UNDERSTANDING OF EPIGENETICS AND DNA METHYLATION

후생유전학 (Epigenetics)과 DNA methylation의 이해

  • Oh, Jung-Hwan (Dept. of Oral & Maxillofacial Surgery, Kyung-Hee University Dental School) ;
  • Kwon, Young-Dae (Dept. of Oral & Maxillofacial Surgery, Kyung-Hee University Dental School) ;
  • Yoon, Byung-Wook (Dept. of Oral & Maxillofacial Surgery, Kyung-Hee University Dental School) ;
  • Choi, Byung-Jun (Dept. of Oral & Maxillofacial Surgery, Kyung-Hee University Dental School)
  • 오정환 (경희대학교 치의학전문대학원 구강악안면외과학교실) ;
  • 권용대 (경희대학교 치의학전문대학원 구강악안면외과학교실) ;
  • 윤병욱 (경희대학교 치의학전문대학원 구강악안면외과학교실) ;
  • 최병준 (경희대학교 치의학전문대학원 구강악안면외과학교실)
  • Published : 2008.05.30

Abstract

Epigenetic is usually referring to heritable traits that do not involve changes to the underlying DNA sequence. DNA methylation is known to serve as cellular memory. and is one of the most important mechanism of epigenetic. DNA methylation is a covalent modification in which the target molecules for methylation in mammalian DNA are cytosine bases in CpG dinucleotides. The 5' position of cytosine is methylated in a reaction catalyzed by DNA methyltransferases; DNMTl, DNMT3a, and DNMT3b. There are two different regions in the context of DNA methylation: CpG poor regions and CpG islands. The intergenic and the intronic region is considered to be CpG poor, and CpG islands are discrete CpG-rich regions which are often found in promoter regions. Normally, CpG poor regions are usually methylated whereas CpG islands are generally hypomethylated. DNA methylation is involved in various biological processes such as tissue-specific gene expression, genomic imprinting, and X chromosome inactivation. In general. cancer cells are characterized by global genomic hypomethylation and focal hypermethylation of CpG islands, which are generally unmethylated in normal cells. Gene silencing by CpG hypermethylation at the promotors of tumor suppressor genes is probably the most common mechanism of tumor suppressor inactivation in cancer.

DNA 메틸화는 histone modification과 함께 DNA의 염기서열이 유지되면서 유전기능이 변화되고 자손까지 전달 될 수 있는 후생 유전의 중요한 한 부분이다. DNA 메틸화는 크로마틴의 구조를 변경시키는 과정을 통하여 유전자와 repetitive sequence의 표현을 억제시킬 수 있다. DNA 메틸화는 X-불활성화, 유전체 각인, 유전자 발현조절, 암 생성 등에 중요한 역할을 하는 것으로 밝혀졌고, DNA 메틸화 표지자 (DNA methylation marker)들은 종양의 진단과 치료에 대한 반응을 예측하는 지표로 활용되고 있다. 지금까지 많은 연구 성과에도 불구하고 DNA메틸화, 메틸화에 의한 gene silencing, DNA 메틸화의 표적부위 등에 대한 명확한 기전이 아직도 밝혀지지 않고 있어 향후 더 많은 기초적 연구가 필요할 것이다. 최근에는 후생 유전적 변화는 가역적이기 때문에 종양억제유전자를 억압하는 후생 유전적 변화를 제거한다면 그 종양억제유전자를 다시 활성화시킬 수 있다는 개념의 후생유전 치료법 연구로 DNA 메틸화 억제제와 histone deacetyaltion에 관여하는 HDAC의 억제제들이 항암제로서 개발되어 사용되고 있는데 향후 더 많은 약제 개발과 임상적 연구가 진행되어야 할 것이다.

Keywords

References

  1. KH Kang : Epigenetics;Understandings about DNA methylation in carcinogenesis. KMB Co. 2007
  2. Weissbach A : A chronicle of DNA methylation.(1948- 1975). EXS 64 : 1, 1993
  3. Singai R, Ginder GD : DNA methylation. Blood 93 : 4059, 1999
  4. Miranda TB, Johnes PA : DNA methylation: the nuts and bolts of repression. J Cell Physiol 213 : 384, 2007 https://doi.org/10.1002/jcp.21224
  5. Bestor T, Laudano A, Mattaliano R et al : Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells. The carboxyl-terminal domain of the mammalian enzymes in related to bacterial restriction methyltransferase. J Mol Biol 203 : 971, 1988 https://doi.org/10.1016/0022-2836(88)90122-2
  6. Okano M, Bell DW, Haber DA et al : DNA methyltransferase Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99 : 247, 1999 https://doi.org/10.1016/S0092-8674(00)81656-6
  7. Xie S, Wang Z, Okano M et al : Cloning, expression and chromosome location of the human DNMT3 gene family. Gene 236 : 87, 1999 https://doi.org/10.1016/S0378-1119(99)00252-8
  8. Chen T, Ueda Y, Xie S : A novel Dnmt3a isoform produced from an alternative promoter localizes to euchromatin and its exression correlates with active de novo methylation. J Biol Chem 277 : 38746, 2002 https://doi.org/10.1074/jbc.M205312200
  9. Hata K, Okano M, Lei H et al : Dnmt3L cooperates with the Dnmt3 family of de novo DNA methyltransferases to etablish maternal imprints in mice. Development 129 : 1983, 2002
  10. Takai D, Jones PA : Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci USA 99 : 3740, 2002
  11. Ponger L : Determinants of CpG islands : expression in early embryo and isochore structure. Genome Res 11 : 1854, 2001
  12. Sved J, Bird A : The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model. Proc Natl Acad Sci USA 87 : 4692, 1990
  13. Dallosso AR, Hancock AL, Moorwood K et al : Genomic imprinting at the WT1 gene involves a novel coding transcript (AWT1) that shows deregulation in wilms tumors. Hum Mol Genet 13 : 405, 2004 https://doi.org/10.1093/hmg/ddh038
  14. Gronbaek K, Hother C, Jones PA : Epigenetic changes in cancer. APMIS 115 : 1030, 2007
  15. Cheng MK, Disteche CM : Silence of the fathers: early X inactivation. BioEssays 26(8) : 821, 2004 https://doi.org/10.1002/bies.20082
  16. McGrath J, Solter D : completion of mouse embryogenesis requires both the maternal and paternal genomes. Cell 37 : 179, 1984 https://doi.org/10.1016/0092-8674(84)90313-1
  17. Heard E, Clerc P, Avner P : X-chromosome inactivation in mammals. Annu Rev Genet 31 : 571, 1997 https://doi.org/10.1146/annurev.genet.31.1.571
  18. Plath K, Mlynareczyk-Evans S, Nusinow D et al : Xist RNA and the mechanism of X chromosome inactivation. Annu Rev Genet 36 : 233, 2002 https://doi.org/10.1146/annurev.genet.36.042902.092433
  19. Ohhata T, Hoki Y, Sasaki H et al : Tsix-deficient X chromosome does not undergo inactivation in the embryonic lineage in male: impliations for Tsix-independent silencing of Xist. Cytogeniet Genome Res 113 : 345, 2006 https://doi.org/10.1159/000090851
  20. Heard E, Rougenulle C, Arnaud D et al : Methylation of histone H3 at Lys-9 is an early mark on the X chromosome during X inactivation. Cell 107 : 727, 2001 https://doi.org/10.1016/S0092-8674(01)00598-0
  21. Tycko B, Morison JM : Physiological functions of imprinted genes. J Cell Physiol 192 : 245, 2002 https://doi.org/10.1002/jcp.10129
  22. Reik W, Walter J : Genomic imprinting: parental influence on the genome. Nat Rev Genet 2 : 21, 2001
  23. Jaenisch R, Bird A : Epigenetic reulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 33 suppl : 245, 2003 https://doi.org/10.1038/ng1089
  24. IIsles, AR, Holland AJ : Imprinted genes and mother-offspring interactions. Early Hum Dev 81(1) : 73, 2005 https://doi.org/10.1016/j.earlhumdev.2004.10.006
  25. Constancia M : Resourceful imprinting. Nature 432(7013) : 53, 2004 https://doi.org/10.1038/432053a
  26. Temple IK : Imprinting in human disease with special reference to transient neonatal diabetes and Beckwith- Wiedemann syndrome. Endocr Dev 12 : 113, 2007
  27. Higashimoto K, Soejima H, Saito T et al : Imprinting disruption of the CDKN1C/KCNQ1OT1 domain: the molecular mechanisms causing Beckwith-Wiedemann syndrome and cancer. Cytogenet Genome Res 113 : 306, 2006 https://doi.org/10.1159/000090846
  28. Galvan-Nanso M, Campistol J, Conill J et al : Analysis of the characteristics of epilepsy in 37 pateints with the molecular diagnosis of Angelman syndrome. Epileptic Disod 7 : 19, 2005
  29. Haig D, Graham C : Genomic imprinting and the strange case of the insulin-like growth factor II receptor. Cell 22 : 1045, 1991
  30. Riggs AD, Jones PA : S-methylcytosine, gene regulation, and cancer. Adv Cancer Res 40 : 1, 1983 https://doi.org/10.1016/S0065-230X(08)60678-8
  31. Johns PA, Baylin SB : The fundamental role of epigenetic events in cancer. Nat Rev Genet 3 : 415, 2002 https://doi.org/10.1038/nrg816
  32. Chalitchagorn K, Shuangshoti S, Hourpai N et al : Distinctive pattern of LINE-1 methylation level in normal tissues and the association with carcinogenesis. Oncogene 23 : 8841, 2004 https://doi.org/10.1038/sj.onc.1208137
  33. Ogishima T, Shiina H, Breault JE : Promoter CpG hypomethylation and transcription factor EGR1 hyperactivate heparanase expression in bladder cancer. Oncogene 24 : 6765, 2005 https://doi.org/10.1038/sj.onc.1208811
  34. Okada H, Kimura MT, Tan D : Frequent trefoil factor 3 (TFF3) overexpression and promoter hypomethylation in mouse and human hepatocellular carcinomas. Int J Oncol 26 : 369, 2005
  35. Smith IM, Mydlarz WK, Nithani SK : DNA global hypomethylation in squamouse cell head and neck cancer associated with smoking, alcohol comsumption and stage. Int J Cancer 15 : 1724, 2007
  36. Wong TS, Man MW, Lam AK et al : The study of p16 and p15 gene methylation in head and neck squamous cell carcinoma and their quantitative evaluation in plasma by real-time PCR. Eur J Cancer 39 : 1881, 2003 https://doi.org/10.1016/S0959-8049(03)00428-3
  37. Hong SH, Kim HG, Chung WB et al : DNA hypermethylation of tumor-related genes in gastric carcinoma. J Kor Med Sci 20 : 236, 2005 https://doi.org/10.3346/jkms.2005.20.2.236
  38. Marsit CJ, Kim DH, Liu M et al : Hypermethylation of RASSF1A and BLU tumor suppressor genes in non-small cell lung cancer: implications for tobacco smoking during adolescence. Int J Cancer 114 : 219, 2005 https://doi.org/10.1002/ijc.20714
  39. Maruyama R, Sugio K, Yoshino K et al : Hypermethylation of FHIT as a prognostic marker in nonsmall cell lung carcinoma. Cancer 100 : 1472, 2004 https://doi.org/10.1002/cncr.20144
  40. Li S, Rong M, Iacopetta B : DNA hypermethylation in breast cancer and its association with clinicopathological features. Cancer Lett 18 : 272, 2005
  41. Yeo W, Wong WL, Wong N et al : High frequency of promoter hypermethylation of RASSF1A in tumorous and non-tumourous tissue of breast cancer. Pathology 37 : 125, 2005 https://doi.org/10.1080/00313020500058623
  42. Park HJ, Yu E. Shim YH : DNA methyltransferase expression and DNA hypermethylation in human hepatocellular carcinoma. Cancer Lett 233 : 271, 2006 https://doi.org/10.1016/j.canlet.2005.03.017
  43. Bai AH, Tong JH, To KF et al : Promoter hypermethylation of tumor-related genes in the progression of colorectal neoplasia. Int J Cancer 112 : 846, 2004 https://doi.org/10.1002/ijc.20485
  44. Lee S, Hwang KS, Lee HJ et al : Aberrant CpG island hypermethylation of multiple genes in colorectal neoplasia. Lab Invest 84 : 884, 2004 https://doi.org/10.1038/labinvest.3700108
  45. Ishida E, Nakamura M, Ikuta M et al : Promotor hypermethylation of p14ARF is a key alteration for progression of oral squamous cell carcinoma. Oral Oncol 41 : 614, 2005 https://doi.org/10.1016/j.oraloncology.2005.02.003
  46. Viswanathan M, Tsuchida N, Shanmugam G : Promoter hypermethylation profile of tumor-associated genes p16, p15, hMLH1, MGMT and E-cadherin in oral squamous cell carcinoma. Int J Cancer 105 : 41, 2003 https://doi.org/10.1002/ijc.11028
  47. Maruya SI, Issa JP, Weber RS et al : Differential methylation status of tumor-associated genes in head and neck squamous carcinoma: incidence and potential implications. Clin Cancer Res 10 : 3825, 2004 https://doi.org/10.1158/1078-0432.CCR-03-0370
  48. Puri SK, Si L, Fan CY et al : Aberrant promoter hypermethylation of multiple genes in head and neck squamous cell carcinoma. Am J Otolaryngol 26 : 12, 2005 https://doi.org/10.1016/j.amjoto.2004.06.007