The non-coding oncogene: A case of missing DNA evidence?

Frontiers in Genetics

Volumn 3, Issue SEP, 2012, Pages

  Shahrouki, Puja ^a   Larsson, Erik ^a  

^a UNIVERSITY OF GOTHENBURG   (Sweden)

Author keywords

Cancer; Lincrna; LncRNA; MicroRNA; Mutation; Non coding RNA; Somatic alteration; T UCR

Indexed keywords

EID: 84876124685     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2012.00170     Document Type: Article

References (81)

1. Arvey, A., Larsson, E., Sander, C., Leslie, C. S., and Marks, D. S. (2010). Target mRNA abundance dilutes microRNA and siRNA activity. Mol. Syst. Biol. 6, 363.
2. Augello, C., Vaira, V., Caruso, L., Destro, A., Maggioni, M., Park, Y. N., Mon-torsi, M., Santambrogio, R., Ron-calli, M., and Bosari, S. (2012). MicroRNA profiling of hepatocar-cinogenesis identifies C19MC cluster as a novel prognostic biomarker in hepatocellular carcinoma. Liver Int. 32, 772-782.
3. Bartel, D. P. (2009). MicroRNAs: target recognition and regulatory functions. Cell 136,215-233.
4. Bejerano, G., Pheasant, M., Makunin, I., Stephen, S., Kent, W. J., Mattick, J. S., and Haussler, D. (2004). Ultraconserved elements in the human genome. Science 304, 1321-1325.
5. Bernard, D., Prasanth, K. V., Tripathi, V., Colasse, S., Nakamura, T., Xuan, Z., Zhang, M. Q., Sedel, F., Jourdren, L., Coulpier, F., Triller, A., Spector, D. L., and Bessis, A. (2010). A long nuclear-retained non-coding RNA regulates synaptogenesis by modu lating gene expression. EMBO J. 29, 3082-3093.
6. Bernstein, E., Kim, S. Y., Carmell, M. A., Murchison, E. P., Alcorn, H., Li, M. Z., Mills, A. A., Elledge, S. J., Anderson, K. V., and Hannon, G. J. (2003). Dicer is essential for mouse development. Nat. Genet. 35, 215-217.
7. Birney, E., Stamatoyannopoulos, J. A., Dutta, A., Guigo, R., Gingeras, T. R., Margulies, E. H., Weng, Z., Snyder, M., Dermitzakis, E. T., Thurman, R. E., Kuehn, M. S., Taylor, C. M., Neph, S., Koch, C. M., Asthana, S., Malhotra, A., Adzhubei, I., Green-baum, J. A., Andrews, R. M., Flicek, P., Boyle, P. J., Cao, H., Carter, N. P., Clelland, G. K., Davis, S., Day, N., Dhami, P., Dillon, S. C., Dorschner, M. O., Fiegler, H., Giresi, P. G., Goldy, J., Hawrylycz, M., Haydock, A., Humbert, R., James, K. D., Johnson, B. E., Johnson, E. M., Frum, T. T., Rosenzweig, E. R., Karnani, N., Lee, K., Lefebvre, G. C., Navas, P. A., Neri, F., Parker, S. C., Sabo, P. J., Sandstrom, R., Shafer, A., Vetrie, D., Weaver, M., Wilcox, S., Yu, M., Collins, E S., Dekker, J., Lieb, J. D., Tullius, T. D., Crawford, G. E., Sun-yaev, S., Noble, W. S., Dunham, I., Denoeud, F., Reymond, A., Kapra-nov, P., Rozowsky, J., Zheng, D., Castelo, R., Frankish, A., Harrow, J., Ghosh, S., Sandelin, A., Hofacker, I. L., Baertsch, R., Keefe, D., Dike, S., Cheng, J., Hirsch, H. A., Sekinger, E. A., Lagarde, J., Abril, J. F., Sha-hab, A., Flamm, C., Fried, C., Hack-ermuller, J., Hertel, J., Lindemeyer, M., Missal, K., Tanzer, A., Washietl, S., Korbel, J., Emanuelsson, O., Ped-ersen, J. S., Holroyd, N., Taylor, R., Swarbreck, D., Matthews, N., Dick-son, M. C., Thomas, D. J., Weirauch, M. T., Gilbert, J., Drenkow, J., Bell, I., Zhao, X., Srinivasan, K. G., Sung, W. K., Ooi, H. S., Chiu, K. P., Fois-sac, S., Alioto, T., Brent, M., Pachter, L., Tress, M. L., Valencia, A., Choo, S. W., Choo, C. Y., Ucla, C., Manzano, C., Wyss, C., Cheung, E., Clark, T. G., Brown, J. B., Ganesh, M., Patel, S., Tammana, H., Chrast, J., Hen-richsen, C. N., Kai, C., Kawai, J., Nagalakshmi, U., Wu, J., Lian, Z., Lian, J., Newburger, P., Zhang, X., Bickel, P., Mattick, J. S., Carninci, P., Hayashizaki, Y., Weissman, S., Hub-bard, T., Myers, R. M., Rogers, J., Stadler, P. F., Lowe, T. M., Wei, C. L., Ruan, Y., Struhl, K., Gerstein, M., Antonarakis, S. E., Fu, Y., Green, E. D., Karaöz, U., Siepel, A., Taylor, J., Liefer, L. A., Wetterstrand, K. A., Good, P. J., Feingold, E. A., Guyer, M. S., Cooper, G. M., Asi-menos, G., Dewey, C. N., Hou, M., Nikolaev, S., Montoya-Burgos, J. I., Löytynoja, A., Whelan, S., Pardi, F., Massingham, T., Huang, H., Zhang, N. R., Holmes, I., Mullikin, J. C., Ureta-Vidal, A., Paten, B., Sering-haus, M., Church, D., Rosenbloom, K., Kent, W J., Stone, E. A., NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute, Batzoglou, S., Goldman, N., Hardison, R. C., Haussler, D., Miller, W., Sidow, A., Trinklein, N. D., Zhang, Z. D., Barrera, L., Stuart, R., King, D. C., Ameur, A., Enroth, S., Bieda, M. C., Kim, J., Bhinge, A. A., Jiang, N., Liu, J., Yao, F., Vega, V. B., Lee, C. W., Ng, P., Shahab, A., Yang, A., Moqtaderi, Z., Zhu, Z., Xu, X., Squazzo, S., Oberley, M. J., Inman, D., Singer, M. A., Richmond, T. A., Munn, K. J., Rada-Iglesias, A., Wallerman, O., Komorowski, J., Fowler, J. C., Couttet, P., Bruce, A. W., Dovey, O. M., Ellis, P. D., Lang-ford, C. F., Nix, D. A., Euskirchen, G., Hartman, S., Urban, A. E., Kraus, P., Van Calcar, S., Heintzman, N., Kim, T. H., Wang, K., Qu, C., Hon, G., Luna, R., Glass, C. K., Rosen-feld, M. G., Aldred, S. F., Cooper, S. J., Halees, A., Lin, J. M., Shulha, H. P., Zhang, X., Xu, M., Haidar, J. N., Yu, Y., Ruan, Y., Iyer, V R., Green, R. D., Wadelius, C., Farn-ham, P. J., Ren, B., Harte, R. A., Hin-richs, A. S., Trumbower, H., Claw-son, H., Hillman-Jackson, J., Zweig, A. S., Smith, K., Thakkapallayil, A., Barber, G., Kuhn, R. M., Karolchik, D., Armengol, L., Bird, C. P., de Bakker, P. I., Kern, A. D., Lopez Bigas, N., Martin, J. D., Stranger, B. E., Woodroffe, A., Davydov, E., Dimas, A., Eyras, E., Hallgrímsdóttir, I. B., Huppert, J., Zody, M. C., Abecasis, G. R., Estivill, X., Bouffard, G. G., Guan, X., Hansen, N. F., Idol, J. R., Maduro, V V, Maskeri, B., Mcdowell, J. C., Park, M., Thomas, P. J., Young,A. C.,Blakesley,R.W.,Muzny, D. M., Sodergren, E., Wheeler, D. A., Worley, K. C., Jiang, H., Weinstock, G. M., Gibbs, R. A., Graves, T., Fulton, R., Mardis, E. R., Wilson, R. K., Clamp, M., Cuff, J., Gnerre, S., Jaffe, D. B., Chang, J. L., Lindblad-Toh, K., Lander, E. S., Koriabine, M., Nefedov, M., Osoegawa, K., Yoshi-naga, Y., Zhu, B., and de Jong, P. J. (2007). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799-816.
8. Boehm, J. S., and Hahn, W. C. (2011). Towards systematic functional characterization of cancer genomes. Nat. Rev. Genet. 12, 487-498.
9. Calin, G. A., Dumitru, C. D., Shimizu, M., Bichi, R., Zupo, S., Noch, E., Aldler, H., Rattan, S., Keating, M., Rai, K., Rassenti, L., Kipps, T., Negrini, M., Bullrich, F., and Croce, C. M. (2002). Frequent deletions and down-regulation of micro RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc. Natl. Acad. Sci. U.S.A. 99, 15524-15529.
10. Calin, G. A., Ferracin, M., Cimmino, A., Di Leva, G., Shimizu, M., Woj-cik, S. E., Iorio, M. V., Visone, R., Sever, N. I., Fabbri, M., Iuliano, R., Palumbo, T., Pichiorri, F., Roldo, C., Garzon, R., Sevignani, C., Rassenti, L., Alder, H., Volinia, S., Liu, C. G., Kipps, T. J., Negrini, M., and Croce, C. M. (2005). A microRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N Engl. J. Med. 353, 1793-1801.
11. Calin, G. A., Liu, C. G., Ferracin, M., Hyslop, T., Spizzo, R., Sevignani, C., Fabbri, M., Cimmino, A., Lee, E. J., Wojcik, S. E., Shimizu, M., Tili, E., Rossi, S., Taccioli, C., Pichiorri, F., Liu, X., Zupo, S., Herlea, V., Gra-mantieri, L., Lanza, G., Alder, H., Rassenti, L., Volinia, S., Schmittgen, T. D., Kipps, T. J., Negrini, M., and Croce, C. M. (2007). Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas. Cancer Cell 12, 215-229.
12. Cancer Genome Atlas Research Network. (2011). Integrated genomic analyses of ovarian carcinoma. Nature 474, 609-615.
13. Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C., Kodzius, R., Shimokawa, K., Bajic, V. B., Brenner, S. E., Bat-alov, S., Forrest, A. R., Zavolan, M., Davis, M. J., Wilming, L. G., Aidinis, V., Allen, J. E., Ambesi-Impiombato, A., Apweiler, R., Aturaliya, R. N., Bailey, T. L., Bansal, M., Baxter, L., Beisel, K. W., Bersano, T., Bono, H., Chalk, A. M., Chiu, K. P., Choud-hary, V., Christoffels, A., Clutterbuck, D R., Crowe, M. L., Dalla, E., Dal-rymple, B. P., De Bono, B., Della Gatta, G., Di Bernardo, D., Down, T., Engstrom, P., Fagiolini, M., Faulkner, G., Fletcher, C. F., Fukushima, T., Furuno, M., Futaki, S., Gariboldi, M., Georgii-Hemming, P., Gingeras, T. R., Gojobori, T., Green, R. E., Gustincich, S., Harbers, M., Hayashi, Y., Hensch, T. K., Hirokawa, N., Hill, D., Huminiecki, L., Iacono, M., Ikeo, K., Iwama, A., Ishikawa, T., Jakt, M., Kanapin, A., Katoh, M., Kawasawa, Y., Kelso, J., Kitamura, H., Kitano, H., Kollias, G., Krishnan, S. P., Kruger, A., Kummerfeld, S. K., Kurochkin, I. V., Lareau, L. E, Lazarevic, D., Lipovich, L., Liu, J., Liuni, S., Mcwilliam, S., Madan Babu, M., Madera, M., Marchionni, L., Matsuda, H., Matsuzawa, S., Miki, H., Mignone, F., Miyake, S., Morris, K., Mottagui-Tabar, S., Mul der, N., Nakano, N., Nakauchi, H., Ng, P., Nilsson, R., Nishiguchi, S., Nishikawa, S., Nori, F., Ohara, O., Okazaki, Y., Orlando, V., Pang, K. C., Pavan, W. J., Pavesi, G., Pesole, G., Petrovsky, N., Piazza, S., Reed, J., Reid, J. F., Ring, B. Z., Ringwald, M., Rost, B., Ruan, Y., Salzberg, S. L., Sandelin, A., Schneider, C., Schön-bach, C., Sekiguchi, K., Semple, C. A., Seno, S., Sessa, L., Sheng, Y., Shibata, Y., Shimada, H., Shimada, K., Silva, D., Sinclair, B., Sperling, S., Stupka, E., Sugiura, K., Sultana, R., Takenaka, Y., Taki, K., Tammoja, K., Tan, S. L., Tang, S., Taylor, M. S., Tegner, J., Teichmann, S. A., Ueda, H. R., van Nimwegen, E., Verardo, R., Wei, C. L., Yagi, K., Yamanishi, H., Zabarovsky, E., Zhu, S., Zimmer, A., Hide, W., Bult, C., Grimmond, S. M., Teasdale, R. D., Liu, E. T., Brusic, V., Quackenbush, J., Wahlestedt, C., Mattick, J. S., Hume, D. A., Kai, C., Sasaki, D., Tomaru, Y., Fukuda, S., Kanamori-Katayama, M., Suzuki, M.,Aoki,J.,Arakawa, T., Iida, J.,Imamura, K., Itoh, M., Kato, T., Kawaji, H., Kawagashira, N., Kawashima, T., Kojima, M., Kondo, S., Konno, H., Nakano, K., Ninomiya, N., Nishio, T., Okada, M., Plessy, C., Shibata, K., Shiraki, T., Suzuki, S., Tagami, M., Waki, K., Watahiki, A., Okamura-Oho, Y., Suzuki, H., Kawai, J., Hayashizaki, Y., FANTOM Consortium, RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group). (2005). The transcriptional landscape of the mammalian genome. Science 309, 1559-1563.
14. Cimmino, A., Calin, G. A., Fabbri, M., Iorio, M. V., Ferracin, M., Shimizu, M., Wojcik, S. E., Aqeilan, R. I., Zupo, S., Dono, M., Rassenti, L., Alder, H., Volinia, S., Liu, C. G., Kipps, T. J., Negrini, M., and Croce, C. M. (2005). miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc. Natl. Acad. Sci. U.S.A. 102, 13944-13949.
15. Costinean, S., Zanesi, N., Pekarsky, Y., Tili, E., Volinia, S., Heerema, N., and Croce, C. M. (2006). Pre-B cell proliferation and lymphoblas-tic leukemia/high-grade lymphoma in E(mu)-miR155 transgenic mice. Proc. Natl. Acad. Sci. U.S.A. 103, 7024-7029.
16. Diederichs, S., and Haber, D. A. (2006). Sequence variations of microRNAs in human cancer: alterations in predicted secondary structure do not affect processing. Cancer Res. 66, 6097-6104.
17. Dong, X. Y., Guo, P., Boyd, J., Sun, X., Li, Q., Zhou, W., and Dong, J. T. (2009). Implication of snoRNAU50 in human breast cancer. J. Genet. Genomics 36,447-454.
18. Dong, X. Y., Rodriguez, C., Guo, P., Sun, X., Talbot, J. T., Zhou, W., Pet-ros, J., Li, Q., Vessella, R. L., Kibel, A. S., Stevens, V. L., Calle, E. E., and Dong, J. T. (2008). SnoRNA U50 is a candidate tumor-suppressor gene at 6q14.3 with a mutation associated with clinically significant prostate cancer. Hum. Mol. Genet. 17,1031-1042.
19. Eis, P. S., Tam, W., Sun, L., Chad-burn, A., Li, Z., Gomez, M. F., Lund, E., and Dahlberg, J. E. (2005). Accumulation of miR-155 and BIC RNA in human B cell lymphomas. Proc. Natl. Acad. Sci. U.S.A. 102, 3627-3632.
20. Futreal, P. A., Coin, L., Marshall, M., Down, T., Hubbard, T., Wooster, R., Rahman, N., and Stratton, M. R. (2004). A census of human cancer genes. Nat. Rev. Cancer 4, 177-183.
21. Gupta, R. A., Shah, N., Wang, K. C., Kim, J., Horlings, H. M., Wong, D. J., Tsai, M. C., Hung, T., Argani, P., Rinn, J. L., Wang, Y., Brzoska, P., Kong, B., Li, R., West, R. B., Van De Vijver, M. J., Sukumar, S., and Chang, H. Y. (2010). Long non-coding RNA HOTAIR repro-grams chromatin state to promote cancer metastasis. Nature 464, 1071-1076.
22. Guttman, M., Amit, I., Garber, M., French, C., Lin, M. F., Feldser, D., Huarte, M., Zuk, O., Carey, B. W., Cassady, J. P., Cabili, M. N., Jaenisch, R., Mikkelsen, T. S., Jacks, T., Haco-hen, N., Bernstein, B. E., Kellis, M., Regev, A., Rinn, J. L., and Lander, E. S. (2009). Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223-227.
23. Guttman, M., Donaghey, J., Carey, B. W., Garber, M., Grenier, J. K., Mun-son, G., Young, G., Lucas, A. B., Ach, R., Bruhn, L., Yang, X., Amit, I., Meissner, A., Regev, A., Rinn, J. L., Root, D. E., and Lander, E. S. (2011). lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477, 295-300.
24. Guttman, M., Garber, M., Levin, J. Z., Donaghey, J., Robinson, J., Adico-nis, X., Fan, L., Koziol, M. J., Gnirke, A., Nusbaum, C., Rinn, J. L., Lander, E. S., and Regev, A. (2010). Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotech-nol. 28, 503-510.
25. Hanahan, D., and Weinberg, R. A. (2011). Hallmarks of cancer: the next generation. Cell 144, 646-674.
26. Harrow, J., Denoeud, F., Frankish, A., Reymond, A., Chen, C. K., Chrast, J., Lagarde, J., Gilbert, J. G., Storey, R., Swarbreck, D., Rossier, C., Ucla, C., Hubbard, T., Antonarakis, S. E., and Guigo, R. (2006). GENCODE: producing a reference annotation for ENCODE. Genome Biol. 7(Suppl. 1), S4 1-9.
27. He, L., Thomson, J. M., Hemann, M. T., Hernando-Monge, E., Mu, D., Goodson, S., Powers, S., Cordon-Cardo, C., Lowe, S. W., Hannon, G. J., and Hammond, S. M. (2005). A microRNA polycistron as a potential human oncogene. Nature 435, 828-833.
28. Heravi-Moussavi, A., Anglesio, M. S., Cheng, S. W., Senz, J., Yang, W., Prentice, L., Fejes, A. P., Chow, C., Tone, A., Kalloger, S. E., Hamel, N., Roth, A., Ha, G., Wan, A. N., Maines-Bandiera, S., Salamanca, C., Pasini, B., Clarke, B. A., Lee, A. E, Lee, C. H., Zhao, C., Young, R. H., Aparicio, S. A., Sorensen, P. H., Woo, M. M., Boyd, N., Jones, S. J., Hirst, M., Marra, M. A., Gilks, B., Shah, S. P., Foulkes, W. D., Morin, G. B., and Huntsman, D. G. (2012). Recurrent somatic DICER1 mutations in nonepithelial ovarian cancers. N. Engl. J. Med. 366, 234-242.
29. Huarte, M., Guttman, M., Feldser, D., Garber, M., Koziol, M. J., Kenzelmann-Broz, D., Khalil, A. M., Zuk, O., Amit, I., Rabani,M., Attar di, L. D., Regev, A., Lander, E. S., Jacks, T., and Rinn, J. L. (2010). A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142, 409-419.
30. International Human Genome Sequencing Consortium. (2004). Finishing the euchromatic sequence of the human genome. Nature 431, 931-945.
31. Jeggari, A., Marks, D. S., and Lars-son, E. (2012). miRcode: a map of putative microRNA target sites in the long non-coding transcriptome. Bioinformatics 28, 2062-2063.
32. Ji, P., Diederichs, S., Wang, W., Boing, S., Metzger, R., Schneider, P. M., Tidow, N., Brandt, B., Buerger, H., Bulk, E., Thomas, M., Berdel, W. E., Serve, H., and Muller-Tidow, C. (2003). MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene 22, 8031-8041.
33. Kapranov, P., Cawley, S. E., Drenkow, J., Bekiranov, S., Strausberg, R. L., Fodor, S. P., and Gingeras, T. R. (2002). Large-scale transcriptional activity in chromosomes 21 and 22. Science 296, 916-919.
34. Katayama, S., Tomaru, Y., Kasukawa, T., Waki, K., Nakanishi, M., Nakamura, M., Nishida, H., Yap, C. C., Suzuki, M., Kawai, J., Suzuki, H., Carninci, P., Hayashizaki, Y., Wells, C., Frith, M., Ravasi, T., Pang, K. C., Halli-nan, J., Mattick, J., Hume, D. A., Lipovich, L., Batalov, S., Engstrom, P. G., Mizuno, Y., Faghihi, M. A., Sandelin, A., Chalk,A. M., Mottagui-Tabar, S., Liang, Z., Lenhard, B., and Wahlestedt, C. (2005). Anti-sense transcription in the mammalian transcriptome. Science 309, 1564-1566.
35. Kim, M. S., Oh, J. E., Kim, Y R., Park, S. W., Kang, M. R., Kim, S. S., Ahn, C. H., Yoo, N. J., and Lee, S. H. (2010). Somatic mutations and losses of expression of microRNA regulation-related genes AGO2 and TNRC6A in gastric and colorectal cancers. J. Pathol. 221, 139-146.
36. Kino, T., Hurt, D. E., Ichijo, T., Nader, N.,and Chrousos,G. P. (2010). Non-coding RNA gas5 is a growth arrest-and starvation-associated repressor of the glucocorticoid receptor. Sci. Signal. 3, ra8.
37. Klein, U., Lia, M., Crespo, M., Siegel, R., Shen, Q., Mo, T., Ambesi-Impiombato, A., Califano, A., Migli-azza, A., Bhagat, G., and Dalla-Favera, R. (2010). The DLEU2/miR-15a/16-1 cluster controls B cell proliferation and its deletion leads to chronic lymphocytic leukemia. Cancer Cell 17,28-40.
38. Knudson, A. G. (1993). Antioncogenes and human cancer. Proc. Natl. Acad. Sci. U.S.A. 90, 10914-10921.
39. Li, R., Wang, H., Bekele, B. N., Yin, Z., Caraway, N. P., Katz, R. L., Stass, S. A., and Jiang, E (2006). Identification of putative oncogenes in lung adeno-carcinoma by a comprehensive functional genomic approach. Oncogene 25,2628-2635.
40. Liao, J., Yu, L., Mei, Y., Guarnera, M., Shen, J., Li, R., Liu, Z., and Jiang, E (2010). Small nucleolar RNA signatures as biomarkers for non-small-cell lung cancer. Mol. Cancer 9, 198.
41. Lionetti, M., Agnelli, L., Mosca, L., Fab-ris, S., Andronache, A., Todoerti, K., Ronchetti, D., Deliliers, G. L., and Neri, A. (2009). Integrative high-resolution microarray analysis of human myeloma cell lines reveals deregulated miRNA expression associated with allelic imbalances and gene expression profiles. Genes Chromosomes Cancer 48, 521-531.
42. Liu, A. M., Zhang, C., Burchard, J., Fan, S. T., Wong, K. F., Dai, H., Poon, R. T., and Luk, J. M. (2011). Global regulation on microRNA in hepatitis B virus-associated hepatocellular carcinoma. OMICS 15, 187-191.
43. Lu, J., Getz, G., Miska, E. A., Alvarez-Saavedra, E., Lamb, J., Peck, D., Sweet-Cordero, A., Ebert, B. L., Mak, R. H., Ferrando, A. A., Downing, J. R., Jacks, T., Horvitz, H. R., and Golub, T. R. (2005). MicroRNA expression profiles classify human cancers. Nature 435, 834-838.
44. Lujambio, A., and Lowe, S. W (2012). The microcosmos of cancer. Nature 482, 347-355.
45. Mavrakis, K. J., Wolfe, A. L., Oricchio, E., Palomero, T., De Keersmaecker, K., Mcjunkin, K., Zuber, J., James, T., Khan, A. A., Leslie, C. S., Parker, J. S., Paddison, P. J., Tam, W., Ferrando, A., and Wendel, H. G. (2010). Genome-wide RNA-mediated interference screen identifies miR-19 targets in Notch-induced T-cell acute lymphoblastic leukaemia. Nat. Cell Biol. 12, 372-379.
46. Mei, Y P., Liao, J. P., Shen, J., Yu, L., Liu, B. L., Liu, L., Li, R. Y., Ji, L., Dorsey, S. G., Jiang, Z. R., Katz, R. L., Wang, J. Y., and Jiang, E (2012). Small nucleolar RNA 42 acts as an oncogene in lung tumorigenesis. Oncogene 31, 2794-2804.
47. Mestdagh, P., Fredlund, E., Pattyn, F., Rihani, A., Van Maerken, T., Ver-meulen, J., Kumps, C., Menten, B., De Preter, K., Schramm, A., Schulte, J., Noguera, R., Schleiermacher, G., Janoueix-Lerosey, I., Laureys, G., Powel, R., Nittner, D., Marine, J. C., Ringner, M., Speleman, F., and Vandesompele, J. (2010). An integrative genomics screen uncovers ncRNA T-UCR functions in neu-roblastoma tumours. Oncogene 29, 3583-3592.
48. Meyerson, M., Gabriel, S., and Getz, G. (2010). Advances in understanding cancer genomes through second-generation sequencing. Nat. Rev. Genet. 11,685-696.
49. Nakamura, Y., Takahashi, N., Kakegawa, E., Yoshida, K., Ito, Y., Kayano, H., Niitsu, N., Jinnai, I., and Bessho, M. (2008). The GAS5 (growth arrest-specific transcript 5) gene fuses to BCL6 as a result of t(1;3)(q25;q27) in a patient with B-cell lym-phoma. Cancer Genet. Cytogenet. 182,144-149.
50. Nowell, P. C. (1976). The clonal evolution of tumor cell populations. Science 194,23-28.
51. Nowell, P. C., and Hungerford, D. A. (1961). Chromosome studies in human leukemia. II. Chronic granu-locytic leukemia.J. Natl. Cancer Inst. 27, 1013-1035.
52. Olive, V., Bennett, M. J., Walker, J. C., Ma, C., Jiang, I., Cordon-Cardo, C., Li, Q. J., Lowe, S. W., Hannon, G. J., and He, L. (2009). miR-19 is a key oncogenic component of mir-17-92. Genes Dev. 23, 2839-2849.
53. Ota, A., Tagawa, H., Karnan, S., Tsuzuki, S., Karpas, A., Kira, S., Yoshida, Y., and Seto, M. (2004). Identification and characterization of a novel gene, C13orf25, as a target for 13q31-q32 amplification in malignant lym-phoma. Cancer Res. 64, 3087-3095.
54. Ouillette, P., Collins, R., Shakhan, S., Li, J., Li, C., Shedden, K., and Malek, S. N. (2011). The prognostic significance of various 13q14 deletions in chronic lymphocytic leukemia. Clin. Cancer Res. 17,6778-6790.
55. Pasic, I., Shlien, A., Durbin, A. D., Stavropoulos, D. J., Baskin, B., Ray, P. N., Novokmet, A., and Malkin, D. (2010). Recurrent focal copy-number changes and loss of het-erozygosity implicate two noncod-ing RNAs and one tumor suppressor gene at chromosome 3q13.31 in osteosarcoma. Cancer Res. 70, 160-171.
56. Perez, D. S., Hoage, T. R., Pritchett, J. R., Ducharme-Smith, A. L., Halling, M. L., Ganapathiraju, S. C., Streng, P. S., and Smith, D. I. (2008). Long, abundantly expressed non-coding transcripts are altered in cancer. Hum. Mol. Genet. 17, 642-655.
57. Plath, K., Fang, J., Mlynarczyk-Evans, S. K., Cao, R., Worringer, K. A., Wang, H., De La Cruz, C. C., Otte, A. P., Panning, B., and Zhang, Y. (2003). Role of histone H3 lysine 27 methy-lation in X inactivation. Science 300, 131-135.
58. Pleasance, E. D., Cheetham, R. K., Stephens, P. J., Mcbride, D. J., Humphray, S. J., Greenman, C. D., Varela, I., Lin, M. L., Ordonez, G. R., Bignell, G. R., Ye, K., Alipaz, J., Bauer, M. J., Beare, D., Butler, A., Carter, R. J., Chen, L., Cox, A. J., Edkins, S., Kokko-Gonzales, P. I., Gormley, N. A., Grocock, R. J., Haudenschild, C. D., Hims, M. M., James, T., Jia, M., Kingsbury, Z., Leroy, C., Marshall, J., Menzies, A., Mudie, L. J., Ning, Z., Royce, T., Schulz-Trieglaff, O. B., Spiridou, A., Stebbings, L. A., Sza-jkowski, L., Teague, J., Williamson, D., Chin, L., Ross, M. T., Campbell, P. J., Bentley, D. R., Futreal, P. A., and Stratton, M. R. (2010). A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463,191-196.
59. Poliseno, L., Salmena, L., Zhang, J., Carver, B., Haveman, W. J., and Pandolfi, P. P. (2010). A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465, 1033-1038.
60. Ponjavic, J., Ponting, C. P., and Lunter, G. (2007). Functionality or tran-scriptional noise? Evidence for selection within long noncoding RNAs. Genome Res. 17,556-565.
61. Prensner, J. R., and Chinnaiyan, A. M. (2011). The emergence of lncRNAs in cancer biology. Cancer Discov. 1, 391-407.
62. Prensner, J. R., Iyer, M. K., Balbin, O. A., Dhanasekaran, S. M., Cao, Q., Brenner, J. C., Laxman, B., Asan-gani, I. A., Grasso, C. S., Komin-sky, H. D., Cao, X., Jing, X., Wang, X., Siddiqui, J., Wei, J. T., Robinson, D., Iyer, H. K., Palanisamy, N., Maher, C. A., and Chinnaiyan, A. M. (2011). Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lin-cRNA implicated in disease progression. Nat. Biotechnol. 29, 742-749.
63. Rao, P. H., Houldsworth, J., Dyomina, K., Parsa, N. Z., Cigudosa, J. C., Louie, D. C., Popplewell, L., Offit, K., Jhanwar, S. C., and Chaganti, R. S. (1998). Chromosomal and gene amplification in diffuse large B-cell lymphoma. Blood 92, 234-240.
64. Reddy, E. P., Reynolds, R. K., Santos, E., and Barbacid, M. (1982). A point mutation is responsible for the acquisition of transforming properties by the T24 human bladder carcinoma oncogene. Nature 300, 149-152.
65. Rinn, J. L., Kertesz, M., Wang, J. K., Squazzo, S. L., Xu, X., Brugmann, S. A., Goodnough, L. H., Helms, J. A., Farnham, P. J., Segal, E., and Chang, H. Y (2007). Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129, 1311-1323.
66. Rosenfeld, N., Aharonov, R., Meiri, E., Rosenwald, S., Spector, Y., Zepe-niuk, M., Benjamin, H., Shabes, N., Tabak, S., Levy, A., Lebanony, D., Goren, Y., Silberschein, E., Targan, N., Ben-Ari, A., Gilad, S., Sion-Vardy, N., Tobar, A., Feinmesser, M., Kharenko, O., Nativ, O., Nass, D., Perelman, M., Yosepovich, A., Shal-mon, B., Polak-Charcon, S., Frid-man, E., Avniel, A., Bentwich, I., Bentwich, Z., Cohen, D., Chajut, A., and Barshack, I. (2008). MicroR-NAs accurately identify cancer tissue origin. Nat. Biotechnol. 26, 462-469.
67. Ryland, G. L., Bearfoot, J. L., Doyle, M. A., Boyle, S. E., Choong, D. Y., Rowley, S. M., Tothill, R. W., Gorringe, K. L., and Campbell, I. G. (2012). MicroRNA genes and their target 3'-untranslated regions are infrequently somaticallymutatedin ovarian cancers. PLoS ONE 7, e35805. doi:10.1371/journal.pone.0035805
68. Sandelin, A., Bailey, P., Bruce, S., Engstrom, P. G., Klos, J. M., Wasser-man, W. W., Ericson, J., and Lenhard, B. (2004). Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. BMC Genomics 5,99. doi:10.1186/1471-2164-5-99
69. Saunders, M. A., and Lim, L. P. (2009). (micro)Genomic medicine: microR-NAs as therapeutics and biomarkers. RNA Biol. 6, 324-328.
70. Shao, C., Yu, Y., Yu, L., Pei, Y., Feng, Q., Chu, F., Fang, Z., and Zhou, Y (2012). Amplification and up-regulation of microRNA-30b in oral squamous cell cancers. Arch. Oral Biol. 57, 1012-1017.
71. Sumazin, P., Yang, X., Chiu, H. S., Chung, W J., Iyer, A., Llobet-Navas, D., Rajbhandari, P., Bansal, M., Guarnieri, P., Silva, J., and Califano, A. (2011). An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell 147,370-381.
72. Tabin, C. J., Bradley, S. M., Bargmann, C. I., Weinberg, R. A., Papageorge, A. G., Scolnick, E. M., Dhar, R., Lowy, D. R., and Chang, E. H. (1982). Mechanism of activation of a human oncogene. Nature 300, 143-149.
73. Ulitsky, I., Shkumatava, A., Jan, C. H., Sive, H., and Bartel, D. P. (2011). Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell 147, 1537-1550.
74. Volinia, S., Calin, G. A., Liu, C. G., Ambs, S., Cimmino, A., Petrocca, F., Visone, R., Iorio, M., Roldo, C., Fer-racin, M., Prueitt, R. L., Yanaihara, N., Lanza, G., Scarpa, A., Vecchione, A., Negrini, M., Harris, C. C., and Croce, C. M. (2006). A microRNA expression signature of human solid tumors defines cancer gene targets. Proc. Natl. Acad. Sci. U.S.A. 103, 2257-2261.
75. Von Hansemann, D. (1890). Ueber asymmetrische Zelltheilung in Epithelhresbsen und deren biologische bedeutung. Vir-chows Arch. A Pathol. Anat. 119, 299-326.
76. Weinberg, R. A. (1982). Fewer and fewer oncogenes. Cell 30, 3-4.
77. Williams, G. T., and Farzaneh, F. (2012). Are snoRNAs and snoRNA host genes new players in cancer? Nat. Rev. Cancer 12, 84-88.
78. Wojcik, S. E., Rossi, S., Shimizu, M., Nicoloso, M. S., Cimmino, A., Alder, H., Herlea, V., Rassenti, L. Z., Rai, K. R., Kipps, T. J., Keating, M. J., Croce, C. M., and Calin, G. A. (2010). Non-codingRNA sequence variations in human chronic lym-phocytic leukemia and colorectal cancer. Carcinogenesis 31,208-215.
79. Xu, C., Yang, M., Tian, J., Wang, X., and Li, Z. (2011). MALAT-1: a long non-coding RNA and its important 3' end functional motif in colorectal cancer metastasis. Int. J. Oncol. 39, 169-175.
80. Ying, L., Chen, Q., Wang, Y., Zhou, Z., Huang, Y., and Qiu, F. (2012). Upregulated MALAT-1 contributes to bladder cancer cell migration by inducing epithelial-to-mesenchymal transition. Mol. Biosyst. 8, 2289-2294.
81. Zhang, L., Huang, J., Yang, N., Greshock, J., Megraw, M. S., Giannakakis, A., Liang, S., Naylor, T. L., Barchetti, A., Ward, M. R., Yao, G., Medina, A., O'brien-Jenkins, A., Katsaros, D., Hatzigeorgiou, A., Gimotty, P. A., Weber, B. L., and Coukos, G. (2006). microRNAs exhibit high frequency genomic alterations in human cancer. Proc. Natl. Acad. Sci. U.S.A. 103, 9136-9141.