Protein Binding Protects Sites on Stable Episomes and in the Chromosome from De Novo Methylation

REFERENCES

• Bird, A. P.. 1986. CpG-rich islands and the function of DNA methylation. Nature 321:209–213.
   PubMed Web of Science ®Google Scholar
• Brandeis, M., D. Frank, I. Keshet, Z. Siegfried, M. Mendelsohn, A. Nemes, V. Temper, A. Razin, and H. Cedar. 1994. Sp1 elements protect a CpG island from de novo methylation. Nature 371:435–438.
   PubMed Web of Science ®Google Scholar
• Brown, M., J. Figge, U. Hansen, C. Wright, K.-T. Jeang, G. Khoury, D. M. Livingston, and T. M. Roberts. 1987. lac repressor can regulate expression from a hybrid SV40 early promoter containing a lac operator in animal cells. Cell 49:603–612.
   PubMedGoogle Scholar
• Costello, J. F., M. C. Fruhwald, D. J. Smiraglia, L. J. Rush, G. P. Robertson, X. Gao, F. A. Wright, J. D. Feramisco, P. Peltomaki, J. C. Lang, D. E. Schuller, L. Yu, C. D. Bloomfield, M. A. Caligiuri, A. Yates, R. Nishikawa, H. Su Huang, N. J. Petrelli, X. Zhang, M. S. O'Dorisio, W. A. Held, W. K. Cavenee, and C. Plass. 2000. Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nat. Genet. 24:132–138.
   PubMed Web of Science ®Google Scholar
• Devereux, T. R., I. Horikawa, C. H. Anna, L. A. Annab, C. A. Afshari, and J. C. Barrett. 1999. DNA methylation analysis of the promoter region of the human telomerase reverse transcriptase (hTERT) gene. Cancer Res. 59:6087–6090.
   PubMed Web of Science ®Google Scholar
• Grawunder, U., N. Finnie, S. P. Jackson, B. Riwar, and R. Jessberger. 1996. Expression of DNA-dependent protein kinase holoenzyme upon induction of lymphocyte differentiation and V(D)J recombination. Eur. J. Biochem. 241:931–940.
   PubMedGoogle Scholar
• Hirt, B.. 1967. Selective extraction of polyoma DNA from infected mouse cultures. J. Mol. Biol. 26:365–369.
   PubMed Web of Science ®Google Scholar
• Hsieh, C.-L.. 1994. Dependence of transcriptional repression on CpG methylation density. Mol. Cell. Biol. 14:5487–5494.
   PubMed Web of Science ®Google Scholar
• Hsieh, C.-L.. 1999. Evidence that protein binding specifies sites of DNA demethylation. Mol. Cell. Biol. 19:46–56.
   PubMedGoogle Scholar
• Hsieh, C.-L.. 1999. In vivo activity of murine de novo methyltransferases, Dnmt3a and Dnmat3b. Mol. Cell. Biol. 19:8211–8218.
   PubMed Web of Science ®Google Scholar
• Jones, P. A.. 1999. The DNA methylation paradox. Trends Genet. 15:34–37.
   PubMed Web of Science ®Google Scholar
• Kladde, M. P., and R. T. Simpson. 1994. Positioned nucleosomes inhibit Dam methylation in vivo. Proc. Natl. Acad. Sci. USA 91:1361–1365.
   PubMedGoogle Scholar
• Kladde, M. P., M. Xu, and R. T. Simpson. 1996. Direct study of DNA-protein interactions in repressed and active chromatin in living cells. EMBO J. 15:6290–6300.
   PubMedGoogle Scholar
• Lin, I. G., T. J. Tomzynski, Q. Ou, and C.-L. Hsieh. 2000. Modulation of DNA binding protein affinity directly affects target site demethylation. Mol. Cell. Biol. 20:2343–2349.
   PubMedGoogle Scholar
• Lin, I. G., and C.-L. Hsieh. 2001. Chromosomal DNA demethylation specified by protein binding. EMBO Rep. 2:108–112.
   PubMedGoogle Scholar
• Lyko, F., B. H. Ramasahoye, H. Kashevsky, M. Tudor, M.-A. Mastrangelo, T. L. Orr-Weaver, and R. Jaenish. 1999. Mammalian (cytosine-5) methyltransferases cause genomic DNA methylation and lethality in Drosophila. Nat. Genet. 23:363–366.
   PubMed Web of Science ®Google Scholar
• Macleod, D., J. Charlton, J. Mullins, and A. Bird. 1994. Sp1 sites in the mouse aprt gene promoter are required to prevent methylation of the CpG island. Genes Dev. 8:2282–2292.
   PubMed Web of Science ®Google Scholar
• Okano, M., S. Xie, and E. Li. 1998. Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases. Nat. Genet. 19:219–220.
   PubMed Web of Science ®Google Scholar
• Pfeifer, G. P., and A. D. Riggs. 1991. Chromatin differences between active and inactive X chromosomes revealed by genomic footprinting of permeabilized cells using DNase I and ligation-mediated PCR. Genes Dev. 5:1102–1113.
   PubMedGoogle Scholar
• Pfeifer, G. P., S. D. Steigerwald, R. S. Hansen, S. M. Gartler, and A. D. Riggs. 1990. Polymerase chain reaction-aided genomic sequencing of an X chromosome-linked CpG island; methylation patterns suggest clonal inheritance, CpG site autonomy, and an explanation of activity state stability. Proc. Natl. Acad. Sci. USA 87:8252–8256.
   PubMed Web of Science ®Google Scholar
• Pfeifer, G. P., R. L. Tanguay, S. D. Steigerwald, and A. D. Riggs. 1990. In vivo footprint and methylation analysis by PCR-aided genomic sequencing: comparison of active and inactive X chromosomal DNA at the CpG island and promoter of human PGK-1. Genes Dev. 4:1277–1287.
   PubMed Web of Science ®Google Scholar
• Riggs, A. D.. 1989. DNA methylation and cell memory. Cell Biophys. 15:1–13.
   PubMedGoogle Scholar
• Riggs, A. D., and P. A. Jones. 1983. 5-Methylcytosine, gene regulation, and cancer. Adv. Cancer Res. 40:1–30.
   PubMed Web of Science ®Google Scholar
• Riggs, A. D., Z. Xiong, L. Wang, and J. M. LeBon. 1998. Methylation dynamics, epigenetic fidelity and X chromosome structure. Novartis Found. Symp. 214:214–232.
   PubMedGoogle Scholar
• Selker, E. C.. 1990. DNA methylation and chromatin structure: a view from below. Trends Biochem. Sci. 15:103–107.
   PubMed Web of Science ®Google Scholar
• Singer, J., J. Roberts-Ems, E. W. Luthardt, and A. D. Riggs. 1979. Methylation of DNA in mouse early embryos, teratocarcinoma cells and adult tissues of mouse and rabbit. Nucleic Acids Res. 20:2369–2385.
   Google Scholar
• Singh, J., and A. J. S. Klar. 1992. Active genes in budding yeast display enhanced in vivo accessibility to foreign DNA methylases: a novel in vivo probe for chromatin structure of yeast. Genes Dev. 6:186–196.
   PubMed Web of Science ®Google Scholar
• Sugden, B., K. Marsh, and J. Yates. 1985. A vector that replicates as a plasmid and can be efficiently selected in B-lymphoblasts transformed by Epstein-Barr virus. Mol. Cell. Biol. 5:410–413.
   PubMedGoogle Scholar
• Tavazoie, S., and G. M. Church. 1998. Quantitative whole-genome analysis of DNA-protein interaction by in vivo methylase protection in E. coli. Nat. Biotechnol. 16:566–571.
   PubMed Web of Science ®Google Scholar
• Vu, T. H., T. Li, D. Nguyen, B. T. Nguyen, X. M. Yao, J. F. Hu, and A. R. Hoffman. 2000. Symmetric and asymmetric DNA methylation in the human IGF2–H19 imprinted region. Genomics 64:132–143.
   PubMed Web of Science ®Google Scholar
• Wang, M. X., and G. M. Church. 1992. A whole genome approach to in vivo DNA-protein interactions in E. coli. Nature 360:606–610.
   PubMedGoogle Scholar
• Warnecke, P. M., J. R. Mann, M. Frommer, and S. J. Clark. 1998. Bisulfite sequencing in preimplantation embryos: DNA methylation profile of the upstream region of the mouse imprinted H19 gene. Genomics 51:182–190.
   PubMed Web of Science ®Google Scholar
• Warnecke, P. M., and S. J. Clark. 1999. DNA methylation profile of the mouse skeletal alpha-actin promoter during development and differentiation. Mol. Cell. Biol. 19:164–172.
   PubMedGoogle Scholar
• Wigler, M., R. Sweet, G. K. Sim, B. Wold, A. Pellicer, E. Lacy, T. Maniatis, S. Silverstein, and R. Axel. 1979. Transformation of mammalian cells with genes from prokaryotes and eukaryotes. Cell 16:777–785.
   PubMed Web of Science ®Google Scholar
• Wolffe, A. P., and D. Pruss. 1996. Targeting chromatin disruption: transcription regulators that acetylate histones. Cell 84:817–819.
   PubMed Web of Science ®Google Scholar
• Xu, M., R. T. Simpson, and M. P. Kladde. 1998. Gal4p-mediated chromatin remodelling depends on binding site position in nucleosomes but does not require DNA replication. Mol. Cell. Biol. 18:1201–1212.
   PubMedGoogle Scholar