Epigenetic regulation of miRNA genes and their role in human melanomas

Epigenomics

Volumn 4, Issue 1, 2012, Pages 81-90

  Perera, Ranjan J ^a   Ray, Animesh ^b  

^a BURNHAM INSTITUTE   (United States)

^b KECK GRADUATE INSTITUTE   (United States)

Author keywords

chromatin; CpG island; epigenetic; melanoma; methylation; miRNA; ncRNA

Indexed keywords

MICRORNA; UNTRANSLATED RNA;

CANCER GENETICS; CARCINOGENESIS; CAUSAL ATTRIBUTION; EPIGENETICS; GENE CONTROL; HUMAN; MELANOCYTE; MELANOMA; PRIORITY JOURNAL; REVIEW; SIGNAL TRANSDUCTION;

DNA METHYLATION; EPIGENESIS, GENETIC; HUMANS; MELANOMA; MICRORNAS; SKIN NEOPLASMS; TUMOR SUPPRESSOR PROTEIN P53; ULTRAVIOLET RAYS;

EID: 84857309805     PISSN: 17501911     EISSN: 1750192X     Source Type: Journal    
DOI: 10.2217/epi.11.114     Document Type: Review

References (93)

1. Clark WH Jr, Elder DE, Guerry DT, Epstein MN, Greene MH, Van Horn M. A study of tumor progression: the precursor lesions of superficial spreading and nodular melanoma. Hum. Pathol. 15(12), 1147-1165 (1984). (Pubitemid 15128121)
2. Moan J, Dahlback A, Setlow RB. Epidemiological support for an hypothesis for melanoma induction indicating a role for UVA radiation. Photochem. Photobiol. 70(2), 243-247 (1999). (Pubitemid 129549215)
3. Runkle GP, Zaloznik AJ. Malignant melanoma. Am. Fam. Physician 49(1), 91-98, 102-104 (1994).
4. Kuchelmeister C, Schaumburg-Lever G, Garbe C. Acral cutaneous melanoma in caucasians. clinical features, histopathology and prognosis in 112 patients. Br. J. Dermatol. 143(2), 275-280 (2000). (Pubitemid 30650393)
5. Situm M, Bolanca Z, Buljan M. Lentigo maligna melanoma-the review. Coll. Antropol. 34(Suppl. 2), 299-301 (2010).
6. Adler MJ, White CR Jr. Amelanotic malignant melanoma. Semin. Cutan. Med. Surg. 16(2), 122-130 (1997). (Pubitemid 27287727)
7. Forman SB, Ferringer TC, Peckham SJ et al. Is superficial spreading melanoma still the most common form of malignant melanoma? J. Am. Acad. Dermatol. 58(6), 1013-1020 (2008). (Pubitemid 351657607)
8. Curtin JA, Fridlyand J, Kageshita T et al. Distinct sets of genetic alterations in melanoma. N. Engl. J. Med. 353(20), 2135-2147 (2005). (Pubitemid 41653105)
9. Ren S, Liu S, Howell P Jr et al. The impact of genomics in understanding human melanoma progression and metastasis. Cancer Control 15(3), 202-215 (2008).
10. Carr KM, Bittner M, Trent JM. Gene-expression profiling in human cutaneous melanoma. Oncogene 22(20), 3076-3080 (2003). (Pubitemid 36713758)
11. Houghton AN, Polsky D. Focus on melanoma. Cancer Cell 2(4), 275-278 (2002). (Pubitemid 41043961)
12. Hoek K, Rimm DL, Williams KR et al. Expression profiling reveals novel pathways in the transformation of melanocytes to melanomas. Cancer Res. 64(15), 5270-5282 (2004). (Pubitemid 39006547)
13. Alonso SR, Tracey L, Ortiz P et al. A high-throughput study in melanoma identifies epithelial-mesenchymal transition as a major determinant of metastasis. Cancer Res. 67(7), 3450-3460 (2007). (Pubitemid 46724886)
14. Kudo-Saito C, Shirako H, Takeuchi T, Kawakami Y. Cancer metastasis is accelerated through immunosuppression during Snail-induced EMT of cancer cells. Cancer Cell 15(3), 195-206 (2009).
15. Bennett DC. How to make a melanoma. what do we know of the primary clonal events? Pigment Cell Melanoma Res. 21(1), 27-38 (2008). (Pubitemid 351421467)
16. Johnson JM, Edwards S, Shoemaker D, Schadt EE. Dark matter in the genome. evidence of widespread transcription detected by microarray tiling experiments. Trends Genet. 21(2), 93-102 (2005). (Pubitemid 40127353)
17. Van Bakel H, Nislow C, Blencowe BJ, Hughes TR. Most ?dark matter? transcripts are associated with known genes. PLoS Biol. 8(5), e1000371 (2010).
18. Clark MB, Amaral PP, Schlesinger FJ et al. The reality of pervasive transcription. PLoS Biol. 9(7), e1000625; discussion e1001102 (2011).
19. Calin GA, Croce CM. MicroRNAs and chromosomal abnormalities in cancer cells. Oncogene 25(46), 6202-6210 (2006). (Pubitemid 44527851)
20. Chen CZ. MicroRNAs as oncogenes and tumor suppressors. N. Engl. J. Med. 353(17), 1768-1771 (2005)
21. Dalmay T, Edwards DR. MicroRNAs and the hallmarks of cancer. Oncogene 25(46), 6170-6175 (2006). (Pubitemid 44527847)
22. Esquela-Kerscher A, Slack FJ. Oncomirs - microRNAs with a role in cancer. Nat. Rev. Cancer 6(4), 259-269 (2006).
23. Hwang HW, Mendell JT. MicroRNAs in cell proliferation, cell death, and tumorigenesis. Br. J. Cancer 94(6), 776-780 (2006).
24. Lee YS, Dutta A. MicroRNAs. small but potent oncogenes or tumor suppressors. Curr. Opin. Investig. Drugs 7(6), 560-564 (2006). (Pubitemid 43891035)
25. Slack FJ, Weidhaas JB. MicroRNAs as a potential magic bullet in cancer. Future Oncol. 2(1), 73-82 (2006).
26. Volinia S, Calin GA, Liu CG et al. A microRNA expression signature of human solid tumors defines cancer gene targets. Proc. Natl Acad. Sci. USA 103(7), 2257-2261 (2006). (Pubitemid 43271657)
27. Zhang B, Pan X, Cobb GP, Anderson TA. microRNAs as oncogenes and tumor suppressors. Dev. Biol. 302(1), 1-12 (2007). (Pubitemid 46096921)
28. Saito Y, Jones PA. Epigenetic activation of tumor suppressor microRNAs in human cancer cells. Cell Cycle 5(19), 2220-2222 (2006). (Pubitemid 44546557)
29. Voorhoeve PM, Le Sage C, Schrier M et al. A genetic screen implicates miRNA-372 and miRNA-373 as oncogenes in testicular germ cell tumors. Cell 124(6), 1169-1181 (2006).
30. Ruvkun G. Clarifications on miRNA and cancer. Science 311(5757), 36-37 (2006).
31. Hammond SM. MicroRNAs as oncogenes. Curr. Opin. Genet. Dev. 16(1), 4-9 (2006). (Pubitemid 43089605)
32. Tam W, Dahlberg JE. miR-155/BIC as an oncogenic microRNA. Genes Chromosomes Cancer 45(2), 211-212 (2006). (Pubitemid 43191028)
33. Hede K. Studies define role of microRNA in cancer. J. Natl Cancer Inst. 97(15), 1114-1115 (2005). (Pubitemid 41511207)
34. Eder M, Scherr M. MicroRNA and lung cancer. N. Engl. J. Med. 352(23), 2446-2448 (2005). (Pubitemid 40958446)
35. Mcmanus MT. MicroRNAs and cancer. Semin Cancer Biol 13(4), 253-258 (2003).
36. Calin GA, Cimmino A, Fabbri M et al. MiR-15a and miR-16-11 cluster functions in human leukemia. Proc. Natl Acad. Sci. USA 105(13), 5166-5171 (2008). (Pubitemid 351738528)
37. Xia L, Zhang D, Du R et al. miR-15b and miR-16 modulate multidrug resistance by targeting BCL2 in human gastric cancer cells. Int. J. Cancer 123(2), 372-379 (2008). (Pubitemid 351842022)
38. Mazar J, Deyoung K, Khaitan D et al. The regulation of miRNA-211 expression and its role in melanoma cell invasiveness. PLoS ONE 5(11), e13779 (2010).
39. Bird A. Perceptions of epigenetics. Nature 447(7143), 396-398 (2007). (Pubitemid 46816744)
40. Vinod Saladi S, Marathe H, De La Serna IL. SWItching on the transcriptional circuitry in melanoma. Epigenetics 5(6), 469-475 (2010).
41. Brait M, Sidransky D. Cancer epigenetics. above and beyond. Toxicol. Mech. Methods 21(4), 275-288 (2011).
42. Portela A, Esteller M. Epigenetic modifications and human disease. Nat. Biotechnol. 28(10), 1057-1068 (2010).
43. Grewal SI, Moazed D. Heterochromatin and epigenetic control of gene expression. Science 301(5634), 798-802 (2003). (Pubitemid 36962612)
44. Robertson KD. DNA methylation and human disease. Nat. Rev. Genet. 6(8), 597-610 (2005). (Pubitemid 41044297)
45. Okano M, Bell DW, Haber DA, Li E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99(3), 247-257 (1999). (Pubitemid 29519904)
46. Bestor T, Laudano A, Mattaliano R, Ingram V. Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells. The carboxyl-terminal domain of the mammalian enzymes is related to bacterial restriction methyltransferases. J. Mol. Biol. 203(4), 971-983 (1988).
47. Li E, Bestor TH, Jaenisch R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69(6), 915-926 (1992).
48. Gonzalgo ML, Bender CM, You EH et al. Low frequency of p16/CDKN2A methylation in sporadic melanoma. comparative approaches for methylation analysis of primary tumors. Cancer Res. 57(23), 5336-5347 (1997). (Pubitemid 27516372)
49. Worm J, Bartkova J, Kirkin AF et al. Aberrant p27Kip1 promoter methylation in malignant melanoma. Oncogene 19(44), 5111-5115 (2000).
50. Worm J, Christensen C, Gronbaek K, Tulchinsky E, Guldberg P. Genetic and epigenetic alterations of the APC gene in malignant melanoma. Oncogene 23(30), 5215-5226 (2004). (Pubitemid 38980354)
51. Hoon DS, Spugnardi M, Kuo C, Huang SK, Morton DL, Taback B. Profiling epigenetic inactivation of tumor suppressor genes in tumors and plasma from cutaneous melanoma patients. Oncogene 23(22), 4014-4022 (2004). (Pubitemid 38747930)
52. Guan X, Sagara J, Yokoyama T et al. ASC/ TMS1, a caspase-1 activating adaptor, is downregulated by aberrant methylation in human melanoma. Int. J. Cancer 107(2), 202-208 (2003). (Pubitemid 37152898)
53. Gaur A, Jewell DA, Liang Y et al. Characterization of microRNA expression levels and their biological correlates in human cancer cell lines. Cancer Res. 67(6), 2456-2468 (2007). (Pubitemid 46548930)
54. Fabbri M, Garzon R, Cimmino A et al. MicroRNA-29 family reverts aberrant methylation in lung cancer by targeting DNA methyltransferases 3A and 3B. Proc. Natl Acad. Sci. USA 104(40), 15805-15810 (2007). (Pubitemid 350035380)
55. Fazi F, Racanicchi S, Zardo G et al. Epigenetic silencing of the myelopoiesis regulator microRNA-223 by the AML1/ETO oncoprotein. Cancer Cell 12(5), 457-466 (2007). (Pubitemid 350046404)
56. Grady WM, Parkin RK, Mitchell PS et al. Epigenetic silencing of the intronic microRNA hsa-miR-342 and its host gene EVL in colorectal cancer. Oncogene 27(27) 3880-3888 (2008). (Pubitemid 351862055)
57. Lehmann U, Hasemeier B, Christgen M et al. Epigenetic inactivation of microRNA gene hsa-mir-9-1 in human breast cancer. J. Pathol. 214(1), 17-24 (2008).
58. Rothhammer T, Bosserhoff AK. Epigenetic events in malignant melanoma. Pigment Cell Res. 20(2), 92-111 (2007). (Pubitemid 46439524)
59. Maat W, Van Der Velden PA, Out-Luiting C et al. Epigenetic inactivation of RASSF1a in uveal melanoma. Invest. Ophthalmol. Vis. Sci. 48(2), 486-490 (2007). (Pubitemid 351260675)
60. Jeffery L, Nakielny S. Components of the DNA methylation system of chromatin control are RNA-binding proteins. J. Biol. Chem. 279(47), 49479-49487 (2004). (Pubitemid 39625835)
61. Bernstein E, Allis CD. RNA meets chromatin. Genes Dev. 19(14), 1635-1655 (2005). (Pubitemid 41058358)
62. Robins H, Li Y, Padgett RW. Incorporating structure to predict microRNA targets. Proc. Natl Acad. Sci. USA 102(11), 4006-4009 (2005). (Pubitemid 40388546)
63. Kim VN, Nam JW. Genomics of microRNA. Trends Genet. 22(3), 165-173 (2006). (Pubitemid 43290020)
64. Hill AE, Hong JS, Wen H et al. Micro-RNA-like effects of complete intronic sequences. Front Biosci. 11, 1998-2006 (2006). (Pubitemid 43253411)
65. Ying SY, Lin SL. Intronic microRNAs. Biochem. Biophys. Res. Commun. 326(3), 515-520 (2005).
66. Ying SY, Lin SL. Intron-derived microRNAs - fine tuning of gene functions. Gene 342(1), 25-28 (2004).
67. Ying SY, Lin SL. Current perspectives in intronic micro RNAs (miRNAs). J. Biomed. Sci. 13(1), 5-15 (2006).
68. Stolc V, Samanta MP, Tongprasit W et al. Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proc. Natl Acad. Sci. USA 102(12), 4453-4458 (2005). (Pubitemid 40397133)
69. Robins H, Press WH. Human microRNAs target a functionally distinct population of genes with AT-rich 3? UTRs. Proc. Natl Acad. Sci. USA 102(43), 15557-15562 (2005). (Pubitemid 41528095)
70. Xie X, Lu J, Kulbokas EJ et al. Systematic discovery of regulatory motifs in human promoters and 3? UTRs by comparison of several mammals. Nature 434(7031), 338-345 (2005). (Pubitemid 40469170)
71. Jing Q, Huang S, Guth S et al. Involvement of microRNA in AU-rich element-mediated mRNA instability. Cell 120(5), 623-634 (2005). (Pubitemid 40343075)
72. Ambros V, Lee RC, Lavanway A, Williams PT, Jewell D. MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr. Biol. 13(10), 807-818 (2003). (Pubitemid 36573248)
73. Tijsterman M, Plasterk RH. Dicers at RISC; the mechanism of RNAi. Cell 117(1), 1-3 (2004).
74. Yang WJ, Yang DD, Na S, Sandusky GE, Zhang Q, Zhao G. Dicer is required for embryonic angiogenesis during mouse development. J. Biol. Chem. 280(10), 9330-9335 (2005). (Pubitemid 40409626)
75. Lee YS, Nakahara K, Pham JW et al. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 117(1), 69-81 (2004). (Pubitemid 38469899)
76. Suzuki H, Takatsuka S, Akashi H et al. Genome-wide profiling of chromatin signatures reveals epigenetic regulation of microRNA genes in colorectal cancer. Cancer Res. 71(17), 5646-5658 (2011).
77. Braconi C, Kogure T, Valeri N et al. microRNA-29 can regulate expression of the long non-coding RNA gene MEG3 in hepatocellular cancer. Oncogene 30(47), 4750-4756 (2011)
78. Cao Q, Mani RS, Ateeq B et al. Coordinated regulation of polycomb group complexes through microRNAs in cancer. Cancer Cell 20(2), 187-199 (2011).
79. So AY, Jung JW, Lee S, Kim HS, Kang KS. DNA methyltransferase controls stem cell aging by regulating BMI1 and EZH2 through microRNAs. PLoS ONE 6(5), e19503 (2011).
80. Mazar J, Deblasio D, Govindarajan SS, Zhang S, Perera RJ. Epigenetic regulation of microRNA-375 and its role in melanoma development in humans. FEBS Lett. 585(15), 2467-2476 (2011).
81. Khaitan D, Dinger ME, Mazar J et al. The melanoma-upregulated long noncoding RNA SPRY4-IT1 modulates apoptosis and invasion. Cancer Res. 71(11), 3852-3862 (2011).
82. Lujambio A, Calin GA, Villanueva A et al. A microRNA DNA methylation signature for human cancer metastasis. Proc. Natl Acad. Sci. USA 105(36), 13556-13561 (2008).
83. De Souza Rocha Simonini P, Breiling A, Gupta N et al. Epigenetically deregulated microRNA-375 is involved in a positive feedback loop with estrogen receptor alpha in breast cancer cells. Cancer Res. 70(22), 9175-9184 (2010).
84. Ding L, Xu Y, Zhang W et al. MiR-375 frequently downregulated in gastric cancer inhibits cell proliferation by targeting JAK2. Cell Res. 20(7), 784-793 (2010).
85. Tsukamoto Y, Nakada C, Noguchi T et al. MicroRNA-375 is downregulated in gastric carcinomas and regulates cell survival by targeting PDK1 and 14-13-3zeta. Cancer Res. 70(6), 2339-2349 (2010).
86. Dhawan P, Singh AB, Ellis DL, Richmond A. Constitutive activation of Akt/protein kinase B in melanoma leads to up-regulation of nuclear factor-kappaB and tumor progression. Cancer Res. 62(24), 7335-7342 (2002). (Pubitemid 36025257)
87. Ura K, Araki M, Saeki H et al. ATP-dependent chromatin remodeling facilitates nucleotide excision repair of UV-induced DNA lesions in synthetic dinucleosomes. EMBO J. 20(8), 2004-2014 (2001). (Pubitemid 32397402)
88. Martini E, Roche DM, Marheineke K, Verreault A, Almouzni G. Recruitment of phosphorylated chromatin assembly factor 1 to chromatin after UV irradiation of human cells. J. Cell Biol. 143(3), 563-575 (1998). (Pubitemid 28512554)
89. Ferraiuolo MA, Lee CS, Ler LW et al. A nuclear translation-like factor eIF4AIII is recruited to the mRNA during splicing and functions in nonsense-mediated decay. Proc. Natl Acad. Sci. USA 101(12), 4118-4123 (2004). (Pubitemid 38405893)
90. Lejeune F, Ranganathan AC, Maquat LE. eIF4G is required for the pioneer round of translation in mammalian cells. Nat. Struct. Mol. Biol. 11(10), 992-1000 (2004). (Pubitemid 39315304)
91. Brumbaugh KM, Otterness DM, Geisen C et al. The mRNA surveillance protein hSMG-1 functions in genotoxic stress response pathways in mammalian cells. Mol. Cell 14(5), 585-598 (2004). (Pubitemid 38739082)
92. Chiu SY, Lejeune F, Ranganathan AC, Maquat LE. The pioneer translation initiation complex is functionally distinct from but structurally overlaps with the steady-state translation initiation complex. Genes Dev. 18(7), 745-754 (2004). (Pubitemid 38480887)
93. Maquat LE. Nonsense-mediated mRNA decay. splicing, translation and mRNP dynamics. Nat. Rev. Mol. Cell Biol. 5(2), 89-99 (2004). (Pubitemid 38160252)