750
Views
19
CrossRef citations to date
0
Altmetric
Point of View

Human non-CG methylation

Are human stem cells plant-like?

, , , &
Pages 569-572 | Received 18 May 2010, Accepted 16 Jun 2010, Published online: 01 Oct 2010

References

  • Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, et al. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 2001; 292:30 - 33
  • Cao X, Aufsatz W, Zilberman D, Mette MF, Huang MS, Matzke M, et al. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Curr Biol 2003; 13:2212 - 2217
  • 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
  • Toth M, Muller U, Doerfler W. Establishment of de novo DNA methylation patterns. Transcription factor binding and deoxycytidine methylation at CpG and non-CpG sequences in an integrated adenovirus promoter. J Mol Biol 1990; 214:673 - 683
  • Clark SJ, Harrison J, Frommer M. CpNpG methylation in mammalian cells. Nat Genet 1995; 10:20 - 27
  • Woodcock DM, Lawler CB, Linsenmeyer ME, Doherty JP, Warren WD. Asymmetric methylation in the hypermethylated CpG promoter region of the human L1 retrotransposon. J Biol Chem 1997; 272:7810 - 7816
  • Tasheva ES, Roufa DJ. A mammalian origin of bidirectional DNA replication within the Chinese hamster RPS14 locus. Mol Cell Biol 1994; 14:5628 - 5635
  • Tasheva ES, Roufa DJ. Densely methylated DNA islands in mammalian chromosomal replication origins. Mol Cell Biol 1994; 14:5636 - 5644
  • Franchina M, Kay PH. Evidence that cytosine residues within 5′-CCTGG-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
  • 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
  • Woodcock DM, Linsenmeyer ME, Doherty JP, Warren WD. DNA methylation in the promoter region of the p16 (CDKN2/MTS-1/INK4A) gene in human breast tumours. Br J Cancer 1999; 79:251 - 256
  • Buryanov YI, Shevchuk TV, Zakharchenko NS, D'yachenko OV, Marinich DV, Vorob'ev IA. The absence of the CpNpG methylation at the 5′-terminal region of the human calcitonin gene in norm and leukemias. Russ J Bioorg Chem 2000; 26:358 - 360
  • Clark J, Smith SS. Secondary structure at a hot spot for DNA methylation in DNA from human breast cancers. Cancer Genomics Proteomics 2008; 5:241 - 251
  • Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009; 462:315 - 322
  • 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
  • Gupta PB, Chaffer CL, Weinberg RA. Cancer stem cells: mirage or reality?. Nat Med 2009; 15:1010 - 1012
  • Pfeifer GP, Steigerwald SD, Mueller PR, Wold B, Riggs AD. Genomic sequencing and methylation analysis by ligation mediated PCR. Science 1989; 246:810 - 813
  • Raghavan SC, Chastain P, Lee JS, Hegde BG, Houston S, Langen R, et al. Evidence for a triplex DNA conformation at the bcl-2 major breakpoint region of the t(14;18) translocation. J Biol Chem 2005; 280:22749 - 22760
  • Cao X, Springer NM, Muszynski MG, Phillips RL, Kaeppler S, Jacobsen SE. Conserved plant genes with similarity to mammalian de novo DNA methyltransferases. Proc Natl Acad Sci USA 2000; 97:4979 - 4984
  • Svoboda P, Stein P, Filipowicz W, Schultz RM. Lack of homologous sequence-specific DNA methylation in response to stable dsRNA expression in mouse oocytes. Nucleic Acids Res 2004; 32:3601 - 3606
  • Taira K. Induction of DNA methylation and gene silencing by short interfering RNAs in human cells. Nature 2006; 441:1176
  • Castanotto D, Tommasi S, Li M, Li H, Yanow S, Pfeifer GP, et al. Short hairpin RNA-directed cytosine (CpG) methylation of the RASSF1A gene promoter in HeLa cells. Mol Ther 2005; 12:179 - 183
  • Morris KV, Chan SW, Jacobsen SE, Looney DJ. Small interfering RNA-induced transcriptional gene silencing in human cells. Science 2004; 305:1289 - 1292
  • Kim JW, Zhang YH, Zern MA, Rossi JJ, Wu J. Short hairpin RNA causes the methylation of transforming growth factor-beta receptor II promoter and silencing of the target gene in rat hepatic stellate cells. Biochem Biophys Res Commun 2007; 359:292 - 297
  • Ting AH, Schuebel KE, Herman JG, Baylin SB. Short double-stranded RNA induces transcriptional gene silencing in human cancer cells in the absence of DNA methylation. Nat Genet 2005; 37:906 - 910
  • Tan Y, Zhang B, Wu T, Skogerbo G, Zhu X, Guo X, et al. Transcriptional inhibiton of Hoxd4 expression by miRNA-10a in human breast cancer cells. BMC Mol Biol 2009; 10:12
  • Smith SS. Biological implications of the mechanism of action of human DNA (cytosine-5)methyltransferase. Prog Nucleic Acid Res Mol Biol 1994; 49:65 - 111
  • Tanasijevic B, Dai B, Ezashi T, Livingston K, Roberts RM, Rasmussen TP. Progressive accumulation of epigenetic heterogeneity during human ES cell culture. Epigenetics 2009; 4:330 - 338
  • Shevchuk T, Kretzner L, Munson K, Axume J, Clark J, Dyachenko OV, et al. Transgene-induced CCWGG methylation does not alter CG methylation patterning in human kidney cells. Nucleic Acids Res 2005; 33:6124 - 6136
  • McClelland M, Ivarie R. Asymmetrical distribution of CpG in an ‘average’ mammalian gene. Nucleic Acids Res 1982; 10:7865 - 7877
  • Adams RL, Davis T, Rinaldi A, Eason R. CpG deficiency, dinucleotide distributions and nucleosome positioning. Eur J Biochem 1987; 165:107 - 115
  • Cooper DN, Gerber-Huber S. DNA methylation and CpG suppression. Cell Differ 1985; 17:199 - 205
  • Cooper DN, Youssoufian H. The CpG dinucleotide and human genetic disease. Hum Genet 1988; 78:151 - 155
  • Watson B, Munson K, Clark J, Shevchuk T, Smith SS. Distribution of CWG and CCWGG in the human genome. Epigenetics 2007; 2:151 - 154
  • Free A, Wakefield RI, Smith BO, Dryden DT, Barlow PN, Bird AP. DNA recognition by the methyl-CpG binding domain of MeCP2. J Biol Chem 2001; 276:3353 - 3360
  • Smith SS, Baker DJ. Stalling of human methyltransferase at single-strand conformers from the Huntington's locus. Biochem Biophys Res Commun 1997; 234:73 - 78
  • Kho MR, Baker DJ, Laayoun A, Smith SS. Stalling of human DNA (cytosine-5) methyltransferase at single-strand conformers from a site of dynamic mutation. J Mol Biol 1998; 275:67 - 79
  • Clark J, Shevchuk T, Kho MR, Smith SS. Methods for the design and analysis of oligodeoxynucleotide-based DNA (cytosine-5) methyltransferase inhibitors. Anal Biochem 2003; 321:50 - 64
  • Smith SS. Gilbert's conjecture: the search for DNA (cytosine-5) demethylases and the emergence of new functions for eukaryotic DNA (cytosine-5) methyltransferases. J Mol Biol 2000; 302:1 - 7
  • The Human DNA Methylone 2010; 2 5 [Internet]. San Diego Epigenome Center Available from: http://neomorph.salk.edu/human_methylome/
  • Herman JG, Graff JR, Myohanen S, Nelkin BD, Baylin SB. Methylation-specificPCR: a novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci USA 1996; 93:9821 - 9826
  • Boyd VL, Moody KI, Karger AE, Livak KJ, Zon G, Burns JW. Methylation-dependent fragment separation: Direct detection of DNA methylation by capillary electrophoresis of PCR products from bisulfite-converted genomic DNA. Anal Biochem 2006; 354:266 - 273
  • Munson K, Clark J, Lamparska-Kupsik K, Smith SS. Recovery of bisulfite-converted genomic sequences in the methylation-sensitive QPCR. Nucleic Acids Research 2007; 35:2893 - 2903
  • Sneddon JB, Werb Z. Location, location, location: the cancer stem cell niche. Cell Stem Cell 2007; 1:607 - 611
  • McGovern M, Voutev R, Maciejowski J, Corsi AK, Hubbard EJ. A “latent niche” mechanism for tumor initiation. Proc Natl Acad Sci USA 2009; 106:11617 - 11622
  • Rauch TA, Pfeifer GP. The MIRA method for DNA methylation analysis. Methods Mol Biol 2009; 507:65 - 75
  • Yegnasubramanian S, Lin X, Haffner MC, DeMarzo AM, Nelson WG. Combination of methylated-DNA precipitation and methylation-sensitive restriction enzymes (COMPARE-MS) for the rapid, sensitive and quantitative detection of DNA methylation. Nucleic Acids Res 2006; 34:19
  • Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL, et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 2005; 37:853 - 862

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.