karouzakis, S Strietholt, et al. (2010) Epigenetics and rheumatoid arthritis: the role of SENP1 in the regulation of MMP-1 expression. J Autoimmun 35 15-22
97. I Meinecke, A Cinski, A Baier, et al. (2007) Modification of nuclear PML protein by SUMO-1 regulates Fas-induced apoptosis in rheumatoid arthritis synovial fibroblasts. Proc Natl Acad Sci U S A 104 5073-5978
98. C Willyard (2010) The saving switch. Nat Med 16 18-21
99. CS Mitsiades, NS Mitsiades, CJ McMullan, et al. (2004) Transcriptional signature of histone deacetylase inhibition in multiple myeloma: biological and clinical implications. Proc Natl Acad Sci U S A 101 540-545
100. RE Lanford, ES Hildebrandt-Eriksen, A Petri, et al. (2010) Therapeutic silencing of microRNA-122 in primates with chronic hepatitis C virus infection. Science 327 198-201