Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs

Nucleic Acids Research

Volumn 40, Issue 14, 2012, Pages 6391-6400

  Moran, Victoria A ^a   Perera, Ranjan J ^d   Khalil, Ahmad M ^a,b,c  

^a Center for RNA Molecular Biology   (United States)

^b Department of Genetics and Genome Sciences ^*  (United States)

^c CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d BURNHAM INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA METHYLTRANSFERASE; LONG UNTRANSLATED RNA; MEMBRANE PROTEIN; METASTASIS ASSOCIATED LUNG ADENOCARCINOMA TRANSCRIPT 1; NUCLEAR ENRICHED AUTOSOMAL TRANSCRIPT 1; POLYCOMB GROUP PROTEIN; RIBONUCLEOPROTEIN; RNA POLYMERASE; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

CELL DIFFERENTIATION; CHROMATIN CONDENSATION; CHROMATIN IMMUNOPRECIPITATION; CHROMOSOME INACTIVATION; CPG ISLAND; DNA BINDING; DNA METHYLATION; ENZYME SPECIFICITY; EPIGENETICS; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE LOCUS; GENE SILENCING; GENETIC TRANSCRIPTION; GENOME IMPRINTING; HUMAN; INTRON; MOLECULAR DYNAMICS; NONHUMAN; OPEN READING FRAME; POLYADENYLATION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; PROTEIN PHOSPHORYLATION; REVIEW; RNA ANALYSIS; RNA STRUCTURE; UBIQUITINATION; X CHROMOSOME;

ANIMALS; DISEASE; GENE EXPRESSION REGULATION; HUMANS; MAMMALS; RNA, UNTRANSLATED;

EID: 84864927713     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks296     Document Type: Review

References (103)

1. Cabili, M.N., Trapnell, C., Goff, L., Koziol, M., Tazon-Vega, B., Regev, A. and Rinn, J.L. (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev., 25, 1915-1927.
2. Orom, U.A., Derrien, T., Beringer, M., Gumireddy, K., Gardini, A., Bussotti, G., Lai, F., Zytnicki, M., Notredame, C., Huang, Q. et al. (2010) Long noncoding RNAs with enhancer-like function in human cells. Cell, 143, 46-58.
3. Ponting, C.P., Oliver, P.L. and Reik, W. (2009) Evolution and functions of long noncoding RNAs. Cell, 136, 629-641.
4. Khalil, A.M., Guttman, M., Huarte, M., Garber, M., Raj, A., Rivea Morales, D., Thomas, K., Presser, A., Bernstein, B.E., van Oudenaarden, A. et al. (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl Acad. Sci. USA, 106, 11667-11672.
5. Guttman, M., Amit, I., Garber, M., French, C., Lin, M.F., Feldser, D., Huarte, M., Zuk, O., Carey, B.W., Cassady, J.P. et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 458, 223-227.
6. Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M.C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C. et al. (2005) The transcriptional landscape of the mammalian genome. Science, 309, 1559-1563.
7. Mercer, T.R., Dinger, M.E. and Mattick, J.S. (2009) Long non-coding RNAs: insights into functions. Nat. Rev. Genet., 10, 155-159.
8. Brown, C.J., Hendrich, B.D., Rupert, J.L., Lafreniere, R.G., Xing, Y., Lawrence, J. and Willard, H.F. (1992) The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell, 71, 527-542.
9. Brockdorff, N., Ashworth, A., Kay, G.F., McCabe, V.M., Norris, D.P., Cooper, P.J., Swift, S. and Rastan, S. (1992) The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus. Cell, 71, 515-526.
10. Brown, C.J., Ballabio, A., Rupert, J.L., Lafreniere, R.G., Grompe, M., Tonlorenzi, R. and Willard, H.F. (1991) A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome. Nature, 349, 38-44. (Pubitemid 21912005)
11. Wang, K.C. and Chang, H.Y. (2011) Molecular mechanisms of long noncoding RNAs. Mol. Cell, 43, 904-914.
12. Nagano, T. and Fraser, P. (2011) No-nonsense functions for long noncoding RNAs. Cell, 145, 178-181.
13. Clark, M.B. and Mattick, J.S. (2011) Long noncoding RNAs in cell biology. Semin. Cell Dev. Biol., 22, 366-376.
14. Mattick, J.S., Amaral, P.P., Dinger, M.E., Mercer, T.R. and Mehler, M.F. (2009) RNA regulation of epigenetic processes. Bioessays, 31, 51-59.
15. Wapinski, O. and Chang, H.Y. (2011) Long noncoding RNAs and human disease. Trends Cell Biol., 21, 354-361.
16. Qureshi, I.A., Mattick, J.S. and Mehler, M.F. (2010) Long non-coding RNAs in nervous system function and disease. Brain Res., 1338, 20-35.
17. Geisler, S., Lojek, L., Khalil, A.M., Baker, K.E. and Coller, J. (2012) Decapping of long noncoding RNAs regulates inducible genes. Mol. Cell, 45, 279-291.
18. Pauli, A., Valen, E., Lin, M.F., Garber, M., Vastenhouw, N.L., Levin, J.Z., Fan, L., Sandelin, A., Rinn, J.L., Regev, A. et al. (2012) Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res, 22, 577-591.
19. Lee, J.T., Davidow, L.S. and Warshawsky, D. (1999) Tsix, a gene antisense to Xist at the X-inactivation centre. Nat. Genet., 21, 400-404. (Pubitemid 29159577)
20. Brown, C.J., Lafreniere, R.G., Powers, V.E., Sebastio, G., Ballabio, A., Pettigrew, A.L., Ledbetter, D.H., Levy, E., Craig, I.W. and Willard, H.F. (1991) Localization of the X inactivation centre on the human X chromosome in Xq13. Nature, 349, 82-84. (Pubitemid 21912021)
21. Brannan, C.I., Dees, E.C., Ingram, R.S. and Tilghman, S.M. (1990) The product of the H19 gene may function as an RNA. Mol. Cell. Biol., 10, 28-36.
22. Okazaki, Y., Furuno, M., Kasukawa, T., Adachi, J., Bono, H., Kondo, S., Nikaido, I., Osato, N., Saito, R., Suzuki, H. et al. (2002) Analysis of the mouse transcriptome based on functional annotation of 60, 770 full-length cDNAs. Nature, 420, 563-573. (Pubitemid 35477049)
23. He, Y., Vogelstein, B., Velculescu, V.E., Papadopoulos, N. and Kinzler, K.W. (2008) The antisense transcriptomes of human cells. Science, 322, 1855-1857.
24. Katayama, S., Tomaru, Y., Kasukawa, T., Waki, K., Nakanishi, M., Nakamura, M., Nishida, H., Yap, C.C., Suzuki, M., Kawai, J. et al. (2005) Antisense transcription in the mammalian transcriptome. Science, 309, 1564-1566.
25. Werner, A., Carlile, M. and Swan, D. (2009) What do natural antisense transcripts regulate? RNA Biol., 6, 43-48.
26. Kampa, D., Cheng, J., Kapranov, P., Yamanaka, M., Brubaker, S., Cawley, S., Drenkow, J., Piccolboni, A., Bekiranov, S., Helt, G. et al. (2004) Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res., 14, 331-342. (Pubitemid 38380391)
27. Rinn, J.L., Euskirchen, G., Bertone, P., Martone, R., Luscombe, N.M., Hartman, S., Harrison, P.M., Nelson, F.K., Miller, P., Gerstein, M. et al. (2003) The transcriptional activity of human Chromosome 22. Genes Dev., 17, 529-540. (Pubitemid 36258766)
28. Mikkelsen, T.S., Ku, M., Jaffe, D.B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.K., Koche, R.P. et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature, 448, 553-560. (Pubitemid 47206934)
29. Barski, A., Cuddapah, S., Cui, K., Roh, T.Y., Schones, D.E., Wang, Z., Wei, G., Chepelev, I. and Zhao, K. (2007) High-resolution profiling of histone methylations in the human genome. Cell, 129, 823-837. (Pubitemid 46802390)
30. Guttman, M., Garber, M., Levin, J.Z., Donaghey, J., Robinson, J., Adiconis, X., Fan, L., Koziol, M.J., Gnirke, A., Nusbaum, C. et al. (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol., 28, 503-510.
31. Schorderet, P. and Duboule, D. (2011) Structural and functional differences in the long non-coding RNA hotair in mouse and human. PLoS Genet., 7, e1002071.
32. Austin, C.P., Battey, J.F., Bradley, A., Bucan, M., Capecchi, M., Collins, F.S., Dove, W.F., Duyk, G., Dymecki, S., Eppig, J.T. et al. (2004) The knockout mouse project. Nat. Genet., 36, 921-924. (Pubitemid 351319639)
33. Amaral, P.P., Dinger, M.E., Mercer, T.R. and Mattick, J.S. (2008) The eukaryotic genome as an RNA machine. Science, 319, 1787-1789. (Pubitemid 351451554)
34. Guttman, M., Donaghey, J., Carey, B.W., Garber, M., Grenier, J.K., Munson, G., Young, G., Lucas, A.B., Ach, R., Bruhn, L. et al. (2011) lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature, 477, 295-300.
35. Loewer, S., Cabili, M.N., Guttman, M., Loh, Y.H., Thomas, K., Park, I.H., Garber, M., Curran, M., Onder, T., Agarwal, S. et al. (2010) Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nat. Genet., 42, 1113-1117.
36. Huarte, M., Guttman, M., Feldser, D., Garber, M., Koziol, M.J., Kenzelmann-Broz, D., Khalil, A.M., Zuk, O., Amit, I., Rabani, M. et al. (2010) A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell, 142, 409-419.
37. Pontier, D.B. and Gribnau, J. (2011) Xist regulation and function explored. Hum. Genet., 130, 223-236.
38. Augui, S., Nora, E.P. and Heard, E. (2011) Regulation of X-chromosome inactivation by the X-inactivation centre. Nat. Rev. Genet., 12, 429-442.
39. Zhao, J., Sun, B.K., Erwin, J.A., Song, J.J. and Lee, J.T. (2008) Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science, 322, 750-756.
40. Carrel, L. and Willard, H.F. (2005) X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature, 434, 400-404. (Pubitemid 40469185)
41. Khalil, A.M. and Driscoll, D.J. (2007) Trimethylation of histone H3 lysine 4 is an epigenetic mark at regions escaping mammalian X inactivation. Epigenetics, 2, 114-118. (Pubitemid 351682005)
42. Tian, D., Sun, S. and Lee, J.T. (2010) The long noncoding RNA, Jpx, is a molecular switch for X chromosome inactivation. Cell, 143, 390-403.
43. Barr, M.L. and Bertram, E.G. (1949) A morphological distinction between neurones of the male and female, and the behaviour of the nucleolar satellite during accelerated nucleoprotein synthesis. Nature, 163, 676.
44. Panning, B. (2004) X inactivation in mouse ES cells: histone modifications and FISH. Methods Enzymol., 376, 419-428. (Pubitemid 38200195)
45. Heard, E., Rougeulle, C., Arnaud, D., Avner, P., Allis, C.D. and Spector, D.L. (2001) Methylation of histone H3 at Lys-9 is an early mark on the X chromosome during X inactivation. Cell, 107, 727-738. (Pubitemid 34033666)
46. Reik, W. and Murrell, A. (2000) Genomic imprinting. Silence across the border. Nature, 405, 408-409. (Pubitemid 30367400)
47. Li, Y. and Sasaki, H. (2011) Genomic imprinting in mammals: its life cycle, molecular mechanisms and reprogramming. Cell Res., 21, 466-473.
48. Mohammad, F., Mondal, T. and Kanduri, C. (2009) Epigenetics of imprinted long noncoding RNAs. Epigenetics, 4, 277-286.
49. Nagano, T., Mitchell, J.A., Sanz, L.A., Pauler, F.M., Ferguson-Smith, A.C., Feil, R. and Fraser, P. (2008) The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science, 322, 1717-1720.
50. Pandey, R.R., Mondal, T., Mohammad, F., Enroth, S., Redrup, L., Komorowski, J., Nagano, T., Mancini-Dinardo, D. and Kanduri, C. (2008) Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol. Cell, 32, 232-246.
51. Mohammad, F., Mondal, T., Guseva, N., Pandey, G.K. and Kanduri, C. (2010) Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1. Development, 137, 2493-2499.
52. 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. et al. (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell, 129, 1311-1323. (Pubitemid 46962090)
53. 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. et al. (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature, 464, 1071-1076.
54. Tsai, M.C., Manor, O., Wan, Y., Mosammaparast, N., Wang, J.K., Lan, F., Shi, Y., Segal, E. and Chang, H.Y. (2010) Long noncoding RNA as modular scaffold of histone modification complexes. Science, 329, 689-693.
55. Hung, T., Wang, Y., Lin, M.F., Koegel, A.K., Kotake, Y., Grant, G.D., Horlings, H.M., Shah, N., Umbricht, C., Wang, P. et al. (2011) Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat. Genet., 43, 621-629.
56. Feng, J., Bi, C., Clark, B.S., Mady, R., Shah, P. and Kohtz, J.D. (2006) The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes Dev., 20, 1470-1484. (Pubitemid 43830654)
57. Loh, Y.H., Wu, Q., Chew, J.L., Vega, V.B., Zhang, W., Chen, X., Bourque, G., George, J., Leong, B., Liu, J. et al. (2006) The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat. Genet., 38, 431-440.
58. 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.
59. Sheik Mohamed, J., Gaughwin, P.M., Lim, B., Robson, P. and Lipovich, L. (2010) Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells. RNA, 16, 324-337.
60. Kretz, M., Webster, D.E., Flockhart, R.J., Lee, C.S., Zehnder, A., Lopez-Pajares, V., Qu, K., Zheng, G.X., Chow, J., Kim, G.E. et al. (2012) Suppression of progenitor differentiation requires the long noncoding RNA ANCR. Genes Dev, 26, 338-343.
61. Clemson, C.M., Hutchinson, J.N., Sara, S.A., Ensminger, A.W., Fox, A.H., Chess, A. and Lawrence, J.B. (2009) An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol Cell, 33, 717-726.
62. Chen, L.L. and Carmichael, G.G. (2009) Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Mol. Cell, 35, 467-478.
63. Bond, C.S. and Fox, A.H. (2009) Paraspeckles: nuclear bodies built on long noncoding RNA. J. Cell Biol., 186, 637-644.
64. Prasanth, K.V., Prasanth, S.G., Xuan, Z., Hearn, S., Freier, S.M., Bennett, C.F., Zhang, M.Q. and Spector, D.L. (2005) Regulating gene expression through RNA nuclear retention. Cell, 123, 249-263. (Pubitemid 41457215)
65. Sunwoo, H., Dinger, M.E., Wilusz, J.E., Amaral, P.P., Mattick, J.S. and Spector, D.L. (2009) MEN varepsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res., 19, 347-359.
66. Mao, Y.S., Sunwoo, H., Zhang, B. and Spector, D.L. (2011) Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs. Nat. Cell Biol., 13, 95-101.
67. Shevtsov, S.P. and Dundr, M. (2011) Nucleation of nuclear bodies by RNA. Nat. Cell Biol., 13, 167-173.
68. Tripathi, V., Ellis, J.D., Shen, Z., Song, D.Y., Pan, Q., Watt, A.T., Freier, S.M., Bennett, C.F., Sharma, A., Bubulya, P.A. et al. (2010) The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol. Cell, 39, 925-938.
69. Bernstein, B.E., Meissner, A. and Lander, E.S. (2007) The mammalian epigenome. Cell, 128, 669-681. (Pubitemid 46273573)
70. Kouzarides, T. (2007) Chromatin modifications and their function. Cell, 128, 693-705. (Pubitemid 46273577)
71. Khalil, A.M. and Rinn, J.L. (2011) RNA-protein interactions in human health and disease. Semin. Cell Dev. Biol., 22, 359-365.
72. Koziol, M.J. and Rinn, J.L. (2010) RNA traffic control of chromatin complexes. Curr. Opin. Genet. Dev., 20, 142-148.
73. Chu, C., Qu, K., Zhong, F.L., Artandi, S.E. and Chang, H.Y. (2011) Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol. Cell, 44, 667-678.
74. Zhao, J., Ohsumi, T.K., Kung, J.T., Ogawa, Y., Grau, D.J., Sarma, K., Song, J.J., Kingston, R.E., Borowsky, M. and Lee, J.T. (2010) Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol. Cell, 40, 939-953.
75. Jeon, Y. and Lee, J.T. (2011) YY1 tethers Xist RNA to the inactive X nucleation center. Cell, 146, 119-133.
76. Taft, R.J., Pang, K.C., Mercer, T.R., Dinger, M. and Mattick, J.S. (2010) Non-coding RNAs: regulators of disease. J. Pathol., 220, 126-139.
77. Kino, T., Hurt, D.E., Ichijo, T., Nader, N. and Chrousos, G.P. (2010) Noncoding RNA gas5 is a growth arrest-and starvation-associated repressor of the glucocorticoid receptor. Sci. Signal., 3, ra8.
78. Franco-Zorrilla, J.M., Valli, A., Todesco, M., Mateos, I., Puga, M.I., Rubio-Somoza, I., Leyva, A., Weigel, D., Garcia, J.A. and Paz-Ares, J. (2007) Target mimicry provides a new mechanism for regulation of microRNA activity. Nat. Genet., 39, 1033-1037. (Pubitemid 47185180)
79. Cesana, M., Cacchiarelli, D., Legnini, I., Santini, T., Sthandier, O., Chinappi, M., Tramontano, A. and Bozzoni, I. (2011) A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell, 147, 358-369.
80. Mattick, J.S. (2009) The genetic signatures of noncoding RNAs. PLoS Genet., 5, e1000459.
81. Kogo, R., Shimamura, T., Mimori, K., Kawahara, K., Imoto, S., Sudo, T., Tanaka, F., Shibata, K., Suzuki, A., Komune, S. et al. (2011) Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res., 71, 6320-6326.
82. Chung, S., Nakagawa, H., Uemura, M., Piao, L., Ashikawa, K., Hosono, N., Takata, R., Akamatsu, S., Kawaguchi, T., Morizono, T. et al. (2011) Association of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility. Cancer Sci., 102, 245-252.
83. Yang, Z., Zhou, L., Wu, L.M., Lai, M.C., Xie, H.Y., Zhang, F. and Zheng, S.S. (2011) Overexpression of long non-coding RNA HOTAIR predicts tumor recurrence in hepatocellular carcinoma patients following liver transplantation. Ann. Surg. Oncol., 18, 1243-1250.
84. Yang, F., Zhang, L., Huo, X.S., Yuan, J.H., Xu, D., Yuan, S.X., Zhu, N., Zhou, W.P., Yang, G.S., Wang, Y.Z. et al. (2011) Long noncoding RNA high expression in hepatocellular carcinoma facilitates tumor growth through enhancer of zeste homolog 2 in humans. Hepatology, 54, 1679-1689.
85. Lai, M.C., Yang, Z., Zhou, L., Zhu, Q.Q., Xie, H.Y., Zhang, F., Wu, L.M., Chen, L.M. and Zheng, S.S. (2011) Long non-coding RNA MALAT-1 overexpression predicts tumor recurrence of hepatocellular carcinoma after liver transplantation. Med. Oncol., June 16 (doi:10.1007/s12032-011-0004-z; epub ahead of print).
86. Calin, G.A., Pekarsky, Y. and Croce, C.M. (2007) The role of microRNA and other non-coding RNA in the pathogenesis of chronic lymphocytic leukemia. Best Pract. Res. Clin. Haematol., 20, 425-437. (Pubitemid 47260321)
87. Calin, G.A., Liu, C.G., Ferracin, M., Hyslop, T., Spizzo, R., Sevignani, C., Fabbri, M., Cimmino, A., Lee, E.J., Wojcik, S.E. et al. (2007) Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas. Cancer Cell, 12, 215-229. (Pubitemid 47333418)
88. Khaitan, D., Dinger, M.E., Mazar, J., Crawford, J., Smith, M.A., Mattick, J.S. and Perera, R.J. (2011) The melanoma-upregulated long noncoding RNA SPRY4-IT1 modulates apoptosis and invasion. Cancer Res., 71, 3852-3862.
89. Huarte, M. and Rinn, J.L. (2010) Large non-coding RNAs: missing links in cancer? Hum. Mol. Genet., 19, R152-R161.
90. Li, L., Feng, T., Lian, Y., Zhang, G., Garen, A. and Song, X. (2009) Role of human noncoding RNAs in the control of tumorigenesis. Proc. Natl Acad. Sci. USA, 106, 12956-12961.
91. Yu, W., Gius, D., Onyango, P., Muldoon-Jacobs, K., Karp, J., Feinberg, A.P. and Cui, H. (2008) Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature, 451, 202-206.
92. Ishii, N., Ozaki, K., Sato, H., Mizuno, H., Saito, S., Takahashi, A., Miyamoto, Y., Ikegawa, S., Kamatani, N., Hori, M. et al. (2006) Identification of a novel non-coding RNA, MIAT, that confers risk of myocardial infarction. J. Hum. Genet., 51, 1087-1099. (Pubitemid 44800728)
93. Pasmant, E., Laurendeau, I., Heron, D., Vidaud, M., Vidaud, D. and Bieche, I. (2007) Characterization of a germ-line deletion, including the entire INK4/ARF locus, in a melanoma-neural system tumor family: identification of ANRIL, an antisense noncoding RNA whose expression coclusters with ARF. Cancer Res., 67, 3963-3969. (Pubitemid 46762186)
94. Faghihi, M.A., Modarresi, F., Khalil, A.M., Wood, D.E., Sahagan, B.G., Morgan, T.E., Finch, C.E., St Laurent, G. 3rd, Kenny, P.J. and Wahlestedt, C. (2008) Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase. Nat. Med., 14, 723-730.
95. Sonkoly, E., Bata-Csorgo, Z., Pivarcsi, A., Polyanka, H., Kenderessy-Szabo, A., Molnar, G., Szentpali, K., Bari, L., Megyeri, K., Mandi, Y. et al. (2005) Identification and characterization of a novel, psoriasis susceptibility-related noncoding RNA gene, PRINS. J. Biol. Chem., 280, 24159-24167. (Pubitemid 40884904)
96. Daughters, R.S., Tuttle, D.L., Gao, W., Ikeda, Y., Moseley, M.L., Ebner, T.J., Swanson, M.S. and Ranum, L.P. (2009) RNA gain-of-function in spinocerebellar ataxia type 8. PLoS Genet., 5, e1000600.
97. Khalil, A.M., Faghihi, M.A., Modarresi, F., Brothers, S.P. and Wahlestedt, C. (2008) A novel RNA transcript with antiapoptotic function is silenced in fragile X syndrome. PLoS One, 3, e1486.
98. Wang, K.C., Yang, Y.W., Liu, B., Sanyal, A., Corces-Zimmerman, R., Chen, Y., Lajoie, B.R., Protacio, A., Flynn, R.A., Gupta, R.A. et al. (2011) A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature, 472, 120-124.
99. Yang, L., Lin, C., Liu, W., Zhang, J., Ohgi, K.A., Grinstein, J.D., Dorrestein, P.C. and Rosenfeld, M.G. (2011) ncRNA-and Pc2 methylation-dependent gene relocation between nuclear structures mediates gene activation programs. Cell, 147, 773-788.
100. 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.
101. Kertesz, M., Wan, Y., Mazor, E., Rinn, J.L., Nutter, R.C., Chang, H.Y. and Segal, E. (2010) Genome-wide measurement of RNA secondary structure in yeast. Nature, 467, 103-107.
102. Ingolia, N.T., Lareau, L.F. and Weissman, J.S. (2011) Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell, 147, 789-802.
103. Zhu, Y., Yu, M., Li, Z., Kong, C., Bi, J., Li, J., Gao, Z. and Li, Z. (2011) ncRAN, a newly identified long noncoding RNA, enhances human bladder tumor growth, invasion, and survival. Urology, 77, 510 e511-e515.