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Progress in Studies of DNA Methylation and Gene Expression Regulation |
SHI Yu-jie1, LI Qing-he2, LIU Xiao-hui1 |
1. Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; 2. College of Biological Sciences, China Agricultural University, Beijing 100193, China |
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Abstract Epigenetic modifications refer to heritable changes that do not alter the DNA sequences which occur on cytosines and histones, including DNA methylation, histone modifications, chromatin remodeling and non-coding RNAs. Epigenetic regulation is a senior means that regulating gene expression. As an important epigenetic modification, DNA methylation is involved in gene expression regulation, transposon silencing, genomic imprinting, X chromosome inactivation and tumorigenesis. The study on genome-wide DNA methylation is in progress accompanying the advancement of research technologies, and DNA methylome of several organisms and cell types had been reported. Genome-wide study on DNA methylation facilitates understanding the characteristics and functions of DNA methylation, and also the regulatory role of DNA methylation. Here we reviewed the recent progress in DNA methylation and gene expression regulation studies, including DNA methylation distribution patterns in the genome and the relationship with gene transcription.
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Received: 11 March 2013
Published: 25 July 2013
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[1] Suzuki M M, Bird A. DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet, 2008, 9(6):465-476. [2] Selker E U, Tountas N A, Cross S H,et al. The methylated component of the Neurospora crassa genome. Nature, 2003, 422(6934):893-897. [3] Ramsahoye B H, Biniszkiewicz D, Lyko F, et al. Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc Natl Acad Sci U S A, 2000, 97(10):5237-5242. [4] Zhang X, Yazaki J, Sundaresan A, et al. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell, 2006, 126(6):1189-1201. [5] Lister R, Pelizzola M, Dowen R H, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature, 2009, 462(7271):315-322. [6] Haines T R, Rodenhiser D I, Ainsworth P J. Allele-specific non-CpG methylation of the Nf1 gene during early mouse development. Dev Biol, 2001, 240(2):585-598. [7] Murrell A, Rakyan V K, Beck S. From genome to epigenome. Hum Mol Genet, 2005, 14 Spec No 1:R3-R10. [8] Moving AHEAD with an international human epigenome project. Nature, 2008, 454(7205):711-715. [9] Zilberman D, Gehring M, Tran R K, et al. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet, 2007, 39(1):61-69. [10] Eckhardt F, Lewin J, Cortese R, et al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet, 2006, 38(12):1378-1385. [11] Xiang H, Zhu J, Chen Q, et al. Single base-resolution methylome of the silkworm reveals a sparse epigenomic map. Nat Biotechnol, 2010, 28(5):516-520. [12] Li Y, Zhu J, Tian G, et al. The DNA methylome of human peripheral blood mononuclear cells. PLoS Biol, 2010, 8(11):e1000533. [13] Barry C, Faugeron G, Rossignol J L. Methylation induced premeiotically in Ascobolus: coextension with DNA repeat lengths and effect on transcript elongation. Proc Natl Acad Sci U S A, 1993, 90(10):4557-4561. [14] Hohn T, Corsten S, Rieke S, et al. Methylation of coding region alone inhibits gene expression in plant protoplasts. Proc Natl Acad Sci U S A, 1996, 93(16):8334-8339. [15] Rountree M R, Selker E U. DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa. Genes Dev, 1997, 11(18):2383-2395. [16] Lorincz M C, Dickerson D R, Schmitt M, et al. Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nat Struct Mol Biol, 2004, 11(11):1068-1075. [17] Zemach A, McDaniel I E, Silva P, et al. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science, 2010, 328(5980):916-919. [18] Furner I J, Matzke M. Methylation and demethylation of the Arabidopsis genome. Curr Opin Plant Biol, 2011, 14(2):137-141. [19] Cokus S J, Feng S, Zhang X, et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature, 2008, 452(7184):215-219. [20] Lister R, O'Malley R C, Tonti-Filippini J, et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell, 2008, 133(3):523-536. [21] Chen P Y, Feng S, Joo J W, et al. A comparative analysis of DNA methylation across human embryonic stem cell lines. Genome Biol, 2011, 12(7):R62. [22] Gruenbaum Y, Naveh-Many T, Cedar H, et al. Sequence specificity of methylation in higher plant DNA. Nature, 1981, 292(5826):860-862. [23] Goll M G, Bestor T H. Eukaryotic cytosine methyltransferases. Annu Rev Biochem, 2005, 74:481-514. [24] Simmen M W, Leitgeb S, Charlton J, et al. Nonmethylated transposable elements and methylated genes in a chordate genome. Science, 1999, 283(5405):1164-1167. [25] Jaillon O, Aury J M, Brunet F, et al. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature, 2004, 431(7011):946-957. [26] Boyes J, Bird A. Repression of genes by DNA methylation depends on CpG density and promoter strength: evidence for involvement of a methyl-CpG binding protein. Embo J, 1992, 11(1):327-333. [27] Lock L F, Takagi N, Martin G R. Methylation of the Hprt gene on the inactive X occurs after chromosome inactivation. Cell, 1987, 48(1):39-46. [28] Jones P A. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet, 2012, 13(7):484-492. [29] Rauch T A, Wu X, Zhong X, et al. A human B cell methylome at 100-base pair resolution. Proc Natl Acad Sci U S A, 2009, 106(3):671-678. [30] Bird A P. Gene number, noise reduction and biological complexity. Trends Genet, 1995, 11(3):94-100. [31] Suzuki M M, Kerr A R, De Sousa D, et al. CpG methylation is targeted to transcription units in an invertebrate genome. Genome Res, 2007, 17(5):625-631. [32] Wang Y, Jorda M, Jones P L, et al. Functional CpG methylation system in a social insect. Science, 2006, 314(5799):645. [33] Feng S, Cokus S J, Zhang X, et al. Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci U S A, 2010, 107(19):8689-8694. [34] Nguyen C T, Gonzales F A, Jones P A. Altered chromatin structure associated with methylation-induced gene silencing in cancer cells: correlation of accessibility, methylation, MeCP2 binding and acetylation. Nucleic Acids Res, 2001, 29(22):4598-4606. [35] Yoder J A, Walsh C P, Bestor T H. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet, 1997, 13(8):335-340. [36] Suzuki M, Shiraishi K, Eguchi A, et al. Aberrant methylation of LINE-1, SLIT2, MAL and IGFBP7 in non-small cell lung cancer. Oncol Rep, 2013, 29(4):1308-1314. [37] Brenet F, Moh M, Funk P, et al. DNA methylation of the first exon is tightly linked to transcriptional silencing. PLoS One, 2011, 6(1):e14524. [38] Laurent L, Wong E, Li G, et al. Dynamic changes in the human methylome during differentiation. Genome Res, 2010, 20(3):320-331. [39] Chodavarapu R K, Feng S, Bernatavichute Y V, et al. Relationship between nucleosome positioning and DNA methylation. Nature, 2010, 466(7304):388-392. [40] Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol, 1987, 196(2):261-282. [41] Takai D, Jones P A. Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci U S A, 2002, 99(6):3740-3745. [42] Lander E S, Linton L M, Birren B, Nusbaum C, et al. Initial sequencing and analysis of the human genome. Nature, 2001, 409(6822):860-921. [43] Bird A. DNA methylation patterns and epigenetic memory. Genes Dev, 2002, 16(1):6-21. [44] Kelly T K, Miranda T B, Liang G, et al. H2A.Z maintenance during mitosis reveals nucleosome shifting on mitotically silenced genes. Mol Cell, 2010, 39(6):901-911. [45] Heller G, Babinsky V N, Ziegler B, et al. Genome-wide CpG island methylation analyses in non-small cell lung cancer patients. Carcinogenesis, 2013, 34(3):513-521. [46] Kobayashi H, Sakurai T, Miura F, et al. High-resolution DNA methylome analysis of primordial germ cells identifies gender-specific reprogramming in mice. Genome Res, 2013. [47] Sin H S, Barski A, Zhang F, et al. RNF8 regulates active epigenetic modifications and escape gene activation from inactive sex chromosomes in post-meiotic spermatids. Genes Dev, 2012, 26(24):2737-2748. [48] Farthing C R, Ficz G, Ng R K, et al. Global mapping of DNA methylation in mouse promoters reveals epigenetic reprogramming of pluripotency genes. PLoS Genet, 2008, 4(6):e1000116. [49] Shen L, Kondo Y, Guo Y, et al. Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters. PLoS Genet, 2007, 3(10):2023-2036. [50] Stadler M B, Murr R, Burger L, et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature, 2011, 480(7378):490-495. [51] Wiench M, John S, Baek S, et al. DNA methylation status predicts cell type-specific enhancer activity. EMBO J, 2011, 30(15):3028-3039. [52] Witcher M, Emerson B M. Epigenetic silencing of the p16(INK4a) tumor suppressor is associated with loss of CTCF binding and a chromatin boundary. Mol Cell, 2009, 34(3):271-284. [53] Bell A C, Felsenfeld G. Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature, 2000, 405(6785):482-485. [54] Lian C G, Xu Y, Ceol C, et al. Loss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma. Cell, 2012, 150(6):1135-1146. [55] Tahiliani M, Koh K P, Shen Y, et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science, 2009, 324(5929):930-935. [56] Kriaucionis S, Heintz N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science, 2009, 324(5929):929-930. |
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