Role of chromatin/epigenetic modifications on DNA accessibility

Drug News and Perspectives

Volumn 20, Issue 9, 2007, Pages 549-556

  Georgel, Philippe T ^a  

^a MARSHALL UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

5 AZA 2' DEOXYCYTIDINE; 5,6 DIHYDROAZACITIDINE; ADENOSINE TRIPHOSPHATASE; AZACITIDINE; DNA BINDING PROTEIN; DNA METHYLTRANSFERASE; DNA METHYLTRANSFERASE INHIBITOR; FAZARABINE; HISTONE; SMALL INTERFERING RNA;

CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN CONDENSATION; CHROMATIN STRUCTURE; CLINICAL TRIAL; CPG ISLAND; DNA METHYLATION; DNA MODIFICATION; DNA RNA HYBRIDIZATION; DRUG DELIVERY SYSTEM; DRUG DESIGN; DRUG DNA BINDING; DRUG MECHANISM; DRUG RESEARCH; DRUG SPECIFICITY; EPIGENETICS; GENE CONTROL; GENE EXPRESSION; GENE TARGETING; HUMAN; NONHUMAN; NUCLEOSOME; PROTEIN DOMAIN; REVIEW; RNA INTERFERENCE; UNSPECIFIED SIDE EFFECT;

CHROMATIN; DNA; DNA-BINDING PROTEINS; DRUG DELIVERY SYSTEMS; DRUG DESIGN; EPIGENESIS, GENETIC; HUMANS; MODELS, BIOLOGICAL; PHARMACEUTICAL PREPARATIONS;

EID: 41649087986     PISSN: 02140934     EISSN: None     Source Type: Journal    
DOI: 10.1358/dnp.2007.20.9.1162241     Document Type: Review

References (69)

1. Woodcock, C.L. and Dimitrov, S. Higher-order structure of chromatin and chromosomes. Curr Opin Genet Dev 2001, 11(2): 130-5.
2. van Holde, K.E. Chromatin. Springer-Verlag: New York 1988.
3. Adkins, N.L., Watts, M. and Georgel P.T. To the 30-nm chromatin fiber and beyond. Biochim Biophys Acta 2004, 1677(1-3): 12-23.
4. Jones, P.A. and Laird, P.W. Cancer epigenetics comes of age. Nat Genet 1999, 21(2): 163-7.
5. Georgel, P.T., Horowitz-Scherer, R.A., Adkins, N., Woodcock, C.L., Wade, P.A. and Hansen, J.C. Chromatin compaction by human MeCP2. Assembly of novel secondary chromatin structures in the absence of DNA methylation. J Biol Chem 2003, 278(34): 32181-8.
6. Robertson, K.D, Keyomarsi, K., Gonzales, F.A., Velicescu, M. and Jones, P.A. Differential mRNA expression of the human DNA methyltransferases (DNMTs) 1, 3a and 3b during the G(0)/G(1) to S phase transition in normal and tumor cells. Nucleic Acids Res 2000, 28(10): 2108-13.
7. Rhee, I., Jair, K.W., Yen, R.W. et al. CpG methylation is maintained in human cancer cells lacking DNMT1. Nature 2000, 404(6781): 1003-7.
8. Robertson, K.D., Uzvolgyi, E., Liang, G. et al. The human DNA methyltransferases (DNMTs) 1, 3a and 3b: coordinate mRNA expression in normal tissues and overexpression in tumors. Nucleic Acids Res 1999, 27(11): 2291-8.
9. Hata, K., Okano, M., Lei, H. and Li, E. Dnmt3L cooperates with the Dnmt3 family of de novo DNA methyltransferases to establish maternal imprints in mice. Development 2002, 129(8): 1983-93.
10. Wade, P.A. Methyl CpG-binding proteins and transcriptional repression. Bioessays 2001, 23(12): 1131-7.
11. Goll, M.G., Kirpekar, F., Maggert, K.A. et al. Methylation of tRNA(Asp) by the DNA methyltransferase homolog Dnmt2. Science 2006, 311(5759): 395-7.
12. Ehrlich M., Buchanan, K.L., Tsien, F. et al. DNA methyltransferase 3B mutations linked to the ICF syndrome cause dysregulation of lymphogenesis genes. Hum Mol Genet 2001, 10(25): 2917-31.
13. Hendrich, B. and Tweedie, S. The methyl-CpG binding domain and the evolving role of DNA methylation in animals. Trends Genet 2003, 19(5): 269-77.
14. Jorgensen, H.F. and Bird, A. MeCP2 and other methyl-CpG binding proteins. Ment Retard Dev Disabil Res Rev 2002, 8(2): 87-93.
15. Jones, P.L., Veenstra, G.J., Wade, P.A. et al. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat Genet 1998, 19(2): 187-91.
16. Sheikhnejad, G., Brank, A., Christman, J.K. et al. Mechanism of inhibition of DNA (cytosine C5)-methyltransferases by oligodeoxyribonucleotides containing 5,6-dihydro-5-azacytosine. J MoI Biol 1999, 285(5): 2021-34.
17. Szyf, M. Targeting DNA methyltransferase in cancer. Cancer Metastasis Rev 1998, 17(2): 219-31.
18. Villar-Garea, A. and Esteller, M. DNA demethylating agents and chromatin-remodeling drigs: Which, how and why? Curr Drug Metab 2003, 4(1): 11-31.
19. Bigey, P., Knox, J.D., Croteau, S., Bhattacharya, S.K., Theberge, J. and Szyf, M. Modified oligonucleotides as bona fide antagonists of proteins interacting with DNA. hairpin antagonists of the human DNA methyltransferase. J Biol Chem 1999, 274(8): 4594-606.
20. Christman, J.K., Price, P., Pedrinan, L. and Acs, G. Correlation between hypomethylation of DNA and expression of globin genes in Friend erythroleukemia cells. Eur J Biochem 1977, 81(1): 53-61.
21. Guo, H., Tan, Y., Kubota, T., Moossa, A.R. and Hoffman, R.M. Methionine depletion modulates the antitumor and antimetastatic efficacy of ethionine. Anticancer Res 1996, 16(5A): 2719-23.
22. Ramchandani, S., MacLeod, A.R., Pinard, M., von Hofe, E. and Szyf, M. Inhibition of tumorigenesis by a cytosine-DNA, methyltransferase, antisense oligodeoxynucleotide. Proc Natl Acad Sci U S A 1997, 94(2): 684-9.
23. Bosher, J.M. and Labouesse, M. RNA interference: genetic wand and genetic watch-dog. Nat Cell Biol 2000, 2(2): E31-6.
24. Bernstein, E., Caudy, A.A., Hammond, S.M. and Hannon, G.J. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 2001, 409(6818): 363-6.
25. Hammond, S.M., Boettcher, S., Caudy, A.A., Kobayashi, R. and Hannon, G.J. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 2001, 293(5532): 1146-50.
26. Shrader, T.E. and Crothers, D.M. Artificial nucleosome positioning sequences. Proc Natl Acad Sci U S A 1989, 86(19): 7418-22.
27. Thastrom, A., Bingham, L.M. and Widom, J. Nucleosomal locations of dominant DNA sequence motifs for histone-DNA interactions and nucleosome positioning. J Mol Biol 2004, 338(4): 695-709.
28. Jenuwein, T. and Allis, C.D. Translating the histone code. Science 2001, 293(5532): 1074-80.
29. Rao, B., Shibata, Y., Strahl, B.D. and Lieb, J.D. Dimethylation of histone H3 at lysine 36 demarcates regulatory and nonregulatory chromatin genome-wide. Mol Cell Biol 2005, 25(21): 9447-59.
30. Orlando, V., Jane, E.P., Chinwalla, V., Harte, P.J. and Paro, R. Binding of Trithorax and Polycomb proteins to the bithorax complex: Dynamic changes during early Drosophila embryogenesis. EMBO J 1998, 17(17): 5141-50.
31. Flanagan, J.F, Mi, L.Z., Chrusczc, M.S. et al. Double chromodomains cooperate to recognize the methylated histone H3 tail. Nature 2005, 438(7071): 1181-5.
32. Tsukiyama T. and Wu, C. Purification and properties of an ATP-dependent nucleosome remodeling factor. Cell 1995, 83(6): 1011-20.
33. Prigent, C. and Dimitrov, S. Phosphorylation of serine 10 in histone H3, what for? J Cell Sci 2003, 116(Pt 18): 3677-85.
34. Moss, T.J. and Wallrath, L.L. Connections between epigenetic gene silencing and human disease. Mutat Res 2007, 618(1-2): 163-74.
35. Kamakaka, R. and Biggins, S. Histone variants: Deviants. Genes Dev 2005, 19(3): 295-310.
36. Thiriet, C. and Hayes, J.J. Chromatin in need of a fix: Phosphorylation of H2AX connects chromatin to DNA repair. Mol Cell 2005, 18(6): 617-22.
37. Rogakou, E.P., Pilch, D.R., Orr, A.H., Ivanova, V.S. and Bonner, W.M. Double-stranded breaks induce histone H2AX phosphorylation on serine 139. J Biol Chem 1998, 273(10): 5858-68.
38. Meneghini, M.D., Wu, M. and Madhani, H.D. Conserved histone variant H2A.Z protects euchromatin from ectopic spread of silent heterochromatin. Cell 2003, 112(5): 725-36.
39. Ausio, J. Histone variants - the structure behind the function. Brief Funct Genomic Proteomic 2006, 5(3): 228-43.
40. Gautier, T., Abbott, D.W., Molla, A., Verdel, A., Ausio, J. and Dimitrov, S. Histone variant H2ABbd confers lower stability to the nucleosome. EMBO Rep 2004, 5(7): 715-20.
41. Costanzi, C., Stein, P., Worrad, D.M., Schultz, R.M. and Pehrson, J.R. Histone macroH2A1 is concentrated in the inactive X chromosome of female preimplantation mouse embryos. Development 2000, 127(11): 2283-9.
42. Zalensky, A.O., Siino, J.S., Gineitis, A.A. et al. Human testis/sperm-specific histone H2B (hTSH2B). Molecular cloning and characterization. J Biol Chem 2002, 277(45): 43474-80.
43. Ahmad, K. and Henikoff, S. The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol Cell 2002, 9(6): 1191-200.
44. Witt, O., Albig, W. and Doenecke, D. Testis-specific expression of a novel human H3 histone gene. Exp Cell Res 1996, 229(2): 301-6.
45. Malik, H.S. and Henikoff, S. Phylogenomics of the nucleosome. Nat Struct Biol 2003, 10(11): 882-91.
46. Sif, S. ATP-dependent nucleosome remodeling complexes: Enzymes tailored to deal with chromatin. J Cell Biochem 2004, 91(6): 1087-98.
47. Choudhary, P. and Varga-Weisz, P. ATP-dependent chromatin remodeling: Action and reaction. Subcell Biochem 2007, 41: 29-43.
48. Winston, F. and Carslon, M. Yeast SNF/SWi transcriptional activators and the SPT/Sin chromatin connection. Trends Genet 1992, 8(11): 387-91.
49. Shen, X., Mizuguchi, G., Hamiche, A. and Wu, C. A chromatin remodeling complex involved in transcription and DNA processing. Nature 2000, 406(6795): 541-4.
50. Hall, J.A. and Georgel, P.T. CHD proteins: A diverse family with strong ties. Biochem Cell Biol, in press.
51. Hamiche, A., Sandaltzopoulos, R., Gdula, D.A. and Wu, C. ATP-dependent histone octamer sliding mediated by the chromatin remodeling complex NURF. Cell 1999, 97(7): 833-42.
52. Langst, G., Bonte, E.J., Corona, D.F. and Becker, P.B. Nucleosome movement by CHRAC and ISWI without disruption or trans-displacement of the histone octamer. Cell 1999, 97(7): 843-52.
53. Varga-Weisz, P.D., Wilm, M., Bonte, E., Dumas, K., Mann, M. and Becker, P.B. Chromatin-remodelling factor CHRAC contains the ATPases ISWI and topoisomerase II. Nature 1997, 388(6642): 598-602.
54. Jacob, F. and Monod, J. Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 1961, 3: 318-56.
55. Avner, P. and Heard, E. X-chromosome inactivation: Counting, choice and initiation. Nat Rev Genet 2001, 2(1): 59-67.
56. Heard, E. Recent advances in X-chromosome inactivation. Curr Opin Cell Biol 2004, 16(3): 247-55.
57. Plath, K., Talbot, D., Hamer, K.M. et al. Developmentally regulated alterations in polycomb repressive complex 1 on the inactive X chromosome. J Cell Biol 2004, 167(6): 1025-35.
58. Guo, S. and Kemphues, K.J. par-1, a gene required for establishing polarity in C. elegans, encodes a putative Ser/Thr kinase that is asymmetrically distributed. Cell 1995, 81(4): 611-20.
59. Knight, S.W. and Bass, B.L. A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science 2001, 293(5538): 2269-71.
60. Song, J.J. and Joshua-Tor, L. Argonaute and RNA- getting into the groove. Curr Opin Struct Biol 2006, 16(1): 5-11.
61. Bernstein, E. and Allis, C.D. RNA meets chromatin. Genes Dev 2005, 19(14): 1635-55.
62. Hall I.M., Shankaranarayana, G.D., Noma, K., Ayoub, N., Cohen, A. and Grewal, S.I. Establishment and maintenance of a heterochromatin domain. Science 2002, 297(5590): 2232-7.
63. Martens, J.H., O'Sullivan, R.J., Braunschweig, U., Opravil, S., Radolf, M., Steinlein, P. and Jenuwein, T. The profile of repeat-associated histone lysine methylation states in the mouse epigenome. EMBO J 2005, 24(4): 800-12.
64. Maison, C., Bailly, D., Peters, A.H.F.M. et al. Higher-order structure in pericentric heterochromatin involves a distinct pattern of histone modifications and anRNA component. Nat Genet 2002, 30(3): 329-34.
65. Paro, R. and Hogness, D. The Polycomb protein shares a homologous domain with heterochromatin-associated protein of Drosophila. Proc Natl Acad Sci U S A 1991, 88(1): 263-7.
66. Morris, K.V., Chan, S.W., Jacobsen, E.E. and Looney, D.J. Small interfering RNA-induced transcriptional gene silencing in human cells. Science 2004, 305(5688): 1289-92.
67. Ekwall, K. and Ruusala, T. Mutations in rik1, clr2, clr3 and clr4 genes asymmetrically derepress the silent mating-type loci in fission yeast. Genetics 1994, 136(1): 53-64.
68. Marchion, D. and Munster, P. Development of histone deacetylase inhibitors for cancer treatment. Expert Rev Anticancer Ther 2007, 7(4): 583-98.
69. Berger, S.L. The complex language of chromatin regulation during transcription. Nature 2007, 447(7143): 407-12.