Long non-coding RNA targeting and transcriptional de-repression

Nucleic Acid Therapeutics

Volumn 23, Issue 1, 2013, Pages 9-14

  Weinberg, Marc S ^a,b   Morris, Kevin V ^a,c  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF THE WITWATERSRAND MEDICAL SCHOOL   (South Africa)

^c UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

LONG UNTRANSLATED RNA; SMALL INTERFERING RNA;

ARTICLE; EPIGENETICS; GENE EXPRESSION; GENE LOCUS; GENE SILENCING; GENE TARGETING; GENETIC TRANSCRIPTION; HUMAN; PRIORITY JOURNAL; RNA INTERFERENCE; TRANSCRIPTION REGULATION;

EPIGENESIS, GENETIC; GENE SILENCING; HUMANS; MODELS, GENETIC; RNA INTERFERENCE; RNA, ANTISENSE; RNA, LONG UNTRANSLATED; TRANSCRIPTION, GENETIC; TRANSCRIPTIONAL ACTIVATION;

EID: 84873626217     PISSN: 21593337     EISSN: None     Source Type: Journal    
DOI: 10.1089/nat.2012.0412     Document Type: Article

References (39)

1. ALBERTS, B., BRAY, D., LEWIS, J., RAFF, M., ROBERTS, K., and WATSON, J.D. (1994). Molecular Biology of the Cell, 3rd ed. (Garland Science, New York)
2. BANFAI, B., JIA, H., KHATUN, J., WOOD, E., RISK, B., GUNDLING, W.E., JR., KUNDAJE, A., GUNAWARDENA, H.P., YU, Y., XIE, L., et al. (2012). Long noncoding RNAs are rarely translated in two human cell lines. Genome Res. 22, 1646-1657
3. BERNSTEIN, B.E., BIRNEY, E., DUNHAM, I., GREEN, E.D., GUNTER, C., and SNYDER, M. (2012). An integrated encyclopedia ofDNAelements in the human genome.Nature 489, 57-74
4. GREEN, V.A., and WEINBERG, M.S. (2011). Small RNAinduced transcriptional gene regulation in mammals mechanisms, therapeutic applications, and scope within the genome. Prog. Mol. Biol. Transl. Sci. 102, 11-46
5. HAN, J., KIM, D., and MORRIS, K.V. (2007). Promoter-associated RNA is required for RNA-directed transcriptional gene silencing in human cells. Proc. Natl. Acad. Sci. U. S. A. 104, 12422-12427
6. HANNON, G.J., and ROSSI, J.J. (2004). Unlocking the potential of the human genome with RNA interference. Nature 431, 371-378
7. HAWKINS, P.G., and MORRIS, K.V. (2010). Transcriptional regulation of Oct4 by a long non-coding RNA antisense to Oct4-pseudogene 5. Transcription 1, 165-175
8. HAWKINS, P.G., SANTOSO, S., ADAMS, C., ANEST, V., and MORRIS, K.V. (2009). Promoter targeted small RNAs induce long-term transcriptional gene silencing in human cells. Nucleic Acids Res. 37, 2984-2995
9. JANOWSKI, B.A., HUFFMAN, K.E., SCHWARTZ, J.C., RAM, R., NORDSELL, R., SHAMES, D.S., MINNA, J.D., and COREY, D.R. (2006). Involvement of AGO1 and AGO2 in mammalian transcriptional silencing. Nat. Struct. Mol. Biol. 13, 787-792
10. KERIN, T., RAMANATHAN, A., RIVAS, K., GREPO, N., COETZEE, G.A., and CAMPBELL, D.B. (2012). A noncoding RNA antisense to moesin at 5p14.1 in autism. Sci. Transl. Med. 4, 128ra40
11. KIM, D.H., SAETROM, P., SNOVE, O., JR., and ROSSI, J.J. (2008). MicroRNA-directed transcriptional gene silencing in mammalian cells. Proc. Natl. Acad. Sci. U. S. A. 105, 16230- 16235
12. KIM, D.H., VILLENEUVE, L.M., MORRIS, K.V., and ROSSI, J.J. (2006). Argonaute-1 directs siRNA-mediated transcriptional gene silencing in human cells. Nat. Struct. Mol. Biol. 13, 793-797
13. KLASE, Z., KALE, P., WINOGRAD, R., GUPTA, M.V., HEYDARIAN, M., BERRO, R., MCCAFFREY, T., and KASHANCHI, F. (2007). HIV-1 TAR element is processed by Dicer to yield a viral micro-RNA involved in chromatin remodeling of the viral LTR. BMC Mol. Biol. 8, 63
14. LATOS, P.A., and BARLOW, D.P. (2009). Regulation of imprinted expression by macro non-coding RNAs. RNA Biol. 6, 100-106
15. LEE, J.T. (2009). Lessons from X-chromosome inactivation: Long ncRNA as guides and tethers to the epigenome. Genes Dev. 23, 1831-1842
16. LI, L.C., OKINO, S.T., ZHAO, H., POOKOT, D., PLACE, R.F., URAKAMI, S., ENOKIDA, H., and DAHIYA, R. (2006). Small dsRNAs induce transcriptional activation in human cells. Proc. Natl. Acad. Sci. U. S. A. 103, 17337-17342
17. LIPOVICH, L., DACHET, F., CAI, J., BAGLA, S., BALAN, K., JAI, H., and LOEB, J.A. (2012). Activity-dependent human brain coding/non-coding gene regulatory networks. Genetics 192, 1133-1148
18. MATTICK, J.S., and MAKUNIN, I.V. (2006). Non-coding RNA. Hum. Mol. Genet. 15 Spec No 1, R17-29
19. MODARRESI, F., FAGHIHI, M.A., LOPEZ-TOLEDANO, M.A., FATEMI, R.P., MAGISTRI, M., BROTHERS, S.P., VAN DER BRUG, M.P., and WAHLESTEDT, C. (2012). Inhibition of natural antisense transcripts in vivo results in gene-specific transcriptional upregulation. Nat. Biotechnol. 30, 453-459
20. MORRIS, K.V. (2009a). Long antisense non-coding RNAs function to direct epigenetic complexes that regulate transcription in human cells. Epigenetics 4, 296-301
21. MORRIS, K.V. (2009b). Non-coding RNAs, epigenetic memory, and the passage of information to progeny. RNA Biol. 6, 242-247
22. MORRIS, K.V. (2011). The emerging role of RNA in the regulation of gene transcription in human cells. Semin. Cell Dev. Biol. 22, 351-358
23. MORRIS, K.V., SANTOSO, S., TURNER, A.M., PASTORI, C., and HAWKINS, P.G. (2008). Bidirectional transcription directs both transcriptional gene activation and suppression in human cells. PLoS Genet. 4, e1000258. DOI: 10.1371/journal. pgen.1000258
24. MORRIS, K.V., and VOGT, P.K. (2010). Long antisense noncoding RNAs and their role in transcription and oncogenesis. Cell Cycle 9, 2544-2547
25. NAPOLI, S., PASTORI, C., MAGISTRI, M., CARBONE, G.M., and CATAPANO, C.V. (2009). Promoter-specific transcriptional interference and c-myc gene silencing by siRNAs in human cells. EMBO J. 28, 1708-1719
26. OMOTO, S., and FUJII, Y.R. (2005). Regulation of human immunodeficiency virus 1 transcription by nef microRNA. J. Gen. Virol. 86, 751-755
27. OMOTO, S., ITO, M., TSUTSUMI, Y., ICHIKAWA, Y., OKUYAMA, H., BRISIBE, E.A., SAKSENA, N.K., and FUJII, Y.R. (2004). HIV-1 nef suppression by virally encoded micro- RNA. Retrovirology 1, 44
28. PLACE, R.F., LI, L.C., POOKOT, D., NOONAN, E.J., and DAHIYA, R. (2008). MicroRNA-373 induces expression of genes with complementary promoter sequences. Proc. Natl. Acad. Sci. U. S. A. 105, 1608-1613
29. SUZUKI, K., JUELICH, T., LIM, H., ISHIDA, T., WATANEBE, T., COOPER, D.A., RAO, S., and KELLEHER, A.D. (2008). Closed chromatin architecture is induced by an RNA duplex targeting the HIV-1 promoter region. J. Biol. Chem. 283, 23353-23363
30. SUZUKI, K., SHIJUUKU, T., FUKAMACHI, T., ZAUNDERS, J., GUILLEMIN, G., COOPER, D., and KELLEHER, A. (2005). Prolonged transcriptional silencing and CpG methylation induced by siRNAs targeted to the HIV-1 promoter region. J. RNAi Gene Silencing 1, 66-78
31. TAHIRA, A.C., KUBRUSLY, M.S., FARIA, M.F., DAZZANI, B., FONSECA, R.S., MARACAJA-COUTINHO, V., VERJOVSKIALMEIDA, S., MACHADO, M.C., and REIS, E.M. (2011). Long noncoding intronic RNAs are differentially expressed in primary and metastatic pancreatic cancer. Mol. Cancer 10, 141
32. TAN, Y., ZHANG, B., WU, T., SKOGERBO, G., ZHU, X., GUO, X., HE, S., and CHEN, R. (2009). Transcriptional inhibition of Hoxd4 expression by noncoding RNAs in human breast cancer cells. BMC Mol. Biol. 10, 12
33. TOMARI, Y., and ZAMORE, P.D. (2005). Perspective: Machines for RNAi. Genes Dev. 19, 517-529
34. TURNER, A.M., DE LA CRUZ, J., and MORRIS, K.V. (2009). Mobilization- competent lentiviral vector-mediated sustained transcriptional modulation of HIV-1 expression. Mol. Ther. 17, 360-368
35. TURNER, A.M., and MORRIS, K.V. (2010). Controlling transcription with noncoding RNAs in mammalian cells. Biotechniques 48, ix-xvi
36. WEI, J.X., YANG, J., SUN, J.F., JIA, L.T., ZHANG, Y., ZHANG, H.Z., LI, X., MENG, Y.L., YAO, L.B., and YANG, A.G. (2009). Both strands of siRNA have potential to guide posttranscriptional gene silencing in mammalian cells. PLoS One 4, e5382 DOI: 10.1371/journal.pone.0005382
37. WEINBERG, M.S., VILLENEUVE, L.M., EHSANI, A., AMARZGUIOUI, M., AAGAARD, L., CHEN, Z.X., RIGGS, A.D., ROSSI, J.J., and MORRIS, K.V. (2006). The antisense strand of small interfering RNAs directs histone methylation and transcriptional gene silencing in human cells. RNA 12, 256-262
38. 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
39. ZARDO, G., CIOLFI, A., VIAN, L., STARNES, L.M., BILLI, M., RACANICCHI, S., MARESCA, C., FAZI, F., TRAVAGLINI, L., NOGUERA, N., et al. (2012). Polycombs and microRNA- 223 regulate human granulopoiesis by ranscriptional control of target gene expression. Blood 119, 4034-4046