遗传 ›› 2011, Vol. 33 ›› Issue (4): 298-306.doi: 10.3724/SP.J.1005.2011.00298
肖遥, 张华林, 白莉雅, 王晓民, 李文功, 杨利国
收稿日期:2010-08-28
修回日期:2010-10-21
出版日期:2011-04-20
发布日期:2011-04-25
通讯作者:
杨利国
E-mail:yangliguo2006@yahoo.com.cn
基金资助:国家现代农业技术体系项目(编号：nycytx-10)和国家自然科学基金项目(编号：31001007)资助
XIAO Yao, ZHANG Hua-Lin, BAI Li-Ya, WANG Xiao-Ming, LI Wen-Gong, YANG Li-Guo
Received:2010-08-28
Revised:2010-10-21
Online:2011-04-20
Published:2011-04-25
Contact:
YANG Li-Guo
E-mail:yangliguo2006@yahoo.com.cn
摘要： DNA甲基化是一种相对稳定且可遗传的表观遗传标记, 在植物和动物细胞中均发现有DNA主动去甲基化现象, 其机制在植物中已基本得到阐释, 但在哺乳动物中尚未鉴定出一种有效的DNA去甲基化酶, 并且DNA主动去甲基化途径也存在争议。文章综合分析了近期的文献资料, 阐述了哺乳动物中发生DNA主动去甲基化的时空特异性, 并从细胞和组织特异性角度介绍DNA主动去甲基化的可能通路和机制, 即5-甲基胞嘧啶的氧化作用、5-甲基胞嘧啶脱氨基以及DNA修复等, 旨在为破译表观遗传重编程过程提供理论依据。
肖遥，张华林，白莉雅，王晓民，李文功，杨利国. 哺乳动物中的DNA主动去甲基化[J]. 遗传, 2011, 33(4): 298-306.
XIAO Yao, ZHANG Hua-Lin, BAI Chi-Ya, WANG Xiao-Min, LI Wen-Gong, YANG Li-Guo. Active DNA demethylation in mammals[J]. HEREDITAS, 2011, 33(4): 298-306.
| [1] Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature, 2009, 462(7271): 315-322.[2] Bird AP, Wolffe AP. Methylation-induced repression-belts, braces, and chromatin. Cell, 1999, 99(5): 451-454.[3] Jones PA, Takai D. The role of DNA methylation in mammalian epigenetics. Science, 2001, 293(5532): 1068-1070.[4] Cedar H, Bergman Y. Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet, 2009, 10(5): 295-304.[5] Koerner MV, Pauler FM, Huang R, Barlow DP. The function of non-coding RNAs in genomic imprinting. Development, 2009, 136(11): 1771-1783.[6] Park KY, Pfeifer K. Epigenetic interplay. Nat Genet, 2003, 34(2): 126-128.[7] Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse SD, Johnson BE, Hong CB, Nielsen C, Zhao YJ, Turecki G, Delaney A, Varhol R, Thiessen N, Shchors K, Heine VM, Rowitch DH, Xing XY, Fiore C, Schillebeeckx M, Jones SJM, Haussler D, Marra MA, Hirst M, Wang T, Costello JF. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature, 2010, 466(7303): 253-257.[8] Jones PA, Liang GN. Rethinking how DNA methylation patterns are maintained. Nat Rev Genet, 2009, 10(11): 805-811.[9] Law JA, Jacobsen SE. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet, 2010, 11(3): 204-220.[10] Reik W, Dean W, Walter J. Epigenetic reprogramming in mammalian development. Science, 2001, 293(5532): 1089-1093.[11] Reik W, Walter J. Genomic imprinting: parental influence on the genome. Nat Rev Genet, 2001, 2(1): 21-32.[12] Sasaki H, Matsui Y. Epigenetic events in mammalian germ-cell development: reprogramming and beyond. Nat Rev Genet, 2008, 9(2): 129-140.[13] Ooi SKT, Bestor TH. The colorful history of active DNA demethylation. Cell, 2008, 133(7): 1145-1148.[14] Li E. Chromatin modification and epigenetic reprogramming in mammalian development. Nat Rev Genet, 2002, 3(9): 662-673.[15] Reik W. Stability and flexibility of epigenetic gene regulation in mammalian development. Nature, 2007, 447(7143): 425-432.[16] Morgan HD, Santos F, Green K, Dean W, Reik W. Epigenetic reprogramming in mammals. Hum Mol Genet, 2005, 14(Spec 1): R47-R58.[17] Mayer W, Niveleau A, Walter J, Fundele R, Haaf T. Embryogenesis: Demethylation of the zygotic paternal genome. Nature, 2000, 403(6769): 501-502.[18] Oswald J, Engemann S, Lane N, Mayer W, Olek A, Fundele R, Dean W, Reik W, Walter J. Active demethylation of the paternal genome in the mouse zygote. Curr Biol, 2000, 10(8): 475-478.[19] Hajkova P, Erhardt S, Lane N, Haaf T, El-Maarri O, Reik W, Walter J, Surani MA. Epigenetic reprogramming in mouse primordial germ cells. Mech Dev, 2002, 117(1-2): 15-23.[20] Lee JY, Inoue K, Ono R, Ogonuki N, Kohda T, Kaneko-Ishino T, Ogura A, Ishino F. Erasing genomic imprinting memory in mouse clone embryos produced from day 11.5 primordial germ cells. Development, 2002, 129(8): 1807-1817.[21] Zhu JK. Active DNA demethylation mediated by DNA glycosylases. Annu Rev Genet, 2009, 43: 143-166.[22] Monk M, Boubelik M, Lehnert S. Temporal and regional changes in DNA methylation in the embryonic, extraembryonic and germ cell lineages during mouse embryo development. Development, 1987, 99(3): 371-382.[23] Howlett SK, Reik W. Methylation levels of maternal and paternal genomes during preimplantation development. Development, 1991, 113(1): 119-127.[24] Farthing CR, Ficz G, Ng RK, Chan CF, Andrews S, Dean W, Hemberger M, Reik W. Global mapping of DNA methylation in mouse promoters reveals epigenetic reprogramming of pluripotency genes. PLoS Genet, 2008, 4(6): e1000116.[25] McLay DW, Clarke HJ. Remodelling the paternal chromatin at fertilization in mammals. Reproduction, 2003, 125(5): 625-633.[26] Santos F, Hendrich B, Reik W, Dean W. Dynamic reprogramming of DNA methylation in the early mouse embryo. Dev Biol, 2002, 241(1): 172-182.[27] Haaf T. Methylation dynamics in the early mammalian embryo: implications of genome reprogramming defects for development. Curr Top Microbiol Immunol, 2006, 310: 13-22.[28] Barton SC, Arney KL, Shi W, Niveleau A, Fundele R, Surani MA, Haaf T. Genome-wide methylation patterns in normal and uniparental early mouse embryos. Hum Mol Genet, 2001, 10(26): 2983-2987.[29] van der Heijden GW, Dieker JW, Derijck AAHA, Muller S, Berden JHM, Braat DDM, van der Vlag J, de Boer P. Asymmetry in histone H3 variants and lysine methylation between paternal and maternal chromatin of the early mouse zygote. Mech Dev, 2005, 122(9): 1008-1022.[30] Hajkova P, Jeffries SJ, Lee C, Miller N, Jackson SP, Surani MA. Genome-wide reprogramming in the mouse germ line entails the base excision repair pathway. Science, 2010, 329(5987): 78-82.[31] Wossidlo M, Arand J, Sebastiano V, Lepikhov K, Boiani M, Reinhardt R, Schöler H, Walter J. Dynamic link of DNA demethylation, DNA strand breaks and repair in mouse zygotes. EMBO J, 2010, 29(11): 1877-1888.[32] Gehring M, Reik W, Henikoff S. DNA demethylation by DNA repair. Trends Genet, 2009, 25(2): 82-90.[33] Lane N, Dean W, Erhardt S, Hajkova P, Surani A, Walter J, Reik W. Resistance of IAPs to methylation reprogramming may provide a mechanism for epigenetic inheritance in the mouse. Genesis, 2003, 35(2): 88-93.[34] Kim SH, Kang YK, Koo DB, Kang MJ, Moon SJ, Lee KK, Han YM. Differential DNA methylation reprogramming of various repetitive sequences in mouse preimplantation embryos. Biochem Biophys Res Commun, 2004, 324(1): 58-63.[35] Kafri T, Gao X, Razin A. Mechanistic aspects of genome-wide demethylation in the preimplantation mouse embryo. Proc Natl Acad Sci USA, 1993, 90(22): 10558-10562.[36] Olek A, Walter J. The pre-implantation ontogeny of the H19 methylation imprint. Nat Genet, 1997, 17(3): 275-276.[37] Tremblay KD, Duran KL, Bartolomei MS. A 5' 2-kilobase-pair region of the imprinted mouse H19 gene exhibits exclusive paternal methylation throughout development. Mol Cell Biol, 1997, 17(8): 4322-4329.[38] Nakamura T, Arai Y, Umehara H, Masuhara M, Kimura T, Taniguchi H, Sekimoto T, Ikawa M, Yoneda Y, Okabe M, Tanaka S, Shiota K, Nakano T. PGC7/Stella protects against DNA demethylation in early embryogenesis. Nat Cell Biol, 2007, 9(1): 64-71.[39] Li XJ, Ito M, Zhou F, Youngson N, Zuo XP, Leder P, Ferguson-Smith AC. A maternal-zygotic effect gene, Zfp57, maintains both maternal and paternal imprints. Dev Cell, 2008, 15(4): 547-557.[40] Reese KJ, Lin S, Verona RI, Schultz RM, Bartolomei MS. Maintenance of paternal methylation and repression of the imprinted H19 gene requires MBD3. PLoS Genet, 2007, 3(8): e137.[41] Lawson KA, Dunn NR, Roelen BAJ, Zeinstra LM, Davis AM, Wright CVE, Korving JPWFM, Hogan BLM. Bmp4 is required for the generation of primordial germ cells in the mouse embryo. Genes Dev, 1999, 13(4): 424-436.[42] Fujiwara T, Dunn NR, Hogan BLM. Bone morphogenetic protein 4 in the extraembryonic mesoderm is required for allantois development and the localization and survival of primordial germ cells in the mouse. Proc Natl Acad Sci USA, 2001, 98(24): 13739-13744.[43] Ying Y, Zhao GQ. Cooperation of endoderm-derived BMP2 and extraembryonic ectoderm-derived BMP4 in primordial germ cell generation in the mouse. Dev Biol, 2001, 232(2): 484-492.[44] Popp C, Dean W, Feng SH, Cokus SJ, Andrews S, Pellegrini M, Jacobsen SE, Reik W. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature, 2010, 463(7284): 1101-1105.[45] Ginsburg M, Snow MHL, McLaren A. Primordial germ cells in the mouse embryo during gastrulation. Development, 1990, 110(2): 521-528.[46] Seki Y, Hayashi K, Itoh K, Mizugaki M, Saitou M, Matsui Y. Extensive and orderly reprogramming of genome-wide chromatin modifications associated with specification and early development of germ cells in mice. Dev Biol, 2005, 278(2): 440-458.[47] Seki Y, Yamaji M, Yabuta Y, Sano M, Shigeta M, Matsui Y, Saga Y, Tachibana M, Shinkai Y, Saitou M. Cellular dynamics associated with the genome-wide epigenetic reprogramming in migrating primordial germ cells in mice. Development, 2007, 134(14): 2627-2638.[48] Miki H, Inoue K, Kohda T, Honda A, Ogonuki N, Yuzuriha M, Mise N, Matsui Y, Baba T, Abe K, Ishino F, Ogura A. Birth of mice produced by germ cell nuclear transfer. Genesis, 2005, 41(2): 81-86.[49] Yamazaki Y, Low EW, Marikawa Y, Iwahashi K, Bartolomei MS, McCarrey JR, Yanagimachi R. Adult mice cloned from migrating primordial germ cells. Proc Natl Acad Sci USA, 2005, 102(32): 11361-11366.[50] Hajkova P, Ancelin K, Waldmann T, Lacoste N, Lange UC, Cesari F, Lee C, Almouzni G, Schneider R, Surani MA. Chromatin dynamics during epigenetic reprogramming in the mouse germ line. Nature, 2008, 452(7189): 877-881.[51] Briggs R, King TJ. Transplantation of living nuclei from blastula cells into enucleated frogs' eggs. Proc Natl Acad Sci USA, 1952, 38(5): 455-463.[52] Yang XZ, Smith SL, Tian XC, Lewin HA, Renard JP, Wakayama T. Nuclear reprogramming of cloned embryos and its implications for therapeutic cloning. Nat Genet, 2007, 39(3): 295-302.[53] Dean W, Santos F, Stojkovic M, Zakhartchenko V, Walter J, Wolf E, Reik W. Conservation of methylation reprogramming in mammalian development: Aberrant reprogramming in cloned embryos. Proc Natl Acad Sci USA, 2001, 98(24): 13734-13738.[54] Dean W, Santos F, Reik W. Epigenetic reprogramming in early mammalian development and following somatic nuclear transfer. Semin Cell Dev Biol, 2003, 14(1): 93-100.[55] Simonsson S, Gurdon J. DNA demethylation is necessary for the epigenetic reprogramming of somatic cell nuclei. Nat Cell Biol, 2004, 6(10): 984-990.[56] Santos F, Zakhartchenko V, Stojkovic M, Peters A, Jenuwein T, Wolf E, Reik W, Dean W. Epigenetic marking correlates with developmental potential in cloned bovine preimplantation embryos. Curr Biol, 2003, 13(13): 1116-1121.[57] Bourc'his D, Le Bourhis D, Patin D, Niveleau A, Comizzoli P, Renard JP, Viegas-Péquignot E. Delayed and incomplete reprogramming of chromosome methylation patterns in bovine cloned embryos. Curr Biol, 2001, 11(19): 1542-1546.[58] Kang YK, Park JS, Koo DB, Choi YH, Kim SU, Lee KK, Han YM. Limited demethylation leaves mosaic-type methylation states in cloned bovine pre-implantation embryos. EMBO J, 2002, 21(5): 1092-1100.[59] Gurdon JB, Melton DA. Nuclear reprogramming in cells. Science, 2008, 322(5909): 1811-1815.[60] Doi A, Park IH, Wen B, Murakami P, Aryee MJ, Irizarry R, Herb B, Ladd-Acosta C, Rho J, Loewer S, Miller J, Schlaeger T, Daley GQ, Feinberg AP. Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat Genet, 2009, 41(12): 1350-1353.[61] Mikkelsen TS, Hanna J, Zhang XL, Ku M, Wernig M, Schorderet P, Bernstein BE, Jaenisch R, Lander ES, Meissner A. Dissecting direct reprogramming through integrative genomic analysis. Nature, 2008, 454(7200): 49-55.[62] Kim K, Doi A, Wen B, Ng K, Zhao R, Cahan P, Kim J, Aryee MJ, Ji H, Ehrlich LIR, Yabuuchi A, Takeuchi A, Cunniff KC, Hongguang H, McKinney-Freeman S, Naveiras O, Yoon TJ, Irizarry RA, Jung N, Seita J, Hanna J, Murakami P, Jaenisch R, Weissleder R, Orkin SH, Weissman IL, Feinberg AP, Daley GQ. Epigenetic memory in induced pluripotent stem cells. Nature, 2010, 467(7313): 285-290.[63] Bhutani N, Brady JJ, Damian M, Sacco A, Corbel SY, Blau HM. Reprogramming towards pluripotency requires AID-dependent DNA demethylation. Nature, 2010, 463(7284): 1042-1047.[64] Gehring M, Bubb KL, Henikoff S. Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science, 2009, 324(5933): 1447-1451.[65] Hsieh TF, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, Fischer RL, Zilberman D. Genome-wide demethylation of Arabidopsis endosperm. Science, 2009, 324(5933): 1451-1454.[66] Bhattacharya SK, Ramchandani S, Cervoni N, Szyf M. A mammalian protein with specific demethylase activity for mCpG DNA. Nature, 1999, 397(6720): 579-583.[67] Barreto G, Schäfer A, Marhold J, Stach D, Swaminathan SK, Handa V, Döderlein G, Maltry N, Wu W, Lyko F, Niehrs C. Gadd45a promotes epigenetic gene activation by repair-mediated DNA demethylation. Nature, 2007, 445(7128): 671-675.[68] Jin SG, Guo C, Pfeifer GP. GADD45A does not promote DNA demethylation. PLoS Genet, 2008, 4(3): e1000013.[69] Métivier R, Gallais R, Tiffoche C, Le Péron C, Jurkowska RZ, Carmouche RP, Ibberson D, Barath P, Demay F, Reid G, Benes V, Jeltsch A, Gannon F, Salbert G. Cyclical DNA methylation of a transcriptionally active promoter. Nature, 2008, 452(7183): 45-50.[70] Kim MS, Kondo T, Takada I, Youn MY, Yamamoto Y, Takahashi S, Matsumoto T, Fujiyama S, Shirode Y, Yamaoka I, Kitagawa H, Takeyama KI, Shibuya H, Ohtake F, Kato S. DNA demethylation in hormone-induced transcriptional derepression. Nature, 2009, 461(7266): 1007-1012.[71] Schmitz KM, Schmitt N, Hoffmann-Rohrer U, Schäfer A, Grummt I, Mayer C. TAF12 recruits Gadd45a and the nucleotide excision repair complex to the promoter of rRNA genes leading to active DNA demethylation. Mol Cell, 2009, 33(3): 344-353.[72] Ma DK, Jang MH, Guo JU, Kitabatake Y, Chang ML, Pow-Anpongkul N, Flavell RA, Lu BF, Ming GL, Song HJ. Neuronal activity-induced Gadd45b promotes epigenetic DNA demethylation and adult neurogenesis. Science, 2009, 323(5917): 1074-1077.[73] Tahiliani M, Koh KP, Shen YH, Pastor WA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu DR, Aravind L, Rao A. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science, 2009, 324(5929): 930-935.[74] Ito S, D'Alessio AC, Taranova OV, Hong K, Sowers LC, Zhang Y. Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature, 2010, 466(7310): 1129-1133.[75] Okada Y, Yamagata K, Hong K, Wakayama T, Zhang Y. A role for the elongator complex in zygotic paternal genome demethylation. Nature, 2010, 463(7280): 554-558.[76] Niehrs C. Active DNA demethylation and DNA repair. Differentiation, 2009, 77(1): 1-11.[77] Wu SC, Zhang Y. Active DNA demethylation: many roads lead to Rome. Nat Rev Mol Cell Biol, 2010, 11(9): 607-620.[78] Bird A. DNA methylation patterns and epigenetic memory. Genes Dev, 2002, 16(1): 6-21.[79] Sofia HJ, Chen G, Hetzler BG, Reyes-Spindola JF, Miller NE. Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods. Nucleic Acids Res, 2001, 29(5): 1097-1106.[80] Delker RK, Fugmann SD, Papavasiliou FN. A coming-of-age story: activation-induced cytidine deaminase turns 10. Nat Immunol, 2009, 10(11): 1147-1153.[81] Morgan HD, Dean W, Coker HA, Reik W, Petersen-Mahrt SK. Activation-induced cytidine deaminase deaminates 5-methylcytosine in DNA and is expressed in pluripotent tissues: implications for epigenetic reprogramming. J Biol Chem, 2004, 279(50): 52353-52360.[82] Ma DK, Guo JU, Ming GL, Song HJ. DNA excision repair proteins and Gadd45 as molecular players for active DNA demethylation. Cell Cycle, 2009, 8(10): 1526-1531.[83] Engel N, Tront JS, Erinle T, Nguyen N, Latham KE, Sapienza C, Hoffman B, Liebermann DA. Conserved DNA methylation in Gadd45a(-/-) mice. Epigenetics, 2009, 4(2): 98-99.[84] Kangaspeska S, Stride B, Métivier R, Polycarpou-Schwarz M, Ibberson D, Carmouche RP, Benes V, Gannon F, Reid G. Transient cyclical methylation of promoter DNA. Nature, 2008, 452(7183): 112-115.[85] Hardeland U, Bentele M, Jiricny J, Schär P. The versatile thymine DNA-glycosylase: a comparative characterization of the human, Drosophila and fission yeast orthologs. Nucleic Acids Res, 2003, 31(9): 2261-2271.[86] Zhu B, Zheng Y, Hess D, Angliker H, Schwarz S, Siegmann M, Thiry S, Jost JP. 5-methylcytosine-DNA glycosylase activity is present in a cloned G/T mismatch DNA glycosylase associated with the chicken embryo DNA demethylation complex. Proc Natl Acad Sci USA, 2000, 97(10): 5135-5139.[87] Santos F, Dean W. Epigenetic reprogramming during early development in mammals. Reproduction, 2004, 127(6): 643-651. |
| [1] | 宋红卫, 安铁洙, 朴善花, 王春生. 哺乳动物DNA甲基化及其在体细胞诱导重编程中的作用[J]. 遗传, 2014, 36(5): 431-438. |
| [2] | 刘秋香, 薛庆中, 徐建红. 被子植物DNA去甲基化酶基因的进化分析[J]. 遗传, 2014, 36(3): 276-285. |
| [3] | 谢兆辉. DNA合成的忠实性机制[J]. 遗传, 2012, 34(6): 679-686. |
| [4] | 王春生，张志人，朴善花，安铁洙. microRNA在诱导体细胞重编程中的作用[J]. 遗传, 2012, 34(12): 1545-1550. |
| [5] | 李艳凤，张强，朱大海. 泛素介导的蛋白质降解与肿瘤发生[J]. 遗传, 2006, 28(12): 1591-1591~1596. |
| [6] | 朱克军，汪振诚，王学敏. 线粒体DNA修复系统相关酶的研究进展[J]. 遗传, 2004, 26(2): 274-282. |
| 阅读次数 | ||||||
|
全文 |
|
|||||
|
摘要 |
|
|||||
www.chinagene.cn
备案号：京ICP备09063187号-4
总访问:,今日访问:,当前在线:
