Identification of preferential target sites for human DNA methyltransferases

Nucleic Acids Research

Volumn 39, Issue 1, 2011, Pages 104-118

  Choi, Si Ho ^a,b,c   Heo, Kyu ^b,d   Byun, Hyang Min ^a   An, Woojin ^b   Lu, Wange ^b,c   Yang, Allen S ^a  

^a Norris Cancer Center   (United States)

^b Department of Biochemistry and Molecular Biology ^*  (Australia)

^c UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^d Dongnam Institute of Radiological and Medical Science   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

DNA METHYLTRANSFERASE; DNA METHYLTRANSFERASE 1; DNA METHYLTRANSFERASE 3A; DNA METHYLTRANSFERASE 3B; DNA METHYLTRANSFERASE 3L; HISTONE LYSINE METHYLTRANSFERASE; UNCLASSIFIED DRUG;

ARTICLE; CANCER CELL CULTURE; CELL STRAIN HEK293; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; DNA MICROARRAY; DNA SEQUENCE; ENZYME MODIFICATION; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE IDENTIFICATION; GENE TARGETING; GENETIC TRANSCRIPTION; GENETIC TRANSFECTION; HUMAN; HUMAN CELL; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DOMAIN;

EID: 78651314191     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq774     Document Type: Article

References (38)

1. Goll, M.G. and Bestor, T.H. (2005) Eukaryotic cytosine methyltransferases. Annu. Rev. Biochem., 74, 481-514.
2. Ostler, K.R., Davis, E.M., Payne, S.L., Gosalia, B.B., Exposito-Cespedes, J., Le Beau, M.M. and Godley, L.A. (2007) Cancer cells express aberrant DNMT3B transcripts encoding truncated proteins. Oncogene, 26, 5553-5563.
3. Chen, T., Hevi, S., Gay, F., Tsujimoto, N., He, T., Zhang, B., Ueda, Y. and Li, E. (2007) Complete inactivation of DNMT1 leads to mitotic catastrophe in human cancer cells. Nat. Genet., 39, 391-396.
4. Okano, M., Bell, D.W., Haber, D.A. and Li, E. (1999) DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell, 99, 247-257.
5. Ooi, S.K., Qiu, C., Bernstein, E., Li, K., Jia, D., Yang, Z., Erdjument-Bromage, H., Tempst, P., Lin, S.P., Allis, C.D. et al. (2007) DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature, 448, 714-717.
6. Bourc'his, D. and Bestor, T.H. (2004) Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature, 431, 96-99.
7. Bourc'his, D., Xu, G.L., Lin, C.S., Bollman, B. and Bestor, T.H. (2001) Dnmt3L and the establishment of maternal genomic imprints. Science, 294, 2536-2539.
8. Chen, T., Ueda, Y., Dodge, J.E., Wang, Z. and Li, E. (2003) Establishment and maintenance of genomic methylation patterns in mouse embryonic stem cells by Dnmt3a and Dnmt3b. Mol. Cell. Biol., 23, 5594-5605.
9. Biniszkiewicz, D., Gribnau, J., Ramsahoye, B., Gaudet, F., Eggan, K., Humpherys, D., Mastrangelo, M.A., Jun, Z., Walter, J. and Jaenisch, R. (2002) Dnmt1 overexpression causes genomic hypermethylation, loss of imprinting, and embryonic lethality. Mol. Cell. Biol., 22, 2124-2135.
10. Linhart, H.G., Lin, H., Yamada, Y., Moran, E., Steine, E.J., Gokhale, S., Lo, G., Cantu, E., Ehrich, M., He, T. et al. (2007) Dnmt3b promotes tumorigenesis in vivo by gene-specific de novo methylation and transcriptional silencing. Genes Dev., 21, 3110-3122.
11. Soejima, K., Fang, W. and Rollins, B.J. (2003) DNA methyltransferase 3b contributes to oncogenic transformation induced by SV40T antigen and activated Ras. Oncogene, 22, 4723-4733.
12. Kanai, Y., Saito, Y., Ushijima, S. and Hirohashi, S. (2004) Alterations in gene expression associated with the overexpression of a splice variant of DNA methyltransferase 3b, DNMT3b4, during human hepatocarcinogenesis. J. Cancer Res. Clin. Oncol., 130, 636-644.
13. Saito, Y., Kanai, Y., Sakamoto, M., Saito, H., Ishii, H. and Hirohashi, S. (2002) Overexpression of a splice variant of DNA methyltransferase 3b, DNMT3b4, associated with DNA hypomethylation on pericentromeric satellite regions during human hepatocarcinogenesis. Proc. Natl Acad. Sci. USA, 99, 10060-10065.
14. Wang, J., Bhutani, M., Pathak, A.K., Lang, W., Ren, H., Jelinek, J., He, R., Shen, L., Issa, J.P. and Mao, L. (2007) Delta DNMT3B variants regulate DNA methylation in a promoter-specific manner. Cancer Res., 67, 10647-10652.
15. Wang, L., Wang, J., Sun, S., Rodriguez, M., Yue, P., Jang, S.J. and Mao, L. (2006) A novel DNMT3B subfamily, DeltaDNMT3B, is the predominant form of DNMT3B in non-small cell lung cancer. Int. J. Oncol., 29, 201-207.
16. Wang, J., Walsh, G., Liu, D.D., Lee, J.J. and Mao, L. (2006) Expression of {Delta}DNMT3B variants and its association with promoter methylation of p16 and RASSF1A in primary non-small cell lung cancer. Cancer Res., 66, 8361-8366.
17. Kondo, Y., Shen, L., Yan, P.S., Huang, T.H. and Issa, J.P. (2004) Chromatin immunoprecipitation microarrays for identification of genes silenced by histone H3 lysine 9 methylation. Proc. Natl Acad. Sci. USA, 101, 7398-7403.
18. Ohm, J.E., McGarvey, K.M., Yu, X., Cheng, L., Schuebel, K.E., Cope, L., Mohammad, H.P., Chen, W., Daniel, V.C., Yu, W. et al. (2007) A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing. Nat. Genet., 39, 237-242.
19. Widschwendter, M., Fiegl, H., Egle, D., Mueller-Holzner, E., Spizzo, G., Marth, C., Weisenberger, D.J., Campan, M., Young, J., Jacobs, I. et al. (2007) Epigenetic stem cell signature in cancer. Nat. Genet., 39, 157-158.
20. Schlesinger, Y., Straussman, R., Keshet, I., Farkash, S., Hecht, M., Zimmerman, J., Eden, E., Yakhini, Z., Ben-Shushan, E., Reubinoff, B.E. et al. (2007) Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat. Genet., 39, 232-236.
21. Vire, E., Brenner, C., Deplus, R., Blanchon, L., Fraga, M., Didelot, C., Morey, L., Van Eynde, A., Bernard, D., Vanderwinden, J.M. et al. (2006) The Polycomb group protein EZH2 directly controls DNA methylation. Nature, 439, 871-874.
22. Fouse, S.D., Shen, Y., Pellegrini, M., Cole, S., Meissner, A., Van Neste, L., Jaenisch, R. and Fan, G. (2008) Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation. Cell Stem Cell, 2, 160-169.
23. Bernstein, B.E., Mikkelsen, T.S., Xie, X., Kamal, M., Huebert, D.J., Cuff, J., Fry, B., Meissner, A., Wernig, M., Plath, K. et al. (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell, 125, 315-326.
24. Chen, Z.X., Mann, J.R., Hsieh, C.L., Riggs, A.D. and Chedin, F. (2005) Physical and functional interactions between the human DNMT3L protein and members of the de novo methyltransferase family. J. Cell. Biochem., 95, 902-917.
25. Laird, P.W., Zijderveld, A., Linders, K., Rudnicki, M.A., Jaenisch, R. and Berns, A. (1991) Simplified mammalian DNA isolation procedure. Nucleic Acids Res., 19, 4293.
26. Choi, S.H., Byun, H.M., Kwan, J.M., Issa, J.P. and Yang, A.S. (2007) Hydroxycarbamide in combination with azacitidine or decitabine is antagonistic on DNA methylation inhibition. Br. J. Haematol., 138, 616-623.
27. Choi, S.H., Worswick, S., Byun, H.M., Shear, T., Soussa, J.C., Wolff, E.M., Douer, D., Garcia-Manero, G., Liang, G. and Yang, A.S. (2009) Changes in DNA methylation of tandem DNA repeats are different from interspersed repeats in cancer. Int. J. Cancer, 125, 723-729.
28. Uhlmann, K., Brinckmann, A., Toliat, M.R., Ritter, H. and Nurnberg, P. (2002) Evaluation of a potential epigenetic biomarker by quantitative methyl-single nucleotide polymorphism analysis. Electrophoresis, 23, 4072-4079.
29. Weisenberger, D.J., Campan, M., Long, T.I., Kim, M., Woods, C., Fiala, E., Ehrlich, M. and Laird, P.W. (2005) Analysis of repetitive element DNA methylation by MethyLight. Nucleic Acids Res., 33, 6823-6836.
30. Bibikova, M., Lin, Z., Zhou, L., Chudin, E., Garcia, E.W., Wu, B., Doucet, D., Thomas, N.J., Wang, Y., Vollmer, E. et al. (2006) High-throughput DNA methylation profiling using universal bead arrays. Genome Res., 16, 383-393.
31. Houshdaran, S., Cortessis, V.K., Siegmund, K., Yang, A., Laird, P.W. and Sokol, R.Z. (2007) Widespread epigenetic abnormalities suggest a broad DNA methylation erasure defect in abnormal human sperm. PLoS ONE, 2, e1289.
32. Huebert, D.J., Kamal, M., O'Donovan, A. and Bernstein, B.E. (2006) Genome-wide analysis of histone modifications by ChIP-on-chip. Methods, 40, 365-369.
33. Aoki, A., Suetake, I., Miyagawa, J., Fujio, T., Chijiwa, T., Sasaki, H. and Tajima, S. (2001) Enzymatic properties of de novo-type mouse DNA (cytosine-5) methyltransferases. Nucleic Acids Res., 29, 3506-3512.
34. Chen, T., Tsujimoto, N. and Li, E. (2004) The PWWP domain of Dnmt3a and Dnmt3b is required for directing DNA methylation to the major satellite repeats at pericentric heterochromatin. Mol. Cell. Biol., 24, 9048-9058.
35. Kondo, Y., Shen, L., Cheng, A.S., Ahmed, S., Boumber, Y., Charo, C., Yamochi, T., Urano, T., Furukawa, K., Kwabi-Addo, B. et al. (2008) Gene silencing in cancer by histone H3 lysine 27 trimethylation independent of promoter DNA methylation. Nat. Genet., 40, 741-750.
36. Meissner, A., Mikkelsen, T.S., Gu, H., Wernig, M., Hanna, J., Sivachenko, A., Zhang, X., Bernstein, B.E., Nusbaum, C., Jaffe, D.B. et al. (2008) Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature, 454, 766-770.
37. Okitsu, C.Y. and Hsieh, C.L. (2007) DNA methylation dictates histone H3K4 methylation. Mol. Cell. Biol., 27, 2746-2757.
38. Robertson, K.D., Uzvolgyi, E., Liang, G., Talmadge, C., Sumegi, J., Gonzales, F.A. and Jones, P.A. (1999) The human DNA methyltransferases (DNMTs) 1, 3a and 3b: coordinate mRNA expression in normal tissues and overexpression in tumors. Nucleic Acids Res., 27, 2291-2298.