Specific targeting of cytosine methylation to DNA sequences in vivo

Nucleic Acids Research

Volumn 35, Issue 3, 2007, Pages 740-754

  Smith, Alexander E ^a   Ford, Kevin G ^a  

^a ST THOMAS HOSPITAL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; DNA METHYLTRANSFERASE; PLASMID DNA; ZINC FINGER PROTEIN;

ARTICLE; CELL DIVISION; CONTROLLED STUDY; DNA DETERMINATION; DNA METHYLATION; DNA SEQUENCE; ENZYME ACTIVE SITE; ENZYME ACTIVITY; GENE LOCUS; GENETIC CODE; HUMAN; HUMAN CELL; IN VITRO STUDY; IN VIVO STUDY; MAMMAL CELL; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN METHYLATION; PROTEIN TARGETING;

BASE SEQUENCE; CYTOSINE; DNA; DNA METHYLATION; ELECTROPHORETIC MOBILITY SHIFT ASSAY; ESCHERICHIA COLI; GENOME, BACTERIAL; HUMANS; MUTAGENESIS; SITE-SPECIFIC DNA METHYLTRANSFERASE (CYTOSINE-SPECIFIC); ZINC FINGERS;

BACTERIA (MICROORGANISMS); MAMMALIA; PROKARYOTA;

EID: 33847377099     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl1053     Document Type: Article

References (36)

1. Nakao,M. (2001) Epigenetics: Interaction of DNA methylation and chromatin. Gene, 278, 25-31.
2. 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. Nature Genet., 19, 187-191.
3. 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. Nature Genet., 23, 62-66.
4. Robertson,K.D., Ait-Si-Ali,S., Yokochi,T., Wade,P.A., Jones,P.L. and Wolffe,A.P. (2000) DNMT1 forms a complex with Rb, E2F1 and HDAC1 and represses transcription from E2F-responsive promoters. Nature Genet., 25, 338-342.
5. 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. Nature Genet., 25, 269-277.
6. Lorincz,M.C., Dickerson,D.R., Schmitt,M. and Groudine,M. (2004) Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nature Struct. Mol. Biol., 11, 1068-1075.
7. Kawasaki,H. and Taira K. (2004) Induction of DNA methylation and gene silencing by short interfering RNAs in human cells. Nature, 431, 211-217.
8. Morris,K.V., Chan,S.W., Jacobsen,S.E. and Looney,D.J. (2004) Small interfering RNA-induced transcriptional gene silencing in human cells. Science, 305, 1289-1292.
9. Murayama,A., Sakura,K., Nakama,M., Yasuzawa-Tanaka,K., Fujita,E., Tateishi,Y., Wang,Y., Ushijima,T., Baba,T., Shibuya,K. et al. (2006) A specific CpG site demethylation in the human interleukin 2 gene promoter is an epigenetic memory. EMBO J., 25, 1081-1092.
10. Park,C.W., Chen,Z., Kren,B.T. and Steer,C.J. (2004) Double-stranded siRNA targeted to the huntingtin gene does not induce DNA methylation. Biochem. Biophys. Res. Commun., 323, 275-280.
11. Svoboda,P., Stein,P., Filipowicz,W. and Schultz,R.M. (2004) Lack of homologous sequence-specific DNA methylation in response to stable dsRNA expression in mouse oocytes. Nucleic Acids Res., 32, 3601-3606.
12. Ting,A.H., Schuebel,K.E., Herman,J.G. and Baylin,S.B. (2005) Short double-stranded RNA induces transcriptional gene silencing in human cancer cells in the absence of DNA methylation. Nature Genet., 37, 906-910.
13. Ishii,T., Fujishiro,M., Masuda,M., Teramoto,S. and Matsuse,T. (2004) A methylated oligonucleotide induced methylation of GSTP1 promoter and suppressed its expression in A549 lung adenocarcinoma cells. Cancer Lett., 212, 211-223.
14. Yao,X., Hu,J.F., Daniels,M., Shiran,H., Zhou,X., Yan,H., Lu,H., Zeng,Z., Wang,Q., Li,T. et al. (2003) A methylated oligonucleotide inhibits IGF2 expression and enhances survival in a model of hepatocellular carcinoma. J. Clin. Invest., 111, 265-273.
15. Klug,A. (2005) Towards therapeutic applications of engineered zinc-finger proteins. FEBS Lett., 579, 892-894.
16. Xu,G.L. and Bestor,T.H. (1997) Cytosine methylation targetted to pre-determined sequences. Nature Genet., 17, 376-378.
17. Carvin,C.D., Parr,R.D. and Kladde,M.P. (2003) Site-selective in vivo targeting of cytosine-5 DNA methylation by zinc-finger proteins. Nucleic Acids Res., 31, 6493-6501.
18. McNamara,A.R., Hurd,P.J., Smith,A.E. and Ford,K.G. (2002) Characterisation of site-biased DNA methyltransferases: Specificity, affinity and subsite relationships. Nucleic Acids Res., 30, 3818-3830.
19. McNamara,A.R. and Ford,K.G. (2000) A novel four zinc-finger protein targeted against pl90(BcrAb1) fusion oncogene cDNA: Utilisation of zinc-finger recognition codes. Nucleic Acids Res., 228, 4865-4872.
20. Choo,Y., Sanchez-Garcia,I. and Klug,A. (1994) In vivo repression by a site-specific DNA-binding protein designed against an oncogenic sequence. Nature, 372, 642-645.
21. Smith,A.E., Farzaneh,F. and Ford,K.G. (2005) Single zinc-finger extension: Enhancing transcriptional activity and specificity of three-zinc-finger proteins. Biol. Chem., 2386, 95-99.
22. Sambrook,J., Fritsch,E.F. and Maniatis,T. (1989) Molecular Cloning: A laboratory Manual, 2nd edn. Cold Spring Harbor Press, Cold Spring Harbor, NY.
23. Wislon,G.G. (1992) Amino acid sequence arrangements of DNA-methyltransferases. Nucleic Acids Res., 17, 2421-2435.
24. Cheng,X., Kumar,S., Posfai,J., Pflugrath,J.W. and Roberts,R.J. (1993) Crystal structure of the HhaI DNA methyltransferase complexed with S-adenosyl-L-methionine. Cell, 74, 299-307.
25. Klimasauskas,S., Kumar,S., Roberts,A.J. and Cheng,X. (1994) HhaI methyltransferase flips its target base out of the DNA helix. Cell, 76, 357-369.
26. O'Gara,M., Horton J.R., Roberts,R.J. and Cheng,X. (1998) Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base. Nature Struct. Biol., 5, 872-877.
27. Sankpal,U.T. and Rao,D.N. (2002) Mutational analysis of conserved residues in HhaI DNA methyltransferase. Nucleic Acids Res., 30, 2628-2638.
28. Mi,S., Alonso,D. and Roberts,R.J. (1995) Functional analysis of Gln-237 mutants of HhaI methyltransferase. Nucleic Acids Res., 23, 620-627.
29. Vilkaitis,G., Dong,A., Weinhold,E., Cheng,X. and Klimasauskas,S.R. (2000) Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase. J. Biol. Chem., 275, 38722-38730.
30. Liu,Q., Segal,D.J., Ghiara,J.B. and Barbas,C.F., III (1997) Design of polydactyl zinc-finger proteins for unique addressing within complex genomes. Proc. Natl Acad. Sci. USA, 94, 5525-5530.
31. Kim,J.S. and Pabo,C.O. (1998) Getting a handhold on DNA: Design of poly-zinc-finger proteins with femtomolar dissociation constants. Proc. Natl Acad. Sci. USA, 95, 2812-2817.
32. Liang,G., Salem,C.E., Yu,M.C., Nguyen,H.D., Gonzales,F.A., Nguyen,T.T., Nichols,P.W. and Jones,P.A. (1998) DNA methylation differences associated with tumor tissues identified by genome scanning analysis. Genomics, 53, 260-268.
33. Liang,G., Gonzalgo,M.L., Salem,C. and Jones,P.A. (2002) Identification of DNA methylation differences during tumorigenesis by methylation-sensitive arbitrarily primed polymerase chain reaction. Methods, 27, 150-155.
34. Daujoyte,D., Serva,S., Vilaitis,G., Merkiene,E., Venclovas,C. and Klimasauskas,S. (2004) HhaI DNA methyltransferase uses the protruding Gln237 for active flipping of its target cytosine. Structure, 12, 1047-1055.
35. Christiansen,D.H., Andersen,M.K. and Pedersen-Bjergaard,J. (2003) Methylation of pl51NK4B is common, is associated with deletion of genes on chromosome arm 7q and predicts a poor prognosis in therapy-related myelodysplasia and acute myeloid leukemia. Leukemia, 17, 1813-1819.
36. Yates,P.A., Burman,R., Simpson,J., Ponomoreva,O.N., Thayer,M.J. and Turker,M.S. (2003) Silencing of the mouse Aprt is a gradual process in differentiated cells. Mol. Cell. Biol., 23, 4461-4470.