Early demethylation of non-CpG, CpC-rich, elements in the myogenin 5’-flanking region

References

• Li B, Carey M, Workman JL. The role of chromatin during transcription. Cell 2007; 128:707 - 719
   PubMed Web of Science ®Google Scholar
• Klose RJ, Bird AP. Genomic DNA methylation: The mark and its mediators. Trends Biochem Sci 2006; 31:89 - 97
   PubMed Web of Science ®Google Scholar
• Suzuki MM, Bird A. DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 2008; 9:465 - 476
   PubMed Web of Science ®Google Scholar
• Vaissiere T, Sawan C, Herceg Z. Epigenetic interplay between histone modifications and DNA methylation in gene silencing. Mutat Res 2008; 659:40 - 48
   PubMed Web of Science ®Google Scholar
• D'Alessio AC, Szyf M. Epigenetic tete-a-tete: The bilateral relationship between chromatin modifications and DNA methylation. Biochem Cell Biol 2006; 84:463 - 476
   PubMed Web of Science ®Google Scholar
• Turek-Plewa J, Jagodzinski PP. The role of mammalian DNA methyltransferases in the regulation of gene expression. Cell Mol Biol Lett 2005; 10:631 - 647
   PubMed Web of Science ®Google Scholar
• Brown SE, Suderman MJ, Hallett M, Szyf M. DNA demethylation induced by the methyl-CpG-binding domain protein MBD3. Gene 2008; 420:99 - 106
   PubMed Web of Science ®Google Scholar
• Lucarelli M, Fuso A, Strom R, Scarpa S. The dynamics of myogenin site-specific demethylation is strongly correlated with its expression and with muscle differentiation. J Biol Chem 2001; 276:7500 - 7506
   PubMed Web of Science ®Google Scholar
• Ooi SK, Bestor TH. The colorful history of active DNA demethylation. Cell 2008; 133:1145 - 1148
   PubMed Web of Science ®Google Scholar
• Filippova GN. Genetics and epigenetics of the multifunctional protein CTCF. Curr Top Dev Biol 2008; 80:337 - 360
   PubMed Web of Science ®Google Scholar
• Douet V, Heller MB, Le SO. DNA methylation and Sp1 binding determine the tissue-specific transcriptional activity of the mouse Abcc6 promoter. Biochem Biophys Res Commun 2007; 354:66 - 71
   PubMed Web of Science ®Google Scholar
• Inoue S, Oishi M. Effects of methylation of non-CpG sequence in the promoter region on the expression of human synaptotagmin XI (syt11). Gene 2005; 348:123 - 134
   PubMed Web of Science ®Google Scholar
• Malone CS, Miner MD, Doerr JR, Jackson JP, Jacobsen SE, Wall R, et al. CmC(A/T)GG DNA methylation in mature B cell lymphoma gene silencing. Proc Natl Acad Sci USA 2001; 98:10404 - 10409
   PubMed Web of Science ®Google Scholar
• Novik KL, Nimmrich I, Genc B, Maier S, Piepenbrock C, Olek A, et al. Epigenomics: Genome-wide study of methylation phenomena. Curr Issues Mol Biol 2002; 4:111 - 128
   PubMedGoogle Scholar
• Lorincz MC, Groudine M. C(m)C(a/t)GG methylation: a new epigenetic mark in mammalian DNA?. Proc Natl Acad Sci USA 2001; 98:10034 - 10036
   PubMed Web of Science ®Google Scholar
• Lorincz MC, Schubeler D, Hutchinson SR, Dickerson DR, Groudine M. DNA methylation density influences the stability of an epigenetic imprint and Dnmt3a/b-independent de novo methylation. Mol Cell Biol 2002; 22:7572 - 7580
   PubMed Web of Science ®Google Scholar
• Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 2008; 454:776 - 780
   PubMed Web of Science ®Google Scholar
• Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, Rebhan M, et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 2007; 39:457 - 466
   PubMed Web of Science ®Google Scholar
• Brown SE, Fraga MF, Weaver IC, Berdasco M, Szyf M. Variations in DNA methylation patterns during the cell cycle of HeLa cells. Epigenetics 2007; 2:54 - 65
   PubMed Web of Science ®Google Scholar
• Imamura T, Kerjean A, Heams T, Kupiec JJ, Thenevin C, Paldi A. Dynamic CpG and non-CpG methylation of the Peg1/Mest gene in the mouse oocyte and preimplantation embryo. J Biol Chem 2005; 280:20171 - 20175
   PubMed Web of Science ®Google Scholar
• Oakes CC, La SS, Smiraglia DJ, Robaire B, Trasler JM. Developmental acquisition of genome-wide DNA methylation occurs prior to meiosis in male germ cells. Dev Biol 2007; 307:368 - 379
   PubMed Web of Science ®Google Scholar
• Fazzari MJ, Greally JM. Epigenomics: beyond CpG islands. Nat Rev Genet 2004; 5:446 - 455
   PubMed Web of Science ®Google Scholar
• Saxonov S, Berg P, Brutlag DL. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci USA 2006; 103:1412 - 1417
   PubMed Web of Science ®Google Scholar
• Chan QK, Khoo US, Chan KY, Ngan HY, Li SS, Chiu PM, et al. Promoter methylation and differential expression of pi-class glutathione S-transferase in endometrial carcinoma. J Mol Diagn 2005; 7:8 - 16
   PubMed Web of Science ®Google Scholar
• Kitazawa S, Kitazawa R, Maeda S. Transcriptional regulation of rat cyclin D1 gene by CpG methylation status in promoter region. J Biol Chem 1999; 274:28787 - 28793
   PubMed Web of Science ®Google Scholar
• Kouidou S, Agidou T, Kyrkou A, Andreou A, Katopodi T, Georgiou E, et al. Non-CpG cytosine methylation of p53 exon 5 in non-small cell lung carcinoma. Lung Cancer 2005; 50:299 - 307
   PubMed Web of Science ®Google Scholar
• Teng C, Gladwell W, Raphiou I, Liu E. Methylation and expression of the lactoferrin gene in human tissues and cancer cells. Biometals 2004; 17:317 - 323
   PubMed Web of Science ®Google Scholar
• Vu TH, Li T, Nguyen D, Nguyen BT, Yao XM, Hu JF, et al. Symmetric and asymmetric DNA methylation in the human IGF2-H19 imprinted region. Genomics 2000; 64:132 - 143
   PubMed Web of Science ®Google Scholar
• Haines TR, Rodenhiser DI, Ainsworth PJ. Allele-specific non-CpG methylation of the Nf1 gene during early mouse development. Dev Biol 2001; 240:585 - 598
   PubMed Web of Science ®Google Scholar
• Franchina M, Kay PH. Evidence that cytosine residues within 5′-CCT GG-3′ pentanucleotides can be methylated in human DNA independently of the methylating system that modifies 5′-CG-3′ dinucleotides. DNA Cell Biol 2000; 19:521 - 526
   PubMed Web of Science ®Google Scholar
• Ramsahoye BH, Biniszkiewicz D, Lyko F, Clark V, Bird AP, Jaenisch R. Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc Natl Acad Sci USA 2000; 97:5237 - 5242
   PubMed Web of Science ®Google Scholar
• Fuso A, Nicolia V, Pasqualato A, Fiorenza MT, Cavallaro RA, Scarpa S. Changes in Presenilin 1 gene methylation pattern in diet-induced B vitamin deficiency. Neurobiol Aging 2009; 32:187 - 199
   PubMed Web of Science ®Google Scholar
• Aoki A, Suetake I, Miyagawa J, Fujio T, Chijiwa T, Sasaki H, et al. Enzymatic properties of de novo-type mouse DNA (cytosine-5) methyltransferases. Nucleic Acids Res 2001; 29:3506 - 3512
   PubMed Web of Science ®Google Scholar
• Mund C, Musch T, Strodicke M, Assmann B, Li E, Lyko F. Comparative analysis of DNA methylation patterns in transgenic Drosophila overexpressing mouse DNA methyltransferases. Biochem J 2004; 378:763 - 768
   PubMed Web of Science ®Google Scholar
• Gowher H, Jeltsch A. Enzymatic properties of recombinant Dnmt3a DNA methyltransferase from mouse: The enzyme modifies DNA in a non-processive manner and also methylates non-CpG [correction of non-CpA] sites. J Mol Biol 2001; 309:1201 - 1208
   PubMed Web of Science ®Google Scholar
• Li E. Chromatin modification and epigenetic reprogramming in mammalian development. Nat Rev Genet 2002; 3:662 - 673
   PubMed Web of Science ®Google Scholar
• Kangaspeska S, Stride B, Metivier R, Polycarpou-Schwarz M, Ibberson D, Carmouche RP, et al. Transient cyclical methylation of promoter DNA. Nature 2008; 452:112 - 115
   PubMed Web of Science ®Google Scholar
• Metivier R, Gallais R, Tiffoche C, Le PC, Jurkowska RZ, Carmouche RP, et al. Cyclical DNA methylation of a transcriptionally active promoter. Nature 2008; 452:45 - 50
   PubMed Web of Science ®Google Scholar
• Oswald J, Engemann S, Lane N, Mayer W, Olek A, Fundele R, et al. Active demethylation of the paternal genome in the mouse zygote. Curr Biol 2000; 10:475 - 478
   PubMed Web of Science ®Google Scholar
• Bhattacharya SK, Ramchandani S, Cervoni N, Szyf M. A mammalian protein with specific demethylase activity for mCpG DNA. Nature 1999; 397:579 - 583
   PubMed Web of Science ®Google Scholar
• Zhu B, Zheng Y, Hess D, Angliker H, Schwarz S, Siegmann M, et al. 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; 97:5135 - 5139
   PubMed Web of Science ®Google Scholar
• Barreto G, Schafer A, Marhold J, Stach D, Swaminathan SK, Handa V, et al. Gadd45a promotes epigenetic gene activation by repair-mediated DNA demethylation. Nature 2007; 445:671 - 675
   PubMed Web of Science ®Google Scholar
• Sachan M, Raman R. Developmental methylation of the coding region of c-fos occurs perinatally, stepwise and sequentially in the liver of laboratory mouse. Gene 2008; 416:22 - 29
   PubMed Web of Science ®Google Scholar
• Figliola R, Busanello A, Vaccarello G, Maione R. Regulation of p57(KIP2) during muscle differentiation: role of Egr1, Sp1 and DNA hypomethylation. J Mol Biol 2008; 380:265 - 277
   PubMed Web of Science ®Google Scholar
• Palacios D, Summerbell D, Rigby PW, Boyes J. Interplay between DNA methylation and transcription factor availability: implications for developmental activation of the mouse myogenin gene. Mol Cell Biol 2010; 30:3805 - 3815
   PubMed Web of Science ®Google Scholar
• Asakura A, Komaki M, Rudnicki M. Muscle satellite cells are multipotential stem cells that exhibit myogenic, osteogenic and adipogenic differentiation. Differentiation 2001; 68:245 - 253
   PubMed Web of Science ®Google Scholar
• Pownall ME, Gustafsson MK, Emerson CP Jr. Myogenic regulatory factors and the specification of muscle progenitors in vertebrate embryos. Annu Rev Cell Dev Biol 2002; 18:747 - 783
   PubMed Web of Science ®Google Scholar
• Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol 1987; 196:261 - 282
   PubMed Web of Science ®Google Scholar
• Takai D, Jones PA. Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci USA 2002; 99:3740 - 3745
   PubMed Web of Science ®Google Scholar
• Yee SP, Rigby PW. The regulation of myogenin gene expression during the embryonic development of the mouse. Genes Dev 1993; 7:1277 - 1289
   PubMed Web of Science ®Google Scholar
• Woodcock DM, Crowther PJ, Diver WP. The majority of methylated deoxycytidines in human DNA are not in the CpG dinucleotide. Biochem Biophys Res Commun 1987; 145:888 - 894
   PubMed Web of Science ®Google Scholar
• Meissner A, Gnirke A, Bell GW, Ramsahoye B, Lander ES, Jaenisch R. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res 2005; 33:5868 - 5877
   PubMed Web of Science ®Google Scholar
• Jia D, Jurkowska RZ, Zhang X, Jeltsch A, Cheng X. Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature 2007; 449:248 - 251
   PubMed Web of Science ®Google Scholar
• Ferguson-Smith AC, Greally JM. Epigenetics: perceptive enzymes. Nature 2007; 449:148 - 149
   PubMed Web of Science ®Google Scholar
• Fuso A, Cavallaro RA, Orrú L, Buttarelli FR, Scarpa S. Gene silencing by S-adenosylmethionine in muscle differentiation. FEBS Lett 2001; 508:337 - 340
   PubMed Web of Science ®Google Scholar
• Agirre X, Vizmanos JL, Calasanz MJ, Garcia-Delgado M, Larrayoz MJ, Novo FJ. Methylation of CpG dinucleotides and/or CCWGG motifs at the promoter of TP53 correlates with decreased gene expression in a subset of acute lymphoblastic leukemia patients. Oncogene 2003; 22:1070 - 1072
   PubMed Web of Science ®Google Scholar
• Brooks AR, Harkins RN, Wang P, Qian HS, Liu P, Rubanyi GM. Transcriptional silencing is associated with extensive methylation of the CMV promoter following adenoviral gene delivery to muscle. J Gene Med 2004; 6:395 - 404
   PubMed Web of Science ®Google Scholar
• Klenova EM, Nicolas RH, Paterson HF, Carne AF, Heath CM, Goodwin GH, et al. CTCF, a conserved nuclear factor required for optimal transcriptional activity of the chicken c-myc gene, is an 11-Zn-finger protein differentially expressed in multiple forms. Mol Cell Biol 1993; 13:7612 - 7624
   PubMed Web of Science ®Google Scholar
• Yaffe D, Saxel O. Serial passaging and differentiation of myogenic cells isolated from dystrophic mouse muscle. Nature 1977; 270:725 - 727
   PubMed Web of Science ®Google Scholar
• Fuso A, Scarpa S, Grandoni F, Strom R, Lucarelli M. A reassessment of semiquantitative analytical procedures for DNA methylation: comparison of bisulfite- and HpaII polymerase-chain-reaction-based methods. Anal Biochem 2006; 350:24 - 31
   PubMed Web of Science ®Google Scholar
• Clark SJ, Harrison J, Paul CL, Frommer M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res 1994; 22:2990 - 2997
   PubMed Web of Science ®Google Scholar
• Genereux DP, Johnson WC, Burden AF, Stoger R, Laird CD. Errors in the bisulfite conversion of DNA: modulating inappropriate- and failed-conversion frequencies. Nucleic Acids Res 2008; 36:e150
   PubMed Web of Science ®Google Scholar
• Shiraishi M, Hayatsu H. High-speed conversion of cytosine to uracil in bisulfite genomic sequencing analysis of DNA methylation. DNA Res 2004; 11:409 - 415
   PubMed Web of Science ®Google Scholar