Genomic Targeting of Methylated DNA: Influence of Methylation on Transcription, Replication, Chromatin Structure, and Histone Acetylation

REFERENCES

• Bird, A. P., and Wolffe, A. P.. 1999. Methylation-induced repression—belts, braces, and chromatin. Cell 99:451–454
   PubMed Web of Science ®Google Scholar
• Boyes, J., and Bird, A.. 1992. Repression of genes by DNA methylation depends on CpG density and promoter strength: evidence for involvement of a methyl-CpG binding protein. EMBO J. 11:327–333
   PubMed Web of Science ®Google Scholar
• Boyes, J., and Felsenfeld, G.. 1996. Tissue-specific factors additively increase the probability of the all-or-none formation of a hypersensitive site. EMBO J. 15:2496–2507
   PubMedGoogle Scholar
• Brandeis, M., Ariel, M., and Cedar, H.. 1993. Dynamics of DNA methylation during development. Bioessays 15:709–713
   PubMed Web of Science ®Google Scholar
• Carmen, A. A., Griffin, P. R., Calaycay, J. R., Rundlett, S. E., Suka, Y., and Grunstein, M.. 1999. Yeast HOS3 forms a novel trichostatin A-insensitive homodimer with intrinsic histone deacetylase activity. Proc. Natl. Acad. Sci. USA 96:12356–12361
   PubMedGoogle Scholar
• Chen, W. Y., and Townes, T. M.. 2000. Molecular mechanism for silencing virally transduced genes involves histone deacetylation and chromatin condensation. Proc. Natl. Acad. Sci. USA 97:377–382
   PubMed Web of Science ®Google Scholar
• Cimbora, D. M., Schübeler, D., Reik, A., Hamilton, J., Francastel, C., Epner, E. M., and Groudine, M.. 2000. Long-distance control of origin choice and replication timing in the human beta-globin locus are independent of the locus control region. Mol. Cell. Biol. 20:5581–5591
   PubMed Web of Science ®Google Scholar
• Eden, S., Hashimshony, T., Keshet, I., Cedar, H., and Thorne, A. W.. 1998. DNA methylation models histone acetylation. Nature 394: 842
   PubMed Web of Science ®Google Scholar
• Feng, Y. Q., Lorincz M. C., Fiering S., Greally J. M., and Bouhassira E.. Position effects are influenced by the orientation of a transgene with respect to flanking chromatin. Mol. Cell. Biol., in press.
   Google Scholar
• Feng, Y. Q., Seibler, J., Alami, R., Eisen, A., Westerman, K. A., Leboulch, P., Fiering, S., and Bouhassira, E. E.. 1999. Site-specific chromosomal integration in mammalian cells: highly efficient CRE recombinase-mediated cassette exchange. J. Mol. Biol. 292:779–785
   PubMedGoogle Scholar
• Forrester, W. C., Epner, E., Driscoll, M. C., Enver, T., Brice, M., Papayannopoulou, T., and Groudine, M.. 1990. A deletion of the human beta-globin locus activation region causes a major alteration in chromatin structure and replication across the entire beta-globin locus. Genes Dev. 4:1637–1649
   PubMed Web of Science ®Google Scholar
• Forrester, W. C., Fernandez, L. A., and Grosschedl, R.. 1999. Nuclear matrix attachment regions antagonize methylation-dependent repression of long-range enhancer-promoter interactions. Genes Dev. 13:3003–3014
   PubMedGoogle Scholar
• Francastel, C., Walters, M. C., Groudine, M., and Martin, D. I.. 1999. A functional enhancer suppresses silencing of a transgene and prevents its localization close to centrometric heterochromatin. Cell 99:259–269
   PubMedGoogle Scholar
• Fuks, F., Burgers, W. A., Brehm, A., Hughes-Davies, L., and Kouzarides, T.. 2000. DNA methyltransferase Dnmt1 associates with histone deacetylase activity. Nat. Genet. 24:88–91
   PubMed Web of Science ®Google Scholar
• Goldman, M. A., Holmquist, G. P., Gray, M. C., Caston, L. A., and Nag, A.. 1984. Replication timing of genes and middle repetitive sequences. Science 224:686–692
   PubMedGoogle Scholar
• Groudine, M., Peretz, M., and Weintraub, H.. 1981. Transcriptional regulation of hemoglobin switching in chicken embryos. Mol. Cell. Biol. 1:281–288
   PubMed Web of Science ®Google Scholar
• Gu, H., Zou, Y. R., and Rajewsky, K.. 1993. Independent control of immunoglobulin switch recombination at individual switch regions evidenced through Cre-loxP-mediated gene targeting. Cell 73:1155–1164
   PubMed Web of Science ®Google Scholar
• Hendrich, B.. 2000. Methylation moves into medicine. Curr. Biol. 10:R60–R63
   PubMedGoogle Scholar
• Hendrich, B., and Bird, A.. 1998. Identification and characterization of a family of mammalian methyl-CpG binding proteins. Mol. Cell. Biol. 18:6538–6547
   PubMed Web of Science ®Google Scholar
• Henikoff, S.. 1992. Position effect and related phenomena. Curr. Opin. Genet. Dev. 2:907–912
   PubMedGoogle 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
• Iguchi-Ariga, S. M., and Schaffner, W.. 1989. CpG methylation of the cAMP-responsive enhancer/promoter sequence TGACGTCA abolishes specific factor binding as well as transcriptional activation. Genes Dev. 3:612–619
   PubMed Web of Science ®Google Scholar
• Imai, S., Armstrong, C. M., Kaeberlein, M., and Guarente, L.. 2000. Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature 403:795–800
   PubMed Web of Science ®Google Scholar
• Jaenisch, R.. 1997. DNA methylation and imprinting: why bother? Trends Genet. 13:323–329
   PubMed Web of Science ®Google Scholar
• Jones, P. A., and Laird, P. W.. 1999. Cancer epigenetics comes of age. Nat. Genet. 21:163–167
   PubMed Web of Science ®Google Scholar
• Jones, P. L., Veenstra, G. J., Wade, P. A., Vermaak, D., Kass, S. U., Landsberger, N., Strouboulis, J., and Wolffe, A. P.. 1998. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat. Genet. 19:187–191
   PubMed Web of Science ®Google Scholar
• Kadosh, D., and Struhl, K.. 1998. Targeted recruitment of the Sin3-Rpd3 histone deacetylase complex generates a highly localized domain of repressed chromatin in vivo. Mol. Cell. Biol. 18:5121–5127
   PubMed Web of Science ®Google Scholar
• Kass, S. U., Landsberger, N., and Wolffe, A. P.. 1997. DNA methylation directs a time-dependent repression of transcription initiation. Curr. Biol. 7:157–165
   PubMed Web of Science ®Google Scholar
• Keshet, I., Lieman-Hurwitz, J., and Cedar, H.. 1986. DNA methylation affects the formation of active chromatin. Cell 44:535–543
   PubMed Web of Science ®Google Scholar
• Krumm, A., Hickey, L. B., and Groudine, M.. 1995. Promoter-proximal pausing of RNA polymerase II defines a general rate-limiting step after transcription initiation. Genes Dev. 9:559–572
   PubMed Web of Science ®Google Scholar
• Krumm, A., Meulia, T., and Groudine, M.. 1993. Common mechanisms for the control of eukaryotic transcriptional elongation. Bioessays 15:659–665
   PubMedGoogle Scholar
• Li, E., Bestor, T. H., and Jaenisch, R.. 1992. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69:915–926
   PubMed Web of Science ®Google Scholar
• Lorincz, M. C., Schübeler, D., Goeke, S. C., Walters, M., Groudine, M., and Martin, D. I.. 2000. Dynamic analysis of proviral induction and de novo methylation: implications for a histone deacetylase-independent, methylation density-dependent mechanism of transcriptional repression. Mol. Cell. Biol. 20:842–850
   PubMed Web of Science ®Google Scholar
• Matsuo, K., Silke, J., Georgiev, O., Marti, P., Giovannini, N., and Rungger, D.. 1998. An embryonic demethylation mechanism involving binding of transcription factors to replicating DNA. EMBO J. 17:1446–1453
   PubMedGoogle Scholar
• Myers, R. M., Tilly, K., and Maniatis, T.. 1986. Fine structure genetic analysis of a beta-globin promoter. Science 232:613–618
   PubMed Web of Science ®Google Scholar
• Nan, X., Meehan, R. R., and Bird, A.. 1993. Dissection of the methyl-CpG binding domain from the chromosomal protein MeCP2. Nucleic Acids Res. 21:4886–4892
   PubMed Web of Science ®Google Scholar
• Nan, X., Ng, H. H., Johnson, C. A., Laherty, C. D., Turner, B. M., Eisenman, R. N., and Bird, A.. 1998. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393:386–389
   PubMed Web of Science ®Google Scholar
• Ng, H. H., Zhang, Y., Hendrich, B., Johnson, C. A., Turner, B. M., Erdjument-Bromage, H., Tempst, P., Reinberg, D., and Bird, A.. 1999. MBD2 is a transcriptional repressor belonging to the MeCP1 histone deacetylase complex. Nat. Genet. 23:58–61
   PubMed Web of Science ®Google Scholar
• Orlando, V., Strutt, H., and Paro, R.. 1997. Analysis of chromatin structure by in vivo formaldehyde cross-linking. Methods 11:205–214
   PubMed Web of Science ®Google Scholar
• Osborne, C. S., Pasceri, P., Singal, R., Sukonnik, T., Ginder, G. D., and Ellis, J.. 1999. Amelioration of retroviral vector silencing in locus control region beta-globin-transgenic mice and transduced F9 embryonic cells. J. Virol. 73:5490–5496
   PubMedGoogle Scholar
• Pikaart, M. J., Recillas-Targa, F., and Felsenfeld, G.. 1998. Loss of transcriptional activity of a transgene is accompanied by DNA methylation and histone deacetylation and is prevented by insulators. Genes Dev. 12:2852–2862
   PubMed Web of Science ®Google Scholar
• Razin, A.. 1998. CpG methylation, chromatin structure, and gene silencing—a three-way connection. EMBO J. 17:4905–4908
   PubMed Web of Science ®Google Scholar
• Rountree, M. R., Bachman, K. E., and Baylin, S. B.. 2000. DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci. Nat. Genet. 25:269–277
   PubMed Web of Science ®Google Scholar
• Rountree, M. R., and Selker, E. U.. 1997. DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa. Genes Dev. 11:2383–2395
   PubMed Web of Science ®Google Scholar
• Schübeler, D., Francastel, C., Cimbora, D. M., Reik, A., Martin, D. I., and Groudine, M.. 2000. Nuclear localization and histone acetylation: a pathway for chromatin opening and transcriptional activation of the human beta-globin locus. Genes Dev. 14:940–950
   PubMed Web of Science ®Google Scholar
• Seibler, J., Schübeler, D., Fiering, S., Groudine, M., and Bode, J.. 1998. DNA cassette exchange in ES cells mediated by Flp recombinase: an efficient strategy for repeated modification of tagged loci by marker-free constructs. Biochemistry 37:6229–6234
   PubMed Web of Science ®Google Scholar
• Simon, I., and Cedar, H.. 1996. Temporal order of DNA replication DNA replication in eukaryotic cells. DePamphilis, M. 387–408 Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y
   Google Scholar
• Struhl, K.. 1998. Histone acetylation and transcriptional regulatory mechanisms. Genes Dev. 12:599–606
   PubMed Web of Science ®Google Scholar
• Tollefsbol, T. O., Hutchison, C. A.III.. 1997. Control of methylation spreading in synthetic DNA sequences by the murine DNA methyltransferase. J. Mol. Biol. 269:494–504
   PubMedGoogle Scholar
• Wade, P. A., Gegonne, A., Jones, P. L., Ballestar, E., Aubry, F., and Wolffe, A. P.. 1999. Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation. Nat. Genet. 23:62–66
   PubMed Web of Science ®Google Scholar
• Yoder, J. A., Walsh, C. P., and Bestor, T. H.. 1997. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 13:335–340
   PubMed Web of Science ®Google Scholar
• Zhang, Y., Ng, H. H., Erdjument-Bromage, H., Tempst, P., Bird, A., and Reinberg, D.. 1999. Analysis of the NuRD subunits reveals a histone deacetylase core complex and a connection with DNA methylation. Genes Dev. 13:1924–1935
   PubMed Web of Science ®Google Scholar