Reading the DNA methylation signal

Cold Spring Harbor Symposia on Quantitative Biology

Volumn 69, Issue , 2004, Pages 113-118

  Bird, A ^a   Macleod, D ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; METHYL CPG BINDING PROTEIN; DNA METHYLTRANSFERASE 1; HISTONE; TRANSCRIPTION FACTOR;

CHROMATIN STRUCTURE; CONFERENCE PAPER; DNA DETERMINATION; DNA METHYLATION; DNA SEQUENCE; EPIGENETICS; GENE REPRESSION; GENE TARGETING; GENERAL ASPECTS OF DISEASE; LIVER; MALIGNANT NEOPLASTIC DISEASE; MARKER GENE; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROTEIN ANALYSIS; RETT SYNDROME; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; TRANSGENIC MOUSE; ARTICLE; EPIGENETIC REPRESSION; GENE EXPRESSION; GENE MUTATION; HUMAN; TRANSCRIPTION REGULATION; X CHROMOSOME INACTIVATION;

ANIMALS; CPG ISLANDS; DNA METHYLATION; DNA-BINDING PROTEINS; EPIGENESIS, GENETIC; GENE EXPRESSION; MICE; MODELS, GENETIC; NEOPLASMS, EXPERIMENTAL;

MUS MUSCULUS;

EID: 23044499578     PISSN: 00917451     EISSN: None     Source Type: Book Series    
DOI: 10.1101/sqb.2004.69.113     Document Type: Conference Paper

References (54)

1. Amir R.E., Van den Veyver I.B., Wan M., Tran C.Q., Francke U., and Zoghbi H.Y. 1999. Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2. Nat. Genet. 23: 185.
2. Ballestar E., Paz M.F., Valle L., Wei S., Fraga M.F., Espada J., Cigudosa J.C., Huang T.H., and Esteller M. 2003. Methyl-CpG binding proteins identify novel sites of epigenetic inactivation in human cancer. EMBO J. 22: 6335.
3. Bannister A.J., Zegerman P., Partridge J.F., Miska E.A., Thomas J.O., Allshire R.C., and Kouzarides T. 2001. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410: 120.
4. Baylin S. and Bestor T.H. 2002. Altered methylation patterns in cancer cell genomes: Cause or consequence? Cancer Cell 1: 299.
5. Bell A.C. and Felsenfeld G. 2000. Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature 405: 482.
6. Bird A.P. 1980. DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res. 8: 1499.
7. Bird A. and Wolffe A.P. 1999. Methylation-induced repression -Belts, braces and chromatin. Cell 99: 451.
8. Boyes J. and Bird A. 1991. DNA methylation inhibits transcription indirectly via a methyl-CpG binding protein. Cell 64: 1123.
9. Chen R.Z., Akbarian S., Tudor M., and Jaenisch R. 2001. Deficiency of methyl-CpG binding protein-2 in CNS neurons results in a Rett-like phenotype in mice. Nat. Genet. 27: 327.
10. Chen W.G., Chang Q., Lin Y., Meissner A., West A.E., Griffith E.C., Jaenisch R., and Greenberg M.E. 2003. Derepression of BDNF transcription involves calcium-dependent phosphorylation of MeCP2. Science 302: 885.
11. Coulondre C., Miller J.H., Farabough P.J., and Gilbert W. 1978. Molecular basis of base substitution hotspots in Escherichia coli. Nature 274: 775.
12. Cross S.H., Meehan R.R., Nan X., and Bird A. 1997. A component of the transcriptional repressor MeCP1 is related to mammalian DNA methyltransferase and trithorax-like protein. Nat. Genet. 16: 256.
13. Daniel J.M. and Reynolds A.B. 1999. The catenin p120(ctn) interacts with Kaiso, a novel BTB/POZ domain zinc finger transcription factor. Mol. Cell. Biol. 19: 3614.
14. Daniel J.M., Spring C.M., Crawford H.C., Reynolds A.B., and Baig A. 2002. The p120(ctn)-binding partner Kaiso is a bimodal DNA-binding protein that recognizes both a sequencespecific consensus and methylated CpG dinucleotides. Nucleic Acids Res. 30: 2911.
15. Eads C.A., Nickel A.E., and Laird P.W. 2002. Complete genetic suppression of polyp formation and reduction of CpG-island hypermethylation in Apc(Min/+) Dnmt1-hypomorphic mice. Cancer Res. 62: 1296.
16. Fearnhead N.S., Britton M.P., and Bodmer W.F. 2001. The ABC of APC. Hum. Mol. Genet. 10: 721.
17. Feng Q. and Zhang Y. 2001. The MeCP1 complex represses transcription through preferential binding, remodeling, and deacetylating methylated nucleosomes. Genes Dev. 15: 827.
18. Fujita N., Watanabe S., Ichimura T., Ohkuma Y., Chiba T., Saya H., and Nakao M. 2003. MCAF mediates MBD1-dependent transcriptional repression. Mol. Cell. Biol. 23: 2834.
19. Guy J., Hendrich B., Holmes M., Martin J.E., and Bird A. 2001. A mouse Mecp2-null mutation causes neurological symptoms that mimic Rett syndrome. Nat. Genet. 27: 322.
20. Hark A.T., Schoenherr C.J., Katz D.J., Ingram R.S., Levorse J.M., and Tilghman S.M. 2000. CTCF mediates methylationsensitive enhancer-blocking activity at the H19/Igf2 locus. Nature 405: 486.
21. Hendrich B. and Bird A. 1998. Identification and characterization of a family of mammalian methyl-CpG binding proteins. Mol. Cell. Biol. 18: 6538.
22. Hendrich B., Guy J., Ramsahoye B., Wilson V.A., and Bird A. 2001. Closely related proteins Mbd2 and Mbd3 play distinctive but interacting roles in mouse development. Genes Dev. 15: 710.
23. Hendrich B., Hardeland U., Ng H.-H., Jiricny J., and Bird A. 1999. The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites. Nature 401: 301.
24. Hutchins A., Mullen A., Lee H., Barner K., High F., Hendrich B., Bird A., and Reiner S. 2002. Gene silencing quantitatively controls the function of a developmental trans-activator. Mol. Cell 10: 81.
25. Jenuwein T. and Allis C.D. 2001. Translating the histone code. Science 293: 1074.
26. 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.
27. Jorgensen H.F., Ben-Porath I., and Bird A.P. 2004. Mbd1 is recruited to both methylated and nonmethylated CpGs via distinct DNA binding domains. Mol. Cell. Biol. 24: 3387.
28. Kriaucionis S. and Bird A. 2003. DNA methylation and Rett syndrome. Hum. Mol. Genet. (Spec. No. 2) 12: R221.
29. Lachner M., O'Carroll D., Rea S., Mechtler K., and Jenuwein T. 2001. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410: 116.
30. Laird P.W., Jackson-Grusby, Fazeli A., Dickinson S.L., Jung W.E., Li E., Weinberg R.A., and Jaenisch R. 1995. Suppression of intestinal neoplasia by DNA hypomethylation. Cell 81: 197.
31. Levine A., Cantoni G.L., and Razin A. 1992. Methylation in the preinitiation domain suppresses gene transcription by an indirect mechanism. Proc. Natl. Acad. Sci. 89: 10119.
32. Lewis J.D., Meehan R.R., Henzel W.J., Maurer-Fogy I., Jeppesen P., Klein F., and Bird A. 1992. Purification, sequence and cellular localisation of a novel chromosomal protein that binds to methylated DNA. Cell 69: 905.
33. Li E., Bestor T.H., and Jaenisch R. 1992. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69: 915.
34. Lin X. and Nelson W.G. 2003. Methyl-CpG-binding domain protein-2 mediates transcriptional repression associated with hypermethylated GSTP1 CpG islands in MCF-7 breast cancer cells. Cancer Res. 63: 498.
35. Martinowich K., Hattori D., Wu H., Fouse S., He F., Hu Y., Fan G., and Sun Y.E. 2003. DNA methylation-related chromatin remodeling in activity-dependent BDNF gene regulation. Science 302: 890.
36. Meehan R.R., Lewis J.D., McKay S., Kleiner E.L., and Bird A.P. 1989. Identification of a mammalian protein that binds specifically to DNA containing methylated CpGs. Cell 58: 499.
37. Millar C.B., Guy J., Sansom O.J., Selfridge J., MacDougall E., Hendrich B., Keightley P.D., Bishop S.M., Clarke A.R., and Bird A. 2002. Enhanced CpG mutability and tumorigenesis in MBD4-deficient mice. Science 297: 403.
38. Nan X., Campoy J., and Bird A. 1997. MeCP2 is a transcriptional repressor with abundant binding sites in genomic chromatin. Cell 88: 471.
39. 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.
40. Nan X., Tate P., Li E., and Bird A.P. 1996. DNA methylation specifies chromosomal localization of MeCP2. Mol. Cell. Biol. 16: 414.
41. 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.
42. Ng H.-H., Zhang Y., Hendrich B., Johnson C.A., Burner 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.
43. Ohki I., Shimotake N., Fujita N., Nakao M., and Shirakawa M. 1999. Solution structure of the methyl-CpG-binding domain of the methylation-dependent transcriptional repressor MBD1. EMBO J. 18: 6653.
44. Ohki I., Shimotake N., Fujita N., Jee J., Ikegami T., Nakao M., and Shirakawa M. 2001. Solution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA. Cell 105: 487.
45. Prokhortchouk A., Hendrich B., Jorgensen H., Ruzov A., Wilm M., Georgiev G., Bird A., and Prokhortchouk E. 2001. The p120 catenin partner Kaiso is a DNA methylation-dependent transcriptional repressor. Genes Dev. 15: 1613.
46. Sansom O.J., Berger J., Bishop S.M., Hendrich B., Bird A., and Clarke A.R. 2003. Deficiency of Mbd2 suppresses intestinal tumorigenesis. Nat. Genet. 34: 145.
47. Shahbazian M.D. and Zoghbi H.Y. 2002. Rett syndrome and MeCP2: Linking epigenetics and neuronal function. Am. J. Hum. Genet. 71: 1259.
48. Shahbazian M.D., Antalffy B., Armstrong D.L., and Zoghbi H.Y. 2002. Insight into Rett syndrome: MeCP2 levels display tissue- and cell-specific differences and correlate with neuronal maturation. Hum. Mol. Genet. 11: 115.
49. Stancheva I., Collins A.L., Van den Veyver I.B., Zoghbi H., and Meehan R.R. 2003. A mutant form of MeCP2 protein associated with human Rett syndrome cannot be displaced from methylated DNA by notch in Xenopus embryos. Mol. Cell 12: 425.
50. Tudor M., Akbarian S., Chen R.Z., and Jaenisch R. 2002. Transcriptional profiling of a mouse model for Rett syndrome reveals subtle transcriptional changes in the brain. Proc. Natl. Acad. Sci. 99: 15536.
51. 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.
52. Wakefield R.I.D., Smith B.P., Nan X., Free A., Soterious A., Uhrin D., Bird A., and Barlow P.N. 1999. The solution structure of the domain from MeCP2 that binds to methylated DNA. J. Mol. Biol. 291: 1055.
53. Winston F. and Allis C.D. 1999. The bromodomain: A chromatin-targeting module? Nat. Struct. Biol. 6: 601.
54. Yoon H.G., Chan D.W., Reynolds A.B., Qin J., and Wong J. 2003. N-CoR mediates DNA methylation-dependent repression through a methyl CpG binding protein Kaiso. Mol. Cell 12: 723.