高级搜索

DNA甲基化结合蛋白

,  , 

downloadPDF

上一篇

下一篇

邹丹丹, 王晓利, 汪海林. DNA甲基化结合蛋白[J]. 环境化学, 2014, 33(10): 1672-1680. doi: 10.7524/j.issn.0254-6108.2014.10.021
引用本文: 邹丹丹, 王晓利, 汪海林. DNA甲基化结合蛋白[J]. 环境化学, 2014, 33(10): 1672-1680. doi: 10.7524/j.issn.0254-6108.2014.10.021
shu
ZOU Dandan, WANG Xiaoli, WANG Hailin. Methylated DNA binding proteins[J]. Environmental Chemistry, 2014, 33(10): 1672-1680. doi: 10.7524/j.issn.0254-6108.2014.10.021
Citation: ZOU Dandan, WANG Xiaoli, WANG Hailin. Methylated DNA binding proteins[J]. Environmental Chemistry, 2014, 33(10): 1672-1680. doi: 10.7524/j.issn.0254-6108.2014.10.021
shu

DNA甲基化结合蛋白

  • 1.

    中国科学院生态环境研究中心, 北京, 100085;

  • 2.

    山东省科学院分析测试中心, 山东, 249014

Methylated DNA binding proteins

  • 1.

    Research Center for Eco- Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China;

  • 2.

    Analysis and Test Center, Shandong Academy of Sciences, Shandong, 249014, China

  • 摘要: DNA甲基化是哺乳动物细胞中最重要的表观遗传学修饰之一, 大约70%—80%的CpG发生这种甲基化修饰.异常的甲基化在许多癌症中频发, 启动子CpG岛的高甲基化作为普遍的失活机制介导抑癌基因沉默.甲基化信号由甲基化结合蛋白来转译, 它们能够特异性识别并结合至甲基化位点通过募集辅阻遏复合物例如组蛋白去乙酰化酶(Histone Deacetylase, HDAC)等建立沉默的染色质, 从而在DNA甲基化和基因沉默中起桥梁作用.目前, 哺乳动物中已鉴定出的甲基化结合蛋白有三类, 分别是:MBD(Methyl-CpG-Binding Domain)、Kaiso以及SRA(Set and Ring finger-associated) 家族.本文就这三大家族(以MBD为主) 各自的结构、功能、结合甲基化DNA的特性以及它们在某些疾病发生中的作用做一综述.
    Abstract: DNA methylation is one of the most important epigenetic modifications in mammalian cells, approximately 70%—80% CpG dinucleotides are methylated. Dysregulation of DNA methylation occurs in many cancer cells, in which hypermethylation of promoter CpG islands may inactivate some tumor suppressor genes. The methylated DNA signal is read out by methylated DNA binding proteins (MBPs). They can specifically recognize and bind to methylated CpG sites and further recruit co-repressors, such as histone deacetylases (HDAC), to establish silent chromatin, thus providing a link between DNA methylation and gene silencing. In mammals, three structurally distinct types of MBPs have been identified so far: MBD(Methyl-CpG-Binding Domain), Kaiso and SRA(Set and Ring finger-associated) family proteins. Their structure, function, binding properties (focused on MBD protein)to methylated DNA and contribution to human disease process are reviewed and discussed in this article.
  • 加载中
  • [1] Portela A, Esteller M. Epigenetic modifications and human disease [J]. Nature Biotechnology, 2010, 28: 1057-1068
    [2] Shim J, Humphreys G I, Venkatesan B M, et al. Detection and quantification of methylation in DNA using solid-state nanopores [J]. Scientific Reports, 2013, 3: 1389-1396
    [3] Song J, Teplova M, Ishibe-Murakami S, et al. Structure-based mechanistic insights into DNMT1-mediated maintenance DNA methylation [J]. Science, 2012, 335: 709-712
    [4] Baccarelli A, Bollati V. Epigenetics and environmental chemicals [J]. Current Opinion in Pediatrics, 2009, 21: 243-251
    [5] Sasai N, Defossez P A. Many paths to one goal? The proteins that recognize methylated DNA in eukaryotes [J]. The International Journal of Development Biology, 2009, 53: 323-334
    [6] Fraga M F, Ballestar E, Montoya G, et al. The affinity of different MBD proteins for a specific methylated locus depends on their intrinsic binding properties [J]. Nucleic Acids Research, 2003, 31: 1765-1774
    [7] Deng D, Yin P, Yan C, et al. Recognition of methylated DNA by TAL effectors [J]. Cell Research, 2012, 22: 1502-1504
    [8] Clouaire T, Stancheva I. Methyl-CpG binding proteins: Specialized transcriptional repressors or structural components of chromatin? [J]. Cellular and Molecular Life Sciences, 2008, 65: 1509-1522
    [9] Dahl C, Guldberg P. DNA methylation analysis techniques [J]. Biogerontology, 2003, 4: 233-250
    [10] Smith Z D, Chan M M, Mikkelsen T S, et al. A unique regulatory phase of DNA methylation in the early mammalian embryo [J]. Nature, 2012, 484: 339-346
    [11] Lister R, Mukamel E A, Nery J R, et al. Global epigenomic reconfiguration during mammalian brain development [J]. Science, 2013, 341: 629-641
    [12] Ziller M J, Gu H, Muller F, et al. Charting a dynamic DNA methylation landscape of the human genome [J]. Nature, 2013, 500: 477-481
    [13] Maunakea A K, Chepelev I, Cui K, et al. Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition [J]. Cell Research, 2013, 23: 1256-1269
    [14] Rhee K D, Yu J, Zhao C Y, et al. Dnmt1-dependent DNA methylation is essential for photoreceptor terminal differentiation and retinal neuron survival [J]. Cell Death and Disease, 2012, 3: e427
    [15] Grayson D R, GuidottiA. The Dynamics of DNA methylation inschizophrenia and related psychiatric disorders [J]. Neuropsychopharmacology, 2013, 38: 138-166
    [16] Kohli R M, Zhang Y. TET enzymes, TDG and the dynamics of DNA demethylation [J]. Nature, 2013, 502: 472-479
    [17] Kang J, Kalantry S, Rao A. PGC7, H3K9me2 and Tet3: regulators of DNA methylation in zygotes [J]. Cell Research, 2013, 23: 6-9
    [18] Nga C W, Yildirima F, Yapa Y S, et al. Extensive changes in DNA methylation are associated with expression of mutant huntingtin [J]. Proceedings of the National Academy of Sciences, 2013, 110: 2354-2359
    [19] Carmona F J, Davalos V, Vidal E, et al. A comprehensive DNA mthylation proile of epithelial-to-mesenchymal transition [J]. Cancer Research, 2014, 74: OF1-OF12
    [20] Shen H, Laird P W. Interplay between the Cancer Genome and Epigenome [J]. Cell, 2013, 153: 38-55
    [21] Hogg K, Robinson W P, Beristain A G. Activation of endocrine-related gene expression in placental choriocarcinoma cell lines following DNA methylation knock-down [J]. Molecular Human Reproduction, 2014, 20: 677-689
    [22] Portela A, Liz J, Nogales V, et al. DNA methylation determines nucleosome occupancy in the 5'-CpG islands of tumor suppressor genes [J]. Oncogene, 2013, 32: 5421-5428
    [23] Khan S I, Aumsuwan P, Khan I A, et al. Epigenetic events associated with breast cancer and their prevention by dietary components targeting the epigenome [J]. Chemical Research in Toxicology, 2012, 25: 61-73
    [24] Jager P L D, Srivastava G, Lunnon K, et al. Alzheimer's disease: Early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci [J]. Nature Neurscience, 2014, doi:10.1038/nn.3786
    [25] Scherf D B, Sarkisyan N, Jacobsson H, et al. Epigenetic screen identifies genotype-specific promoter DNA methylation and oncogenic potential of CHRNB4 [J]. Oncogene, 2013, 32: 3329-3338
    [26] Yun J, Song S H, Park J, et al. Gene silencing of EREG mediated by DNA methylation and histone modification in human gastric cancers [J]. Laboratory Investigation, 2012, 92: 1033-1044
    [27] Deplus R, Denis1 H, Putmans1 P, et al. Citrullination of DNMT3A by PADI4 regulates its stability and controls DNA methylation [J]. Nucleic Acids Research, 2014, 42: 8285-8296
    [28] Day T K, Bianco-Miotto T. Common gene pathways and families altered by DNA methylation in breast and prostate cancers [J]. Endocrine-Related Cancer, 2013, 20: R215-R232
    [29] Liua H W, Lind H L, Yen J H, et al. Demethylation within the proximal promoter region of human estrogen receptor alpha gene correlates with its enhanced expression: Implications for female bias in lupus [J]. Molecular Immunology, 2014, 61: 28-37
    [30] Volkmar M, Dedeurwaerder S, Cunha D A, et al. DNA methylation profiling identifies epigenetic dysregulation in pancreatic islets from type 2 diabetic patients [J]. The EMBO Journal, 2012, 31: 1405-1426
    [31] Jimenez-Useche I, Ke J, Tian Y, et al. DNA methylation regulated nucleosome dynamics [J]. Scientific Reports, 2013, 3: 1-5
    [32] Nga C W, Yildirima F, Yapa Y S, et al. Aberrantly methylated genes in human papillary thyroid cancer and their association with BRAF/RAS mutation [J]. Frontiers in Genetics, 2013, 4: 1-11
    [33] Zhao X, Yang F, Li S, et al. CpG island methylator phenotype of myelodysplastic syndrome identified through genome-wide profiling of DNA methylation and gene expression [J]. British Journal of Haematology, 2014, 165: 649-658
    [34] Fetahu I S, Hobaus J, Aggarwal A. Calcium-sensing receptor silencing in colorectal cancer is associated with promoter hypermethylation and loss of acetylation on histone 3 [J]. International Journal of Cancer, 2014, 135: 2014-2023
    [35] Das P M, Singal R. J. DNA methylation and cancer [J]. Journal of Clinical Oncology, 2004, 22: 4632-4642
    [36] Buck-Koehntop B A, Defossez P A. On how mammalian transcription factors recognize methylated DNA. Epigenetics, 2013, 8: 131-137
    [37] Qureshi I A, Mehler M F. An evolving view of epigenetic complexity in the brain [J]. Philosophical Transactions of The Royal Society B, 2014, 369: 20130506
    [38] Baubec T, Ivanek R, Lienert F, et al. Methylation-dependent and -independent genomic targeting principles of the MBD protein family [J]. 2013, 153: 480-492
    [39] Shiraishi M, Sekiguchi A, Oates A J, et al. Methyl-CpG binding domain column chromatography as a tool for the analysis of genomic DNA methylat ion [J]. Analytical Biochemistry, 2004, 329: 1-10
    [40] Dhasarathy A, Wade P A. The MBD protein family-reading an epigenetic mark? [J]. Mutation Research, 2008, 647: 39-43
    [41] Klose R J, Sarraf S A, Schmiedeberg L, et al. DNA binding selectivity of MeCP2 due to a requirement for A/T sequences adjacent to methyl-CpG [J]. Molecular Cell, 2005, 19: 667-678
    [42] Lopez-Serra L, Ballestar E, Fraga M F, et al. A profile of methyl-CpG binding domain protein occupancy of hypermethylated promoter CpG islands of tumor suppressor genes in human cancer [J]. Cancer Research, 2006, 66: 8342-8346
    [43] Fuks F, Hurd P J, Wolf D, et al. The methyl-CpG-binding protein MeCP2 links DNA methylation to histone methylation [J]. The Journal of Biologic al Chemistry, 2003, 278: 4035-4040
    [44] Filion G J P, Zhenilo S, Salozhin S, et al. A family of human zinc finger proteins that bind methylated DNA and repress transcription [J]. Molecular and Cellular Biology, 2006, 26: 169-181
    [45] Yang J, Bai W, Niu P, et al. Aberrant hypomethylated STAT3 was identfied as a biomarker of chronic benzene poisoning through integrating DNA methylation and mRNA expression data [J]. Experimental and Molecular Pathology, 2014, 96: 346-353
    [46] Bailey K A, Wu M C, Ward W O, et al. Arsenic and the epigenome: Interindividual differences in arsenic metabolism related to distinct patterns of DNA methylation [J]. J Biochem Molecular Toxicology, 2013, 27: 106-115
    [47] Broberg K, Ahmed S, Engstrm K, et al. Arsenic exposure in early pregnancy alters genome-wide DNA methylation in cord blood, particularly in boys [J]. Journal of Developmental Origins of Health and Disease, 2014, 5: 288-298
    [48] Hanna C W, Bloom M S, Robinson W P, et al. DNA methylation changes in whole blood is associated with exposure to the environmental contamina nts, mercury, lead, cadmium and bisphenol A, in women undergoing ovarian stimulation for IVF [J]. Human Reproduction, 2012, 27: 1401-1410
    [49] Watkins D J, Wellenius G A, Butler R A, et al. Associations between serum perfluo roalkyl acids and LINE-1 DNA methylation [J]. Environment International, 2014, 63: 71-76
    [50] Prins S D, Koppen G, Jacobs G, et al. Inuence of ambient air pollution on global DNA methylation in healthy adults: A seasonal follow-up [J]. Environment International, 2013, 59: 418-424
    [51] Guo L, Byun H M, Zhong J, et al. Effects of short-term exposure to inhalable particulate matter on DNA methylation of tandem repeats [J]. Environ mental and Molecular Mutagenesis, 2014. 55: 322-335
    [52] Huen K, Yousefi P, Bradman A, et al. Effects of age, sex, and persistent organic pollutants on DNA methylation in children [J]. Environmental and Molecular Mutagenesis, 2014, 55: 209-222
    [53] Sun Y V, Smith A K, Conneely K N, et al. Epigenomic association analysis identifies smoking-related DNA methylation sites in African Americans [J]. Human Genetics, 2013, 132: 1027-1037
    [54] Zhao R, Zhang R, Li W, et al. Genome-wide DNA methylation patterns in discordant sib pairs with alcohol dependence [J]. Asia-Pacific Psychiatry, 2013, 5: 39-50
    [55] Sasai N, Nakao M, Defossez P A. Sequence-specific recognition of methylated DNA by human zinc-finger proteins [J]. Nucleic Acids Research, 2010, 38: 5015-5022
    [56] Prokhortchouk E, Defossez P A. The cell biology of DNA methylation in mammals [J]. Biochimica et Biophysica Acta, 2008, 1783: 2167-2173
    [57] Ohki I, Shimotake N, Fujita N, et al. Solution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA [J]. Cell, 2001, 105: 487-497
    [58] Jiang C L, Jin S G, Pfeifer G P. MBD3L1 is a transcriptional repressor that interacts with methyl-CpG-binding protein 2 (MBD2) and components of the NuRD complex [J]. The Journal of Biological Chemistry, 2004, 279: 52456-52464
    [59] Moore L D, Le T, Fan G. DNA Methylation and Its Basic Function [J]. Neuropsychopharmacology, 2013, 38: 23-38
    [60] Nan X, Meehan R R, Bird A. Dissection of the methyl-CpG binding domain from the chromosomal protein MeCP2 [J]. Nucleic Acids Research, 1993, 21: 4886-4892
    [61] Hendrich B, Bird A. Identification and characterization of a family of mammalian methyl-CpG binding proteins [J]. Molecullar and Cellular Biology, 1998, 18: 6538-6547
    [62] Wade P A. Methyl CpG binding proteins: Coupling chromatin architecture to gene regulation [J]. Oncogene, 2001, 20: 3166-3173
    [63] Stuss D P, Cheema M, Ng M K, et al. Impaired in vivo binding of MeCP2 to chromatin in the absence of its DNA methyl-binding domain [J]. Nucleic Acids Research, 2013, 41: 4888-4900
    [64] Ballestar E, Wolffe A P. Methyl-CpG-binding proteins [J]. European Journal of Biochemistry, 2001, 268: 1-6
    [65] Lyst M J, Nan X, Stancheva I. Regulation of MBD1-mediated transcriptional repression by SUMO and PIAS proteins [J]. The EMBO Journal, 2006, 25: 5317-5328
    [66] Jorgensen H F, Ben-Porath I, Bird A P. Mbd1 is recruited to both methylated and nonmethylated CpGs via distinct DNA binding domains [J]. Molecular and cellular biology, 2004, 24: 3387-3395
    [67] Saito M, Ishikawa F J. The mCpG-binding domain of human MBD3 does not bind to mCpG but interacts with NuRD/Mi2 components HDAC1 and MTA2 [J]. The Journal of Biological Chemistry, 2002, 277: 35434-35439
    [68] Jørgensen H F, Adie K, Chaubert P, et al. Engineering a high-affinity methyl-CpG-binding proteins [J]. Nucleic Acids Research, 2006, 34: e96
    [69] Hendrich B, Hardeland U, Ng H H, et al. The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites [J]. Nature, 1999, 401: 301-304
    [70] Ohki I, Shimotake N, Fujita N, et al. Solution structure of the methyl-CpG-binding domain of the methylation-dependent transcriptional repressor MBD1 [J]. The EMBO Journal, 1999, 18: 6653-6661
    [71] Fatemi M, Wade P A. MBD family proteins: Rthe epigenetic code [J]. Journal of Cell Science, 2006, 119: 3033-3037
    [72] Hendrich B, Guy J, Ramsahoye B, et al. Closely related proteins MBD2 and MBD3 play distinctive but interacting roles in mouse development [J]. Genes Development, 2001, 15: 710-723
    [73] Clouaire T, Heras J I, Merusi C, et al. Recruitment of MBD1 to target genes requires sequence-specific interaction of the MBD domain with methylated DNA [J]. Nucleic Acids Research, 2010, 38: 4620-4634
    [74] Ballestar E, Paz M F, Valle L, et al. Methyl-CpG binding proteins identify novel sites of epigenetic inactivation in human cancer [J]. The EMBO Journal, 2003, 22: 6335-6345
    [75] Guezennec X L, Vermeulen M, Brinkman A B, et al. MBD2/NuRD and MBD3/NuRD, two Distinct complexes with different biochemical and functional properties [J]. Molecular and Cellular Biology, 2006, 26: 843-851
    [76] Barr H, Hermann A, Berger J, et al. MBD2 Contributes to DNA methylation-directed repression of the Xist gene [J]. Molecular and Cellular Biology, 2007, 27: 3750-3757
    [77] Feng Q, Zhang Y. The MeCP1 complex represses transcription through preferential binding, remodeling, and deacetylating methylated nucleosomes [J]. Genes Development, 2001, 15: 827-832
    [78] Sarraf S A, Stancheva I. Methyl-CpG binding protein MBD1 couples histone H3 methylation at lysine 9 by SETDB1 to DNA replication and chromatin assembly [J]. Molecular Cell, 2004, 15: 595-605
    [79] Kondo E, Gu Z, Horii A, et al. The thymine DNA glycosylase MBD4 represses transcription and is associated with methylated p16INK4a and hMLH1 genes [J]. Molecular and Cellular Biology, 2005, 25: 4388-4396
    [80] Brero A, Easwaran H P, Nowak D, et al. Methyl CpG-binding proteins induce large-scale chromatin reorganization during terminal differentiation [J]. The Journal of Cell Biology, 2005, 169: 733-743
    [81] Wang L, Liu Y, Han R, et al. Mbd2 promotes Foxp3 demethylation and T-regulatory-cell function [J]. Molecular and Cellular Biology,2013, 33: 4106-4115
    [82] Mukhopadhyay P, Rezzoug F, Kaikaus J, et al. Alcohol modulates expression of DNA methyltranferases and methyl CpG-/CpG domain-binding proteins in murine embryonic fibroblasts [J]. Reproductive Toxicology, 2013, 37: 40-48
    [83] Bebbington A, Downs J, Percy A, et al. The phenotype associated with a large deletion on MECP2 [J]. European Journal of Human Genetics, 2012, 20: 921-927
    [84] Na E S, Nelson E D, Kavalali E T, et al. The impact of MeCP2 loss- or gain-of-function on synaptic plasticity [J]. Neuropsychophar macology, 2013, 38: 212-219
    [85] Banerjee A, Romero-Lorenzo E, Sur M. MeCP2: Making sense of missense in Rett syndrome [J]. Cell Research, 2013, 23: 1244-1246
    [86] Hansen J C, Ghosh R P, Woodcock C L. Binding of the Rett syndrome protein, MeCP2, to methylated and unmethylated DNA and chromatin [J]. Iubmb Life, 2010, 62: 732-738
    [87] Prokhortchouk A, Sansom O, Selfridge J, et al. Kaiso-deficient mice show resistance to intestinal cancer [J]. Molecular and Cellular Biology, 2006, 26: 199-208
    [88] Sharif J, Muto M, Takebayashi S, et al. The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA [J]. Nature, 2007, 450: 908-912
    [89] Avvakumov G V, Walker J R, Xue S, et al. Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1 [J]. Nature, 2008, 455: 822-826
    [90] Rottach A, Frauer C, Pichler G, et al. The multi-domain protein Np95 connects DNA methylation and histone modification [J]. Nucleic Acids Research, 2010, 38: 1796-1804
  • 加载中
WeChat 点击查看大图
计量
  • 文章访问数:  2965
  • HTML全文浏览数:  2965
  • PDF下载数:  1583
  • 施引文献:  0
出版历程
  • 收稿日期:  2014-05-12
邹丹丹, 王晓利, 汪海林. DNA甲基化结合蛋白[J]. 环境化学, 2014, 33(10): 1672-1680. doi: 10.7524/j.issn.0254-6108.2014.10.021
引用本文: 邹丹丹, 王晓利, 汪海林. DNA甲基化结合蛋白[J]. 环境化学, 2014, 33(10): 1672-1680. doi: 10.7524/j.issn.0254-6108.2014.10.021
shu
ZOU Dandan, WANG Xiaoli, WANG Hailin. Methylated DNA binding proteins[J]. Environmental Chemistry, 2014, 33(10): 1672-1680. doi: 10.7524/j.issn.0254-6108.2014.10.021
Citation: ZOU Dandan, WANG Xiaoli, WANG Hailin. Methylated DNA binding proteins[J]. Environmental Chemistry, 2014, 33(10): 1672-1680. doi: 10.7524/j.issn.0254-6108.2014.10.021
shu

DNA甲基化结合蛋白

  • 1.  中国科学院生态环境研究中心, 北京, 100085;
  • 2.  山东省科学院分析测试中心, 山东, 249014
  • 收稿日期:  2014-05-12

摘要: DNA甲基化是哺乳动物细胞中最重要的表观遗传学修饰之一, 大约70%—80%的CpG发生这种甲基化修饰.异常的甲基化在许多癌症中频发, 启动子CpG岛的高甲基化作为普遍的失活机制介导抑癌基因沉默.甲基化信号由甲基化结合蛋白来转译, 它们能够特异性识别并结合至甲基化位点通过募集辅阻遏复合物例如组蛋白去乙酰化酶(Histone Deacetylase, HDAC)等建立沉默的染色质, 从而在DNA甲基化和基因沉默中起桥梁作用.目前, 哺乳动物中已鉴定出的甲基化结合蛋白有三类, 分别是:MBD(Methyl-CpG-Binding Domain)、Kaiso以及SRA(Set and Ring finger-associated) 家族.本文就这三大家族(以MBD为主) 各自的结构、功能、结合甲基化DNA的特性以及它们在某些疾病发生中的作用做一综述.

English Abstract

    全文HTML

参考文献 (90)

返回顶部

目录

/

返回文章
返回

Copyright © 2019 中国科学院生态环境研究中心