Redefining regulation of DNA methylation by RNA interference

Genomics

Volumn 96, Issue 4, 2010, Pages 191-198

  Muthusamy, Viswanathan ^a   Bosenberg, Marcus ^a   Wajapeyee, Narendra ^a  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

DNA methylation; Epigenetics; Imprinting; RNA interference; Transcription

Indexed keywords

HISTONE; RAS ASSOCIATION DOMAIN FAMILY PROTEIN 1A; RAS PROTEIN;

CARCINOGENESIS; DEMETHYLATION; DNA METHYLATION; EPIGENETICS; GENE MUTATION; GENE REPRESSION; GENE SILENCING; GENOME IMPRINTING; HUMAN; MAMMAL CELL; MOLECULAR MECHANICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN MODIFICATION; REVIEW; RNA INTERFERENCE; TRANSCRIPTION REGULATION; TUMOR SUPPRESSOR GENE;

ANIMALS; CHROMOSOME MAPPING; DNA METHYLATION; EPIGENESIS, GENETIC; HUMANS; MAMMALS; MODELS, BIOLOGICAL; RNA INTERFERENCE; RNA, SMALL INTERFERING; TERMINOLOGY AS TOPIC;

MAMMALIA;

EID: 77956882077     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2010.07.001     Document Type: Review

References (47)

1. Maston G.A., Evans S.K., Green M.R. Transcriptional regulatory elements in the human genome. Annu. Rev. Genomics Hum. Genet. 2006, 7:29-59.
2. Palakurthy R.K., Wajapeyee N., Santra M.K., Gazin C., Lin L., Gobeil S., Green M.R. Epigenetic silencing of the RASSF1A tumor suppressor gene through HOXB3-mediated induction of DNMT3B expression. Mol. Cell 2009, 36:219-230.
3. Gazin C., Wajapeyee N., Gobeil S., Virbasius C.M., Green M.R. An elaborate pathway required for Ras-mediated epigenetic silencing. Nature 2007, 449:1073-1077.
4. Klose R.J., Bird A.P. Genomic DNA methylation: the mark and its mediators. Trends Biochem. Sci. 2006, 31:89-97.
5. Ramsahoye B.H., Biniszkiewicz D., Lyko F., Clark V., Bird A.P., Jaenisch R. Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc. Natl. Acad. Sci. U. S. A. 2000, 97:5237-5242.
6. Lister R., Pelizzola M., Dowen R.H., Hawkins R.D., Hon G., Tonti-Filippini J., Nery J.R., Lee L., Ye Z., Ngo Q.M., Edsall L., Antosiewicz-Bourget J., Stewart R., Ruotti V., Millar A.H., Thomson J.A., Ren B., Ecker J.R. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009, 462:315-322.
7. Chen T., Hevi S., Gay F., Tsujimoto N., He T., Zhang B., Ueda Y., Li E. Complete inactivation of DNMT1 leads to mitotic catastrophe in human cancer cells. Nat. Genet. 2007, 39:391-396.
8. Suzuki H., Gabrielson E., Chen W., Anbazhagan R., van Engeland M., Weijenberg M.P., Herman J.G., Baylin S.B. A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer. Nat. Genet. 2002, 31:141-149.
9. Cheng J.C., Yoo C.B., Weisenberger D.J., Chuang J., Wozniak C., Liang G., Marquez V.E., Greer S., Orntoft T.F., Thykjaer T., Jones P.A. Preferential response of cancer cells to zebularine. Cancer Cell 2004, 6:151-158.
10. Ecke I., Petry F., Rosenberger A., Tauber S., Monkemeyer S., Hess I., Dullin C., Kimmina S., Pirngruber J., Johnsen S.A., Uhmann A., Nitzki F., Wojnowski L., Schulz-Schaeffer W., Witt O., Hahn H. Antitumor effects of a combined 5-aza-2'deoxycytidine and valproic acid treatment on rhabdomyosarcoma and medulloblastoma in Ptch mutant mice. Cancer Res. 2009, 69:887-895.
11. Ohm J.E., Baylin S.B. Stem cell chromatin patterns: an instructive mechanism for DNA hypermethylation?. Cell Cycle 2007, 6:1040-1043.
12. Morgan H.D., Santos F., Green K., Dean W., Reik W. Epigenetic reprogramming in mammals. Hum. Mol. Genet. 2005, 14(Spec No 1):R47-58.
13. Bestor T., Laudano A., Mattaliano R., Ingram V. Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells. The carboxyl-terminal domain of the mammalian enzymes is related to bacterial restriction methyltransferases. J. Mol. Biol. 1988, 203:971-983.
14. Okano M., Xie S., Li E. Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases. Nat. Genet. 1998, 19:219-220.
15. Xie S., Wang Z., Okano M., Nogami M., Li Y., He W.W., Okumura K., Li E. Cloning, expression and chromosome locations of the human DNMT3 gene family. Gene 1999, 236:87-95.
16. Dodge J.E., Okano M., Dick F., Tsujimoto N., Chen T., Wang S., Ueda Y., Dyson N., Li E. Inactivation of Dnmt3b in mouse embryonic fibroblasts results in DNA hypomethylation, chromosomal instability, and spontaneous immortalization. J. Biol. Chem. 2005, 280:17986-17991.
17. Vire E., Brenner C., Deplus R., Blanchon L., Fraga M., Didelot C., Morey L., Van Eynde A., Bernard D., Vanderwinden J.M., Bollen M., Esteller M., Di Croce L., de Launoit Y., Fuks F. The polycomb group protein EZH2 directly controls DNA methylation. Nature 2006, 439:871-874.
18. Bostick M., Kim J.K., Esteve P.O., Clark A., Pradhan S., Jacobsen S.E. UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science 2007, 317:1760-1764.
19. Woo C.J., Kharchenko P.V., Daheron L., Park P.J., Kingston R.E. A region of the human HOXD cluster that confers polycomb-group responsiveness. Cell 2010, 140:99-110.
20. Ooi S.K., Bestor T.H. The colorful history of active DNA demethylation. Cell 2008, 133:1145-1148.
21. Mayer W., Niveleau A., Walter J., Fundele R., Haaf T. Demethylation of the zygotic paternal genome. Nature 2000, 403:501-502.
22. Ramakrishnan V. Histone structure and the organization of the nucleosome. Annu. Rev. Biophys. Biomol. Struct. 1997, 26:83-112.
23. Grewal S.I., Moazed D. Heterochromatin and epigenetic control of gene expression. Science 2003, 301:798-802.
24. Creyghton M.P., Markoulaki S., Levine S.S., Hanna J., Lodato M.A., Sha K., Young R.A., Jaenisch R., Boyer L.A. H2AZ is enriched at polycomb complex target genes in ES cells and is necessary for lineage commitment. Cell 2008, 135:649-661.
25. Campos E.I., Reinberg D. Histones: annotating chromatin. Annu. Rev. Genet. 2009, 43:559-599.
26. Snowden A.W., Gregory P.D., Case C.C., Pabo C.O. Gene-specific targeting of H3K9 methylation is sufficient for initiating repression in vivo. Curr. Biol. 2002, 12:2159-2166.
27. Metzger E., Schule R. The expanding world of histone lysine demethylases. Nat. Struct. Mol. Biol. 2007, 14:252-254.
28. Bird A. DNA methylation patterns and epigenetic memory. Genes Dev. 2002, 16:6-21.
29. Shibuya K., Fukushima S., Takatsuji H. RNA-directed DNA methylation induces transcriptional activation in plants. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:1660-1665.
30. Watt F., Molloy P.L. Cytosine methylation prevents binding to DNA of a HeLa cell transcription factor required for optimal expression of the adenovirus major late promoter. Genes Dev. 1988, 2:1136-1143.
31. Jones P.L., Veenstra G.J., Wade P.A., Vermaak D., Kass S.U., Landsberger N., Strouboulis J., Wolffe A.P. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat. Genet. 1998, 19:187-191.
32. Nan X., Ng H.H., Johnson C.A., Laherty C.D., Turner B.M., Eisenman R.N., Bird A. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 1998, 393:386-389.
33. Grewal S.I., Jia S. Heterochromatin revisited. Nat. Rev. Genet. 2007, 8:35-46.
34. Lehnertz B., Ueda Y., Derijck A.A., Braunschweig U., Perez-Burgos L., Kubicek S., Chen T., Li E., Jenuwein T., Peters A.H. Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr. Biol. 2003, 13:1192-1200.
35. Mohn F., Weber M., Rebhan M., Roloff T.C., Richter J., Stadler M.B., Bibel M., Schubeler D. Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Mol. Cell 2008, 30:755-766.
36. Silva J.M., Li M.Z., Chang K., Ge W., Golding M.C., Rickles R.J., Siolas D., Hu G., Paddison P.J., Schlabach M.R., Sheth N., Bradshaw J., Burchard J., Kulkarni A., Cavet G., Sachidanandam R., McCombie W.R., Cleary M.A., Elledge S.J., Hannon G.J. Second-generation shRNA libraries covering the mouse and human genomes. Nat. Genet. 2005, 37:1281-1288.
37. Downward J. Targeting RAS signalling pathways in cancer therapy. Nat. Rev. Cancer 2003, 3:11-22.
38. Peli J., Schroter M., Rudaz C., Hahne M., Meyer C., Reichmann E., Tschopp J. Oncogenic Ras inhibits Fas ligand-mediated apoptosis by downregulating the expression of Fas. EMBO J. 1999, 18:1824-1831.
39. Pruitt K., Ulku A.S., Frantz K., Rojas R.J., Muniz-Medina V.M., Rangnekar V.M., Der C.J., Shields J.M. Ras-mediated loss of the pro-apoptotic response protein Par-4 is mediated by DNA hypermethylation through Raf-independent and Raf-dependent signaling cascades in epithelial cells. J. Biol. Chem. 2005, 280:23363-23370.
40. Jones P.A., Baylin S.B. The epigenomics of cancer. Cell 2007, 128:683-692.
41. Cui H., Cruz-Correa M., Giardiello F.M., Hutcheon D.F., Kafonek D.R., Brandenburg S., Wu Y., He X., Powe N.R., Feinberg A.P. Loss of IGF2 imprinting: a potential marker of colorectal cancer risk. Science 2003, 299:1753-1755.
42. Holm T.M., Jackson-Grusby L., Brambrink T., Yamada Y., Rideout W.M., Jaenisch R. Global loss of imprinting leads to widespread tumorigenesis in adult mice. Cancer Cell 2005, 8:275-285.
43. Hartwell L.H., Szankasi P., Roberts C.J., Murray A.W., Friend S.H. Integrating genetic approaches into the discovery of anticancer drugs. Science 1997, 278:1064-1068.
44. Luo J., Emanuele M.J., Li D., Creighton C.J., Schlabach M.R., Westbrook T.F., Wong K.K., Elledge S.J. A genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene. Cell 2009, 137:835-848.
45. Scholl C., Frohling S., Dunn I.F., Schinzel A.C., Barbie D.A., Kim S.Y., Silver S.J., Tamayo P., Wadlow R.C., Ramaswamy S., Dohner K., Bullinger L., Sandy P., Boehm J.S., Root D.E., Jacks T., Hahn W.C., Gilliland D.G. Synthetic lethal interaction between oncogenic KRAS dependency and STK33 suppression in human cancer cells. Cell 2009, 137:821-834.
46. Takahashi K., Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 2006, 126:663-676.
47. Hochedlinger K., Blelloch R., Brennan C., Yamada Y., Kim M., Chin L., Jaenisch R. Reprogramming of a melanoma genome by nuclear transplantation. Genes Dev. 2004, 18:1875-1885.