DNA Methylation and Its Basic Function
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Aapola U, Kawasaki K, Scott HS, Ollila J, Vihinen M, Heino M et al (2000). Isolation and initial characterization of a novel zinc finger gene, DNMT3L, on 21q22.3, related to the cytosine-5-methyltransferase 3 gene family. Genomics 65: 293–298. Identified Dnmt3L and profiled its expression.
Aapola U, Lyle R, Krohn K, Antonarakis SE, Peterson P (2001). Isolation and initial characterization of the mouse Dnmt3l gene. Cytogenet Cell Genet 92: 122–126.
Achour M, Jacq X, Ronde P, Alhosin M, Charlot C, Chataigneau T et al (2008). The interaction of the SRA domain of ICBP90 with a novel domain of DNMT1 is involved in the regulation of VEGF gene expression. Oncogene 27: 2187–2197.
Amir RE, Van den Veyver IB, Wan M, Tran CQ, Francke U, Zoghbi HY (1999). Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2. Nat Genet 23: 185–188. Discovered MECP2 mutation as the cause of Rett Syndrome and paved way for further study of MECP2 protein role in the nervous system.
Aran D, Toperoff G, Rosenberg M, Hellman A (2011). Replication timing-related and gene body-specific methylation of active human genes. Hum Mol Genet 20: 670–680.
Asaka Y, Jugloff DG, Zhang L, Eubanks JH, Fitzsimonds RM (2006). Hippocampal synaptic plasticity is impaired in the Mecp2-null mouse model of Rett syndrome. Neurobiol Dis 21: 217–227.
Avery OT, Macleod CM, McCarty M (1944). Studies on the chemical nature of the substance inducing transformation of pneumococcal types: induction of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type Iii. J Exp Med 79: 137–158.
Ball MP, Li JB, Gao Y, Lee JH, LeProust EM, Park IH et al (2009). Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol 27: 361–368.
Bellacosa A, Cicchillitti L, Schepis F, Riccio A, Yeung AT, Matsumoto Y et al (1999). MED1, a novel human methyl-CpG-binding endonuclease, interacts with DNA mismatch repair protein MLH1. Proc Natl Acad Sci USA 96: 3969–3974.
Benetti R, Gonzalo S, Jaco I, Munoz P, Gonzalez S, Schoeftner S et al (2008). A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases. Nat Struct Mol Biol 15: 268–279.
Berezikov E (2011). Evolution of microRNA diversity and regulation in animals. Nat Rev Genet 12: 846–860.
Bhutani N, Brady JJ, Damian M, Sacco A, Corbel SY, Blau HM (2010). Reprogramming towards pluripotency requires AID-dependent DNA demethylation. Nature 463: 1042–1047.
Bird AP, Taggart M, Frommer M, Miller OJ, Macleod D (1985). A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Cell 40: 91–99. One of the pioneering studies that first identified CpG islands and described their sequence characteristics.
Bird AP (1980). DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res 8: 1499–1504.
Bostick M, Kim JK, Esteve PO, Clark A, Pradhan S, Jacobsen SE (2007). UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science 317: 1760–1764.
Bourc’his D, Bestor TH (2004). Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431: 96–99.
Bourc’his D, Xu GL, Lin CS, Bollman B, Bestor TH (2001). Dnmt3L and the establishment of maternal genomic imprints. Science 294: 2536–2539. Demonstrated the importance of Dnmt3L in the establishment of genomic imprints.
Brandeis M, Frank D, Keshet I, Siegfried Z, Mendelsohn M, Nemes A et al (1994). Sp1 elements protect a CpG island from de novo methylation. Nature 371: 435–438.
Brenet F, Moh M, Funk P, Feierstein E, Viale AJ, Socci ND et al (2011). DNA methylation of the first exon is tightly linked to transcriptional silencing. PLoS One 6: e14524.
Brenner C, Deplus R, Didelot C, Loriot A, Vire E, De Smet C et al (2005). Myc represses transcription through recruitment of DNA methyltransferase corepressor. EMBO J 24: 336–346.
Brueckner B, Garcia Boy R, Siedlecki P, Musch T, Kliem HC, Zielenkiewicz P et al (2005). Epigenetic reactivation of tumor suppressor genes by a novel small-molecule inhibitor of human DNA methyltransferases. Cancer Res 65: 6305–6311.
Buiting K (2010). Prader-Willi syndrome and Angelman syndrome. Am J Med Genet C Semin Med Genet 154C: 365–376.
Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J et al (2006). Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 38: 626–635.
Caspary T, Cleary MA, Baker CC, Guan XJ, Tilghman SM (1998). Multiple mechanisms regulate imprinting of the mouse distal chromosome 7 gene cluster. Mol Cell Biol 18: 3466–3474.
Cervoni N, Szyf M (2001). Demethylase activity is directed by histone acetylation. J Biol Chem 276: 40778–40787.
Chang Q, Khare G, Dani V, Nelson S, Jaenisch R (2006). The disease progression of Mecp2 mutant mice is affected by the level of BDNF expression. Neuron 49: 341–348.
Chen RZ, Akbarian S, Tudor M, Jaenisch R (2001). Deficiency of methyl-CpG binding protein-2 in CNS neurons results in a Rett-like phenotype in mice. Nat Genet 27: 327–331.
Chen RZ, Pettersson U, Beard C, Jackson-Grusby L, Jaenisch R (1998). DNA hypomethylation leads to elevated mutation rates. Nature 395: 89–93.
Choi JD, Underkoffler LA, Wood AJ, Collins JN, Williams PT, Golden JA et al (2005). A novel variant of Inpp5f is imprinted in brain, and its expression is correlated with differential methylation of an internal CpG island. Mol Cell Biol 25: 5514–5522.
Choi JK (2010). Contrasting chromatin organization of CpG islands and exons in the human genome. Genome Biol 11: R70.
Citterio E, Papait R, Nicassio F, Vecchi M, Gomiero P, Mantovani R et al (2004). Np95 is a histone-binding protein endowed with ubiquitin ligase activity. Mol Cell Biol 24: 2526–2535.
Cohen S, Gabel HW, Hemberg M, Hutchinson AN, Sadacca LA, Ebert DH et al (2011). Genome-wide activity-dependent MeCP2 phosphorylation regulates nervous system development and function. Neuron 72: 72–85.
Compere SJ, Palmiter RD (1981). DNA methylation controls the inducibility of the mouse metallothionein-I gene lymphoid cells. Cell 25: 233–240.
Cortellino S, Xu J, Sannai M, Moore R, Caretti E, Cigliano A et al (2011). Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair. Cell 146: 67–79.
Coulondre C, Miller JH, Farabaugh PJ, Gilbert W (1978). Molecular basis of base substitution hotspots in Escherichia coli. Nature 274: 775–780.
Creusot F, Acs G, Christman JK (1982). Inhibition of DNA methyltransferase and induction of Friend erythroleukemia cell differentiation by 5-azacytidine and 5-aza-2′-deoxycytidine. J Biol Chem 257: 2041–2048.
D’Alessio AC, Weaver IC, Szyf M (2007). Acetylation-induced transcription is required for active DNA demethylation in methylation-silenced genes. Mol Cell Biol 27: 7462–7474. An example of coordinated actions from both histone modification and DNA demethylation in regulating gene regulation.
Daniel JM, Spring CM, Crawford HC, Reynolds AB, Baig A (2002). The p120(ctn)-binding partner Kaiso is a bi-modal DNA-binding protein that recognizes both a sequence-specific consensus and methylated CpG dinucleotides. Nucleic Acids Res 30: 2911–2919.
Dawlaty MM, Ganz K, Powell BE, Hu YC, Markoulaki S, Cheng AW et al (2011). Tet1 is dispensable for maintaining pluripotency and its loss is compatible with embryonic and postnatal development. Cell Stem Cell 9: 166–175.
Deng JV, Rodriguiz RM, Hutchinson AN, Kim IH, Wetsel WC, West AE (2010). MeCP2 in the nucleus accumbens contributes to neural and behavioral responses to psychostimulants. Nat Neurosci 13: 1128–1136.
Devys D, Lutz Y, Rouyer N, Bellocq JP, Mandel JL (1993). The FMR-1 protein is cytoplasmic, most abundant in neurons and appears normal in carriers of a fragile X premutation. Nat Genet 4: 335–340.
Dhayalan A, Rajavelu A, Rathert P, Tamas R, Jurkowska RZ, Ragozin S et al (2010). The Dnmt3a PWWP domain reads histone 3 lysine 36 trimethylation and guides DNA methylation. J Biol Chem 285: 26114–26120.
Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M et al (2006). DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 38: 1378–1385.
Ehrlich M, Gama-Sosa MA, Huang LH, Midgett RM, Kuo KC, McCune RA et al (1982). Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells. Nucleic Acids Res 10: 2709–2721.
Fan G, Beard C, Chen RZ, Csankovszki G, Sun Y, Siniaia M et al (2001). DNA hypomethylation perturbs the function and survival of CNS neurons in postnatal animals. J Neurosci 21: 788–797. One of the pioneering works in investigating the role of Dnmts in the CNS.
Fan G, Martinowich K, Chin MH, He F, Fouse SD, Hutnick L et al (2005). DNA methylation controls the timing of astrogliogenesis through regulation of JAK-STAT signaling. Development 132: 3345–3356.
Fatemi SH, Folsom TD (2011). The role of fragile X mental retardation protein in major mental disorders. Neuropharmacology 60: 1221–1226.
Feng J, Chang H, Li E, Fan G (2005). Dynamic expression of de novo DNA methyltransferases Dnmt3a and Dnmt3b in the central nervous system. J Neurosci Res 79: 734–746.
Feng J, Zhou Y, Campbell SL, Le T, Li E, Sweatt JD et al (2010). Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons. Nat Neurosci 13: 423–430. Demonstrated the importance of continual activity of Dnmts in postmitotic neurons and that the Dnmts exhibit overlapping roles of each other.
Ficz G, Branco MR, Seisenberger S, Santos F, Krueger F, Hore TA et al (2011). Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature 473: 398–402.
Filion GJ, Zhenilo S, Salozhin S, Yamada D, Prokhortchouk E, Defossez PA (2006). A family of human zinc finger proteins that bind methylated DNA and repress transcription. Mol Cell Biol 26: 169–181.
Fouse SD, Shen Y, Pellegrini M, Cole S, Meissner A, Van Neste L et al (2008). Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation. Cell Stem Cell 2: 160–169.
Fuks F, Burgers WA, Brehm A, Hughes-Davies L, Kouzarides T (2000). DNA methyltransferase Dnmt1 associates with histone deacetylase activity. Nat Genet 24: 88–91. Demonstrates physical connection between the two epigenetic mechanisms: DNA methylation and histone modification.
Fuks F, Hurd PJ, Deplus R, Kouzarides T (2003). The DNA methyltransferases associate with HP1 and the SUV39H1 histone methyltransferase. Nucleic Acids Res 31: 2305–2312.
Gaudet F, Rideout III WM, Meissner A, Dausman J, Leonhardt H, Jaenisch R (2004). Dnmt1 expression in pre- and postimplantation embryogenesis and the maintenance of IAP silencing. Mol Cell Biol 24: 1640–1648.
Ge YZ, Pu MT, Gowher H, Wu HP, Ding JP, Jeltsch A et al (2004). Chromatin targeting of de novo DNA methyltransferases by the PWWP domain. J Biol Chem 279: 25447–25454.
Gebhard C, Benner C, Ehrich M, Schwarzfischer L, Schilling E, Klug M et al (2010). General transcription factor binding at CpG islands in normal cells correlates with resistance to de novo DNA methylation in cancer cells. Cancer Res 70: 1398–1407.
Geiman TM, Sankpal UT, Robertson AK, Zhao Y, Zhao Y, Robertson KD (2004). DNMT3B interacts with hSNF2H chromatin remodeling enzyme, HDACs 1 and 2, and components of the histone methylation system. Biochem Biophys Res Commun 318: 544–555.
Ghosh S, Yates AJ, Frühwald MC, Miecznikowski JC, Plass C, Smiraglia D (2010). Tissue specific DNA methylation of CpG islands in normal human adult somatic tissues distinguishes neural from non-neural tissues. Epigenetics 5: 527–538.
Giacometti E, Luikenhuis S, Beard C, Jaenisch R (2007). Partial rescue of MeCP2 deficiency by postnatal activation of MeCP2. Proc Natl Acad Sci USA 104: 1931–1936.
Globisch D, Munzel M, Muller M, Michalakis S, Wagner M, Koch S et al (2010). Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS One 5: e15367.
Golshani P, Hutnick L, Schweizer F, Fan G (2005). Conditional Dnmt1 deletion in dorsal forebrain disrupts development of somatosensory barrel cortex and thalamocortical long-term potentiation. Thalamus Relat Syst 3: 227–233.
Goto K, Numata M, Komura JI, Ono T, Bestor TH, Kondo H (1994). Expression of DNA methyltransferase gene in mature and immature neurons as well as proliferating cells in mice. Differentiation 56: 39–44. Identified DNA methyltransferase mRNA in postmitotic neurons and suggested that DNA methylation served a unique function in neurons.
Guo J, Ma DK, Mo H, Ball MP, Jang MH, Bonaguidi MA et al (2011a). Neuronal activity modifies the DNA methylation landscape in the adult brain. Nat Neurosci 14: 1345–1351. Investigated the extent to which the DNA methylation pattern is modifiable by neural activity in vivo.
Guo J, Su Y, Zhong C, Ming GL, Song H (2011b). Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell 145: 423–434. Also discovered few gene regions, including BDNF, that exhibit demethylation and remethylation cycle in postmitotic neurons.
Guy J, Gan J, Selfridge J, Cobb S, Bird A (2007). Reversal of neurological defects in a mouse model of Rett syndrome. Science 315: 1143–1147.
Guy J, Hendrich B, Holmes M, Martin JE, Bird A (2001). A mouse Mecp2-null mutation causes neurological symptoms that mimic Rett syndrome. Nat Genet 27: 322–326.
Gwynn B, Lueders K, Sands MS, Birkenmeier EH (1998). Intracisternal A-particle element transposition into the murine beta-glucuronidase gene correlates with loss of enzyme activity: a new model for beta-glucuronidase deficiency in the C3H mouse. Mol Cell Biol 18: 6474–6481.
Han L, Witmer PD, Casey E, Valle D, Sukumar S (2007). DNA methylation regulates microRNA expression. Cancer Biol Ther 6: 1284–1288.
Hashimoto H, Horton JR, Zhang X, Bostick M, Jacobsen SE, Cheng X (2008). The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix. Nature 455: 826–829.
Hashimoto H, Horton JR, Zhang X, Cheng X (2009). UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications. Epigenetics 4: 8–14.
Hata K, Okano M, Lei H, Li E (2002). Dnmt3L cooperates with the Dnmt3 family of de novo DNA methyltransferases to establish maternal imprints in mice. Development 129: 1983–1993.
He YF, Li BZ, Li Z, Liu P, Wang Y, Tang Q et al (2011). Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 333: 1303–1307.
Hellman A, Chess A (2007). Gene body-specific methylation on the active X chromosome. Science 315: 1141–1143.
Hendrich B, Bird A (1998). Identification and characterization of a family of mammalian methyl-CpG binding proteins. Mol Cell Biol 18: 6538–6547.
Hendrich B, Hardeland U, Ng HH, Jiricny J, Bird A (1999). The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites. Nature 401: 301–304.
Hermann A, Goyal R, Jeltsch A (2004). The Dnmt1 DNA-(cytosine-C5)-methyltransferase methylates DNA processively with high preference for hemimethylated target sites. J Biol Chem 279: 48350–48359.
Holliday R, Pugh JE (1975). DNA modification mechanisms and gene activity during development. Science 187: 226–232.
Hotchkiss RD (1948). The quantitative separation of purines, pyrimidines, and nucleosides by paper chromatography. J Biol Chem 175: 315–332. Discovered 5-methylcytosine in the mammalian genome.
Huang Y, Pastor WA, Shen Y, Tahiliani M, Liu DR, Rao A (2010). The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS One 5: e8888.
Hutchinson AN, Deng JV, Aryal DK, Wetsel WC, West AE (2012). Differential regulation of MeCP2 phosphorylation in the CNS by dopamine and serotonin. Neuropsychopharmacology 37: 321–337.
Hutnick LK, Golshani P, Namihira M, Xue Z, Matynia A, Yang XW et al (2009). DNA hypomethylation restricted to the murine forebrain induces cortical degeneration and impairs postnatal neuronal maturation. Hum Mol Genet 18: 2875–2888.
Hutnick LK, Huang X, Loo TC, Ma Z, Fan G (2010). Repression of retrotransposal elements in mouse embryonic stem cells is primarily mediated by a DNA methylation-independent mechanism. J Biol Chem 285: 21082–21091.
Illingworth RS, Gruenewald-Schneider U, Webb S, Kerr AR, James KD, Turner DJ et al (2010). Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet 6: e1001134.
Im HI, Hollander JA, Bali P, Kenny PJ (2010). MeCP2 controls BDNF expression and cocaine intake through homeostatic interactions with microRNA-212. Nat Neurosci 13: 1120–1127.
Inano K, Suetake I, Ueda T, Miyake Y, Nakamura M, Okada M et al (2000). Maintenance-type DNA methyltransferase is highly expressed in post-mitotic neurons and localized in the cytoplasmic compartment. J Biochem 128: 315–321.
Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P et al (2009). The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 41: 178–186.
Ito S, D’Alessio AC, Taranova OV, Hong K, Sowers LC, Zhang Y (2010). Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 466: 1129–1133.
Ito S, Shen L, Dai Q, Wu SC, Collins LB, Swenberg JA et al (2011). Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333: 1300–1303.
Jackson-Grusby L, Beard C, Possemato R, Tudor M, Fambrough D, Csankovszki G et al (2001). Loss of genomic methylation causes p53-dependent apoptosis and epigenetic deregulation. Nat Genet 27: 31–39.
Jia D, Jurkowska RZ, Zhang X, Jeltsch A, Cheng X (2007). Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature 449: 248–251.
Jin SG, Wu X, Li AX, Pfeifer GP (2011). Genomic mapping of 5-hydroxymethylcytosine in the human brain. Nucleic Acids Res 39: 5015–5024.
Jones PL, Veenstra GJ, Wade PA, Vermaak D, Kass SU, Landsberger N et al (1998). Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat Genet 19: 187–191.
Jüttermann R, Li E, Jaenisch R (1994). Toxicity of 5-aza-2′-deoxycytidine to mammalian cells is mediated primarily by covalent trapping of DNA methyltransferase rather than DNA demethylation. Proc Natl Acad Sci USA 91: 11797–11801.
Kaneda M, Okano M, Hata K, Sado T, Tsujimoto N, Li E et al (2004). Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting. Nature 429: 900–903.
Kantor B, Kaufman Y, Makedonski K, Razin A, Shemer R (2004). Establishing the epigenetic status of the Prader-Willi/Angelman imprinting center in the gametes and embryo. Hum Mol Genet 13: 2767–2779.
Karagianni P, Amazit L, Qin J, Wong J (2008). ICBP90, a novel methyl K9 H3 binding protein linking protein ubiquitination with heterochromatin formation. Mol Cell Biol 28: 705–717.
Kimura H, Shiota K (2003). Methyl-CpG-binding protein, MeCP2, is a target molecule for maintenance DNA methyltransferase, Dnmt1. J Biol Chem 278: 4806–4812.
Kishi N, Macklis JD (2004). MECP2 is progressively expressed in post-migratory neurons and is involved in neuronal maturation rather than cell fate decisions. Mol Cell Neurosci 27: 306–321.
Klein CJ, Botuyan MV, Wu Y, Ward CJ, Nicholson GA, Hammans S et al (2011). Mutations in DNMT1 cause hereditary sensory neuropathy with dementia and hearing loss. Nat Genet 43: 595–600.
Kovacheva VP, Mellott TJ, Davison JM, Wagner N, Lopez-Coviella I, Schnitzler AC et al (2007). Gestational choline deficiency causes global and Igf2 gene DNA hypermethylation by up-regulation of Dnmt1 expression. J Biol Chem 282: 31777–31788.
Kriaucionis S, Heintz N (2009). The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324: 929–930. This is first paper describing that hydroxymethylcytosine is enriched in postmitotic CNS neurons.
Kuster JE, Guarnieri MH, Ault JG, Flaherty L, Swiatek PJ (1997). IAP insertion in the murine LamB3 gene results in junctional epidermolysis bullosa. Mamm Genome 8: 673–681.
La Salle S, Oakes CC, Neaga OR, Bourc’his D, Bestor TH, Trasler JM (2007). Loss of spermatogonia and wide-spread DNA methylation defects in newborn male mice deficient in DNMT3L. BMC Dev Biol 7: 104.
Ladd-Acosta C, Pevsner J, Sabunciyan S, Yolken RH, Webster MJ, Dinkins T et al (2007). DNA methylation signatures within the human brain. Am J Hum Genet 81: 1304–1315.
LaPlant Q, Vialou V, Covington III HE, Dumitriu D, Feng J, Warren BL et al (2010). Dnmt3a regulates emotional behavior and spine plasticity in the nucleus accumbens. Nat Neurosci 13: 1137–1143.
LaSalle JM, Goldstine J, Balmer D, Greco CM (2001). Quantitative localization of heterogeneous methyl-CpG-binding protein 2 (MeCP2) expression phenotypes in normal and Rett syndrome brain by laser scanning cytometry. Hum Mol Genet 10: 1729–1740.
Le T, Kim KP, Fan G, Faull KF (2011). A sensitive mass spectrometry method for simultaneous quantification of DNA methylation and hydroxymethylation levels in biological samples. Anal Biochem 412: 203–209.
Lee JH, Skalnik DG (2005). CpG-binding protein (CXXC finger protein 1) is a component of the mammalian Set1 histone H3-Lys4 methyltransferase complex, the analogue of the yeast Set1/COMPASS complex. J Biol Chem 280: 41725–41731.
Lee MS, Jun DH, Hwang CI, Park SS, Kang JJ, Park HS et al (2006). Selection of neural differentiation-specific genes by comparing profiles of random differentiation. Stem Cells 24: 1946–1955.
Leonhardt H, Page AW, Weier HU, Bestor TH (1992). A targeting sequence directs DNA methyltransferase to sites of DNA replication in mammalian nuclei. Cell 71: 865–873.
Levenson JM, Roth TL, Lubin FD, Miller CA, Huang IC, Desai P et al (2006). Evidence that DNA (cytosine-5) methyltransferase regulates synaptic plasticity in the hippocampus. J Biol Chem 281: 15763–15773.
Lewis JD, Meehan RR, Henzel WJ, Maurer-Fogy I, Jeppesen P, Klein F et al (1992). Purification, sequence, and cellular localization of a novel chromosomal protein that binds to methylated DNA. Cell 69: 905–914.
Li BZ, Huang Z, Cui QY, Song XH, Du L, Jeltsch A et al (2011a). Histone tails regulate DNA methylation by allosterically activating de novo methyltransferase. Cell Res 21: 1172–1181.
Li E, Bestor TH, Jaenisch R (1992). Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69: 915–926. Developed the Dnmt1 knockout mice.
Li H, Zhong X, Chau KF, Williams EC, Chang Q (2011b). Loss of activity-induced phosphorylation of MeCP2 enhances synaptogenesis, LTP and spatial memory. Nat Neurosci 14: 1001–1008.
Lienert F, Wirbelauer C, Som I, Dean A, Mohn F, Schubeler D (2011). Identification of genetic elements that autonomously determine DNA methylation states. Nat Genet 43: 1091–1097. Demonstrated that transcription factor binding regulates DNA methylation by inserting 50 different DNA elements into the same chromosome region.
Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J et al (2009). Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462: 315–322.
Liutkeviciute Z, Lukinavicius G, Masevicius V, Daujotyte D, Klimasauskas S (2009). Cytosine-5-methyltransferases add aldehydes to DNA. Nat Chem Biol 5: 400–402.
Lopes EC, Valls E, Figueroa ME, Mazur A, Meng FG, Chiosis G et al (2008). Kaiso contributes to DNA methylation-dependent silencing of tumor suppressor genes in colon cancer cell lines. Cancer Res 68: 7258–7263.
Lubin FD, Roth TL, Sweatt JD (2008). Epigenetic regulation of BDNF gene transcription in the consolidation of fear memory. J Neurosci 28: 10576–10586.
Luikenhuis S, Giacometti E, Beard CF, Jaenisch R (2004). Expression of MeCP2 in postmitotic neurons rescues Rett syndrome in mice. Proc Natl Acad Sci USA 101: 6033–6038.
Lujambio A, Calin GA, Villanueva A, Ropero S, Sanchez-Cespedes M, Blanco D et al (2008). A microRNA DNA methylation signature for human cancer metastasis. Proc Natl Acad Sci USA 105: 13556–13561.
Ma DK, Jang MH, Guo JU, Kitabatake Y, Chang ML, Pow-Anpongkul N et al (2009). Neuronal activity-induced Gadd45b promotes epigenetic DNA demethylation and adult neurogenesis. Science 323: 1074–1077.
Macleod D, Charlton J, Mullins J, Bird AP (1994). Sp1 sites in the mouse aprt gene promoter are required to prevent methylation of the CpG island. Genes Dev 8: 2282–2292.
Martin Caballero I, Hansen J, Leaford D, Pollard S, Hendrich BD (2009). The methyl-CpG binding proteins Mecp2, Mbd2 and Kaiso are dispensable for mouse embryogenesis, but play a redundant function in neural differentiation. PLoS One 4: e4315.
Martinowich K, Hattori D, Wu H, Fouse S, He F, Hu Y et al (2003). DNA methylation-related chromatin remodeling in activity-dependent BDNF gene regulation. Science 302: 890–893. Demonstrated that methylation and MeCP2 binding to the BDNF promoter are regulated by neuronal activity.
Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D’Souza C, Fouse SD et al (2010). Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 466: 253–257.
Mayer W, Niveleau A, Walter J, Fundele R, Haaf T (2000). Demethylation of the zygotic paternal genome. Nature 403: 501–502.
McCarty M, Avery OT (1946). Studies on the chemical nature of the substance inducing transformation of pneumococcal types: II. Effect of desoxyribonuclease on the biological activity of the transforming substance. J Exp Med 83: 89–96.
McGowan PO, Sasaki A, D’Alessio AC, Dymov S, Labonte B, Szyf M et al (2009). Epigenetic regulation of the glucocorticoid receptor in human brain associates with childhood abuse. Nat Neurosci 12: 342–348. Observed childhood abuse in suicidal victims associated with higher DNA methylation level in the glucocorticoid receptor promoter in the hippocampus.
Meehan RR, Lewis JD, McKay S, Kleiner EL, Bird AP (1989). Identification of a mammalian protein that binds specifically to DNA containing methylated CpGs. Cell 58: 499–507.
Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A et al (2008). Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454: 766–770.
Michaud EJ, van Vugt MJ, Bultman SJ, Sweet HO, Davisson MT, Woychik RP (1994). Differential expression of a new dominant agouti allele (Aiapy) is correlated with methylation state and is influenced by parental lineage. Genes Dev 8: 1463–1472.
Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G et al (2007). Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448: 553–560.
Mill J, Tang T, Kaminsky Z, Khare T, Yazdanpanah S, Bouchard L et al (2008). Epigenomic profiling reveals DNA-methylation changes associated with major psychosis. Am J Hum Genet 82: 696–711.
Millar CB, Guy J, Sansom OJ, Selfridge J, MacDougall E, Hendrich B et al (2002). Enhanced CpG mutability and tumorigenesis in MBD4-deficient mice. Science 297: 403–405.
Miller CA, Gavin CF, White JA, Parrish RR, Honasoge A, Yancey CR et al (2010). Cortical DNA methylation maintains remote memory. Nat Neurosci 13: 664–666.
Miller CA, Sweatt JD (2007). Covalent modification of DNA regulates memory formation. Neuron 53: 857–869.
Mohn F, Weber M, Rebhan M, Roloff TC, Richter J, Stadler MB et al (2008). Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Mol Cell 30: 755–766.
Moretti P, Levenson JM, Battaglia F, Atkinson R, Teague R, Antalffy B et al (2006). Learning and memory and synaptic plasticity are impaired in a mouse model of Rett syndrome. J Neurosci 26: 319–327.
Morris KV, Chan SW, Jacobsen SE, Looney DJ (2004). Small interfering RNA-induced transcriptional gene silencing in human cells. Science 305: 1289–1292.
Mortusewicz O, Schermelleh L, Walter J, Cardoso MC, Leonhardt H (2005). Recruitment of DNA methyltransferase I to DNA repair sites. Proc Natl Acad Sci USA 102: 8905–8909.
Muramatsu M, Kinoshita K, Fagarasan S, Yamada S, Shinkai Y, Honjo T (2000). Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme. Cell 102: 553–563.
Muto M, Kanari Y, Kubo E, Takabe T, Kurihara T, Fujimori A et al (2002). Targeted disruption of Np95 gene renders murine embryonic stem cells hypersensitive to DNA damaging agents and DNA replication blocks. J Biol Chem 277: 34549–34555.
Nan X, Meehan RR, Bird A (1993). Dissection of the methyl-CpG binding domain from the chromosomal protein MeCP2. Nucleic Acids Res 21: 4886–4892.
Nan X, Ng HH, Johnson CA, Laherty CD, Turner BM, Eisenman RN et al (1998). Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393: 386–389.
Nelson ED, Kavalali ET, Monteggia LM (2006). MeCP2-dependent transcriptional repression regulates excitatory neurotransmission. Curr Biol 16: 710–716.
Ng HH, Zhang Y, Hendrich B, Johnson CA, Turner BM, Erdjument-Bromage H et al (1999). MBD2 is a transcriptional repressor belonging to the MeCP1 histone deacetylase complex. Nat Genet 23: 58–61.
Nguyen S, Meletis K, Fu D, Jhaveri S, Jaenisch R (2007). Ablation of de novo DNA methyltransferase Dnmt3a in the nervous system leads to neuromuscular defects and shortened lifespan. Dev Dyn 236: 1663–1676. Demonstrate that knockout of Dnmt3a in neural tissue during development does not affect development of cortical neurons but results in hypomethylation of the Gfap promoter and improper motor neuron development.
Okano M, Bell DW, Haber DA, Li E (1999). DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99: 247–257. Demonstrated the function of Dnmt3 enzymes by studying both Dnmt3a and Dnmt3b knockout mice.
Ooi SK, Qiu C, Bernstein E, Li K, Jia D, Yang Z et al (2007). DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448: 714–717.
Oswald J, Engemann S, Lane N, Mayer W, Olek A, Fundele R et al (2000). Active demethylation of the paternal genome in the mouse zygote. Curr Biol 10: 475–478.
Paroush Z, Keshet I, Yisraeli J, Cedar H (1990). Dynamics of demethylation and activation of the alpha-actin gene in myoblasts. Cell 63: 1229–1237.
Pastor WA, Pape UJ, Huang Y, Henderson HR, Lister R, Ko M et al (2011). Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature 473: 394–397.
Petronzelli F, Riccio A, Markham GD, Seeholzer SH, Stoerker J, Genuardi M et al (2000). Biphasic kinetics of the human DNA repair protein MED1 (MBD4), a mismatch-specific DNA N-glycosylase. J Biol Chem 275: 32422–32429.
Popp C, Dean W, Feng S, Cokus SJ, Andrews S, Pellegrini M et al (2010). Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature 463: 1101–1105.
Pradhan S, Bacolla A, Wells RD, Roberts RJ (1999). Recombinant human DNA (cytosine-5) methyltransferase. I. Expression, purification, and comparison of de novo and maintenance methylation. J Biol Chem 274: 33002–33010.
Prokhortchouk A, Hendrich B, Jorgensen H, Ruzov A, Wilm M, Georgiev G et al (2001). The p120 catenin partner Kaiso is a DNA methylation-dependent transcriptional repressor. Genes Dev 15: 1613–1618.
Qian X, Shen Q, Goderie SK, He W, Capela A, Davis AA et al (2000). Timing of CNS cell generation: a programmed sequence of neuron and glial cell production from isolated murine cortical stem cells. Neuron 28: 69–80.
Rai K, Huggins IJ, James SR, Karpf AR, Jones DA, Cairns BR (2008). DNA demethylation in zebrafish involves the coupling of a deaminase, a glycosylase, and gadd45. Cell 135: 1201–1212.
Rakyan VK, Hildmann T, Novik KL, Lewin J, Tost J, Cox AV et al (2004). DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project. PLoS Biol 2: e405.
Ramirez-Carrozzi VR, Braas D, Bhatt DM, Cheng CS, Hong C, Doty KR et al (2009). A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell 138: 114–128.
Ramsahoye BH, Biniszkiewicz D, Lyko F, Clark V, Bird AP, Jaenisch R (2000). Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc Natl Acad Sci USA 97: 5237–5242. First study to demonstrate the presence of non-CG methylation in mammalian cells.
Sarraf SA, Stancheva I (2004). Methyl-CpG binding protein MBD1 couples histone H3 methylation at lysine 9 by SETDB1 to DNA replication and chromatin assembly. Mol Cell 15: 595–605.
Sasai N, Nakao M, Defossez PA (2010). Sequence-specific recognition of methylated DNA by human zinc-finger proteins. Nucleic Acids Res 38: 5015–5022.
Sauvageot CM, Stiles CD (2002). Molecular mechanisms controlling cortical gliogenesis. Curr Opin Neurobiol 12: 244–249.
Saxonov S, Berg P, Brutlag DL (2006). A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci USA 103: 1412–1417.
Schulz WA, Steinhoff C, Florl AR (2006). Methylation of endogenous human retroelements in health and disease. Curr Top Microbiol Immunol 310: 211–250.
Shahbazian MD, Antalffy B, Armstrong DL, Zoghbi HY (2002). Insight into Rett syndrome: MeCP2 levels display tissue- and cell-specific differences and correlate with neuronal maturation. Hum Mol Genet 11: 115–124.
Sharif J, Muto M, Takebayashi S, Suetake I, Iwamatsu A, Endo TA et al (2007). The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. Nature 450: 908–912.
Shen L, Kondo Y, Guo Y, Zhang J, Zhang L, Ahmed S et al (2007). Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters. PLoS Genet 3: 2023–2036.
Sinkkonen L, Hugenschmidt T, Berninger P, Gaidatzis D, Mohn F, Artus-Revel CG et al (2008). MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells. Nat Struct Mol Biol 15: 259–267.
Straussman R, Nejman D, Roberts D, Steinfeld I, Blum B, Benvenisty N et al (2009). Developmental programming of CpG island methylation profiles in the human genome. Nat Struct Mol Biol 16: 564–571.
Stresemann C, Brueckner B, Musch T, Stopper H, Lyko F (2006). Functional diversity of DNA methyltransferase inhibitors in human cancer cell lines. Cancer Res 66: 2794–2800.
Suetake I, Shinozaki F, Miyagawa J, Takeshima H, Tajima S (2004). DNMT3L stimulates the DNA methylation activity of Dnmt3a and Dnmt3b through a direct interaction. J Biol Chem 279: 27816–27823.
Szwagierczak A, Bultmann S, Schmidt CS, Spada F, Leonhardt H (2010). Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA. Nucleic Acids Res 38: e181.
Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y et al (2009). Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324: 930–935. The first study to demonstrate the role of Tet enzymes in conversion of 5-methylcytosine to 5-hydroxymethylcytosine, thus leading to recent studies of the DNA demethylation mechanism in the mammalian system.
Takizawa T, Nakashima K, Namihira M, Ochiai W, Uemura A, Yanagisawa M et al (2001). DNA methylation is a critical cell-intrinsic determinant of astrocyte differentiation in the fetal brain. Dev Cell 1: 749–758.
Tao J, Hu K, Chang Q, Wu H, Sherman NE, Martinowich K et al (2009). Phosphorylation of MeCP2 at Serine 80 regulates its chromatin association and neurological function. Proc Natl Acad Sci USA 106: 4882–4887.
Teter B, Osterburg HH, Anderson CP, Finch CE (1994). Methylation of the rat glial fibrillary acidic protein gene shows tissue-specific domains. J Neurosci Res 39: 680–693.
Teter B, Rozovsky I, Krohn K, Anderson C, Osterburg H, Finch C (1996). Methylation of the glial fibrillary acidic protein gene shows novel biphasic changes during brain development. Glia 17: 195–205.
Thomson JP, Skene PJ, Selfridge J, Clouaire T, Guy J, Webb S et al (2010). CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Nature 464: 1082–1086.
Turner G, Webb T, Wake S, Robinson H (1996). Prevalence of fragile X syndrome. Am J Med Genet 64: 196–197.
Ukai H, Ishii-Oba H, Ukai-Tadenuma M, Ogiu T, Tsuji H (2003). Formation of an active form of the interleukin-2/15 receptor beta-chain by insertion of the intracisternal A particle in a radiation-induced mouse thymic lymphoma and its role in tumorigenesis. Mol Carcinog 37: 110–119.
Valinluck V, Tsai HH, Rogstad DK, Burdzy A, Bird A, Sowers LC (2004). Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2). Nucleic Acids Res 32: 4100–4108.
Verkerk AJ, Pieretti M, Sutcliffe JS, Fu YH, Kuhl DP, Pizzuti A et al (1991). Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome. Cell 65: 905–914.
Walsh CP, Chaillet JR, Bestor TH (1998). Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat Genet 20: 116–117.
Weaver IC, Cervoni N, Champagne FA, D’Alessio AC, Sharma S, Seckl JR et al (2004). Epigenetic programming by maternal behavior. Nat Neurosci 7: 847–854. One of the first studies to demonstrate the association of methylation changes in the brain with neural behavior.
Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, Rebhan M et al (2007). Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39: 457–466.
Webster KE, O’Bryan MK, Fletcher S, Crewther PE, Aapola U, Craig J et al (2005). Meiotic and epigenetic defects in Dnmt3L-knockout mouse spermatogenesis. Proc Natl Acad Sci USA 102: 4068–4073.
Weiler IJ, Irwin SA, Klintsova AY, Spencer CM, Brazelton AD, Miyashiro K et al (1997). Fragile X mental retardation protein is translated near synapses in response to neurotransmitter activation. Proc Natl Acad Sci USA 94: 5395–5400.
Wong E, Yang K, Kuraguchi M, Werling U, Avdievich E, Fan K et al (2002). Mbd4 inactivation increases Cright-arrowT transition mutations and promotes gastrointestinal tumor formation. Proc Natl Acad Sci USA 99: 14937–14942.
Wu H, Zhang Y (2011). Tet1 and 5-hydroxymethylation: a genome-wide view in mouse embryonic stem cells. Cell Cycle 10: 2428–2436.
Wu M, Rinchik EM, Wilkinson E, Johnson DK (1997). Inherited somatic mosaicism caused by an intracisternal A particle insertion in the mouse tyrosinase gene. Proc Natl Acad Sci USA 94: 890–894.
Wutz A, Smrzka OW, Schweifer N, Schellander K, Wagner EF, Barlow DP (1997). Imprinted expression of the Igf2r gene depends on an intronic CpG island. Nature 389: 745–749.
Xie S, Wang Z, Okano M, Nogami M, Li Y, He WW et al (1999). Cloning, expression and chromosome locations of the human DNMT3 gene family. Gene 236: 87–95.
Xie W, Barr CL, Kim A, Yue F, Lee AY, Eubanks J et al (2012). Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome. Cell 148: 816–831. Recent article that identified significant levels of non-CpG DNA methylation in the murine frontal cortex.
Yen RW, Vertino PM, Nelkin BD, Yu JJ, el-Deiry W, Cumaraswamy A et al (1992). Isolation and characterization of the cDNA encoding human DNA methyltransferase. Nucleic Acids Res 20: 2287–2291.
Yoon HG, Chan DW, Reynolds AB, Qin J, Wong J (2003). N-CoR mediates DNA methylation-dependent repression through a methyl CpG binding protein Kaiso. Mol Cell 12: 723–734.
Zamudio NM, Scott HS, Wolski K, Lo CY, Law C, Leong D et al (2011). DNMT3L is a regulator of X chromosome compaction and post-meiotic gene transcription. PLoS One 6: e18276.
Zhang F, Pomerantz JH, Sen G, Palermo AT, Blau HM (2007). Active tissue-specific DNA demethylation conferred by somatic cell nuclei in stable heterokaryons. Proc Natl Acad Sci USA 104: 4395–4400.
Zhang Y, Jurkowska R, Soeroes S, Rajavelu A, Dhayalan A, Bock I et al (2010). Chromatin methylation activity of Dnmt3a and Dnmt3a/3L is guided by interaction of the ADD domain with the histone H3 tail. Nucleic Acids Res 38: 4246–4253.
Zhou L, Cheng X, Connolly BA, Dickman MJ, Hurd PJ, Hornby DP (2002). Zebularine: a novel DNA methylation inhibitor that forms a covalent complex with DNA methyltransferases. J Mol Biol 321: 591–599.
Zhou Z, Hong EJ, Cohen S, Zhao WN, Ho HY, Schmidt L et al (2006). Brain-specific phosphorylation of MeCP2 regulates activity-dependent Bdnf transcription, dendritic growth, and spine maturation. Neuron 52: 255–269.