Controlling transcription with noncoding RNAs in mammalian cells

BioTechniques

Volumn 48, Issue 6, 2010, Pages

  Turner, Anne Marie W ^a   Morris, Kevin V ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Antisense; Epigenetic; ncRNA; Noncoding RNA; siRNA; Small RNAs; Transcription

Indexed keywords

SMALL INTERFERING RNA; UNTRANSLATED RNA; CHROMATIN; COMPLEMENTARY RNA; HISTONE; RNA BINDING PROTEIN;

CHROMATIN STRUCTURE; DNA MODIFICATION; GENE ACTIVATION; GENE CONTROL; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE SILENCING; HUMAN; MAMMAL CELL; NONHUMAN; POSTTRANSCRIPTIONAL GENE SILENCING; REVIEW; TRANSCRIPTION REGULATION; TRANSCRIPTION TERMINATION; ANIMAL; BIOLOGICAL MODEL; CHROMATIN; GENETIC EPIGENESIS; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; PHYSIOLOGY;

MAMMALIA;

ANIMALS; CHROMATIN; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION; GENE SILENCING; HISTONES; HUMANS; MODELS, BIOLOGICAL; RNA, ANTISENSE; RNA, UNTRANSLATED; RNA-BINDING PROTEINS; TRANSCRIPTION, GENETIC;

EID: 77954098792     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/000113442     Document Type: Review

References (64)

1. Berger, S.L. 2007. The complex language of chromatin regulation during transcription. Nature 447:407-412. (Pubitemid 46816746)
2. Scherr, M. and M. Eder. 2007. Gene silencing by small regulatory RNAs in mammalian cells. Cell Cycle 6:444-449. (Pubitemid 46393448)
3. Matzke, M., T. Kanno, L. Daxinger, B. Huettel, and A.J.M. Matzke. 2009. RNA-mediated chromatin-based silencing in plants. Curr. Opin. Cell Biol. 21:367-376.
4. Pal-Bhadra, M., U. Bhadra, and J.A. Birchler. 2002. RNAi related mechanisms affect both transcriptional and posttranscriptional transgene silencing in Drosophila. Mol. Cell 9:315-327.
5. Pal-Bhadra, M., B.A. Leibovitch, S.G. Gandhi, M. Rao, U. Bhadra, J.A. Birchler, and S.C.R. Elgin. 2004. Heterochromatic silencing and HP1 localization in Drosophila are dependent on the RNAi machinery. Science 303:669-672.
6. Volpe, T.A., C. Kidner, I.M. Hall, G. Teng, S.I.S. Grewal, and R.A. Martienssen. 2002. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297:1833-1837.
7. Morris, K.V., S.W.L. Chan, S.E. Jacobsen, and D.J. Looney. 2004. Small interfering RNA-induced transcriptional gene silencing in human cells. Science 305:1289-1292.
8. Weinberg, M.S., L.M. Villeneuve, A. Ehsani, M. Amarzguioui, L. Aagaard, Z.-X. Chen, A.D. Riggs, J.J. Rossi, and K.V. Morris. 2006. The antisense strand of small interfering RNAs directs histone methylation and transcriptional gene silencing in human cells. RNA 12:256-262.
9. Suzuki, K., T. Juelich, H. Lim, T. Ishida, T. Watanebe, D.A. Cooper, S. Rao, and A.D. Kelleher. 2008. Closed chromatin architecture is induced by an RNA duplex targeting the HIV-1 promoter region. J. Biol. Chem. 283:23353-23363.
10. Suzuki, K., T. Shijuuku, T. Fukamachi, J. Zaunders, G. Guillemin, D. Cooper, and A. Kelleher. 2005. Prolonged transcriptional silencing and CpG methylation induced by dsRNAs targeted to the HIV-1 promoter region. J. RNAi Gene Silencing 1:66-78.
11. Kim, D.H., L.M. Villeneuve, K.V. Morris, and J.J. Rossi. 2006. Argonaute-1 directs siRNA-mediated transcriptional gene silencing in human cells. Nat. Struct. Mol. Biol. 13:793-797.
12. Janowski, B.A., K.E. Huffman, J.C. Schwartz, R. Ram, D. Hardy, D.S. Shames, J.D. Minna, and D.R. Corey. 2005. Inhibiting gene expression at transcription start sites in chromosomal DNA with antigene RNAs. Nat. Chem. Biol. 1:216-222.
13. Janowski, B.A., K.E. Huffman, J.C. Schwartz, R. Ram, R. Nordsell, D.S. Shames, J.D. Minna, and D.R. Corey. 2006. Involvement of AGO1 and AGO2 in mammalian transcriptional silencing. Nat. Struct. Mol. Biol. 13:787-792.
14. Janowski, B.A., K. Kaihatsu, K.E. Huffman, J.C. Schwartz, R. Ram, D. Hardy, C.R. Mendelson, and D.R. Corey. 2005. Inhibiting transcription of chromosomal DNA with antigene peptide nucleic acids. Nat. Chem. Biol. 1:210-215.
15. Han, J., D. Kim, and K.V. Morris. 2007. Promoter-associated RNA is required for RNA-directed transcriptional gene silencing in human cells. Proc. Natl. Acad. Sci. USA 104:12422-12427.
16. Gonzalez, S., D.G. Pisano, and M. Serrano. 2008. Mechanistic principles of chromatin remodeling guided by siRNAs and miRNAs. Cell Cycle 7:2601-2608.
17. Napoli, S., C. Pastori, M. Magistri, G.M. Carbone, and C.V. Catapano. 2009. Promoter-specific transcriptional interference and c-myc gene silencing by siRNAs in human cells. EMBO J. 28:1708-1719.
18. Ting, A.H., K.E. Schuebel, J.G. Herman, and S.B. Baylin. 2005. Short double-stranded RNA induces transcriptional gene silencing in human cancer cells in the absence of DNA methylation. Nat. Genet. 37:906-910.
19. Kim, J.-W., Y.-H. Zhang, M.A. Zern, J.J. Rossi, and J. Wu. 2007. Short hairpin RNA causes the methylation of transforming growth factor-beta receptor II promoter and silencing of the target gene in rat hepatic stellate cells. Biochem. Biophys. Res. Commun. 359:292-297.
20. Hawkins, P.G., S. Santoso, C. Adams, V. Anest, and K.V. Morris. 2009. Promoter targeted small RNAs induce long-term transcriptional gene silencing in human cells. Nucleic Acids Res. 37:2984-2995.
21. Castanotto, D., S. Tommasi, M.J. Li, H.T. Li, S. Yanow, G.P. Pfeifer, and J.J. Rossi. 2005. Short hairpin RNA-directed cytosine (CpG) methylation of the RASSF1A gene promoter in HeLa cells. Mol. Ther. 12:179-183.
22. Turner, A.-M.W., J. De La Cruz, and K.V. Morris. 2008. Mobilization-competent lentiviral vector-mediated sustained transcriptional modulation of HIV-1 expression. Mol. Ther. 17:360-368.
23. Buhler, M., F. Mohn, L. Stalder, and O. Muhlemann. 2005. Transcriptional silencing of nonsense codon-containing immunoglobulin minigenes. Mol. Cell 18:307-317.
24. Kim, D.H., P. Saetrom, O. Snove, and J.J. Rossi. 2008. microRNA-directed transcriptional gene silencing in mammalian cells. Proc. Natl. Acad. Sci. USA 105:16230-16235.
25. Pulukuri, S.M.K. and J.S. Rao. 2007. Small interfering RNA directed reversal of urokinase plasminogen activator demethylation inhibits prostate tumor growth and metastasis. Cancer Res. 67:6637-6646.
26. Sharma, S., T.K. Kelly, and P.A. Jones. 2010. Epigenetics in cancer. Carcinogenesis 31:27-36.
27. Yuan, G.-C., Y.-J. Liu, M.F. Dion, M.D. Slack, L.F. Wu, S.J. Altschuler, and O.J. Rando. 2005. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309:626-630.
28. Jeffery, L. and S. Nakielny. 2004. Components of the DNA methylation system of chromatin control are RNA-binding proteins. J. Biol. Chem. 279:49479-49487.
29. Vire, E., C. Brenner, R. Deplus, L. Blanchon, M. Fraga, C. Didelot, L. Morey, A. Van Eynde, et al. 2006. The Polycomb group protein EZH2 directly controls DNA methylation. Nature 439:871-874.
30. Fuks, F., W.A. Burgers, N. Godin, M. Kasai, and T. Kouzarides. 2001. Dnmt3a binds deacetylases and is recruited by a sequence-specific repressor to silence transcription. EMBO J. 20:2536-2544.
31. Probst, A.V., E. Dunleavy, and G. Almouzni. 2009. Epigenetic inheritance during the cell cycle. Nat. Rev. Mol. Cell Biol. 10:192-206.
32. Francis, N.J. 2009. Mechanisms of epigenetic inheritance: copying of polycomb repressed chromatin. Cell Cycle 8:3513-3518.
33. Bartel, D.P. 2009. microRNAs. Target recognition and regulatory functions. Cell 136:215-233.
34. Li, L.-C., S.T. Okino, H. Zhao, D. Pookot, R.F. Place, S. Urakami, H. Enokida, and R. Dahiya. 2006. Small dsRNAs induce transcriptional activation in human cells. Proc. Natl. Acad. Sci. USA 103:17337-17342.
35. Janowski, B.A., S.T. Younger, D.B. Hardy, R. Ram, K.E. Huffman, and D.R. Corey. 2007. Activating gene expression in mammalian cells with promoter-targeted duplex RNAs. Nat. Chem. Biol. 3:166-173.
36. Place, R.F., L.-C. Li, D. Pookot, E.J. Noonan, and R. Dahiya. 2008. microRNA-373 induces expression of genes with complementary promoter sequences. Proc. Natl. Acad. Sci. USA 105:1608-1613.
37. Schwartz, J.C., S.T. Younger, N.-B. Nguyen, D.B. Hardy, B.P. Monia, D.R. Corey, and B.A. Janowski. 2008. Antisense transcripts are targets for activating small RNAs. Nat. Struct. Mol. Biol. 15:842-848.
38. Morris, K.V., S. Santoso, A.-M. Turner, C. Pastori, and P.G. Hawkins. 2008. Bidirectional transcription directs both transcriptional gene activation and suppression in human cells. PLoS Genet. 4:e1000258.
39. Huang, V., Y. Qin, J. Wang, X. Wang, R.F. Place, G. Lin, T.F. Lue, and L.-C. Li. 2010. RNAa is conserved in mammalian cells. PLoS One 5:e8848.
40. Amaral, P.P., M.E. Dinger, T.R. Mercer, and J.S. Mattick. 2008. The eukaryotic genome as an RNA machine. Science 319:1787-1789.
41. Conley, A.B., W.J. Miller, and I.K. Jordan. 2008. Human cis natural antisense transcripts initiated by transposable elements. Trends Genet. 24:53-56.
42. Finocchiaro, G., M.S. Carro, S. Francois, P. Parise, V. DiNinni, and H. Muller. 2007. Localizing hotspots of antisense transcription. Nucleic Acids Res. 35:1488-1500.
43. Kapranov, P., J. Cheng, S. Dike, D.A. Nix, R. Duttagupta, A.T. Willingham, P.F. Stadler, J. Hertel, et al. 2007. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316:1484-1488.
44. Timmons, J.A. and L. Good. 2006. Does everything now make (anti)sense? Biochem. Soc. Trans. 34:1148-1150.
45. Yu, W., D. Gius, P. Onyango, K. Muldoon-Jacobs, J. Karp, A.P. Feinberg, and H. Cui. 2008. Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 451:202-206.
46. Lee, J.T. 2009. Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome. Genes Dev. 23:1831-1842.
47. Kerppola, T.K. 2009. Polycomb group complexes - many combinations, many functions. Trends Cell Biol. 19:692-704.
48. van der Vlag, J. and A.P. Otte. 1999. Transcriptional repression mediated by the human polycomb-group protein EED involves histone deacetylation. Nat. Genet. 23:474-478.
49. Rinn, J.L., M. Kertesz, J.K. Wang, S.L. Squazzo, X. Xu, S.A. Brugmann, L.H. Goodnough, J.A. Helms, et al. 2007. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129:1311-1323.
50. Nagano, T. and P. Fraser. 2009. Emerging similarities in epigenetic gene silencing by long noncoding RNAs. Mamm. Genome 20:557-562.
51. Core, L.J., J.J. Waterfall, and J.T. Lis. 2008. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322:1845-1848.
52. He, Y., B. Vogelstein, V.E. Velculescu, N. Papadopoulos, and K.W. Kinzler. 2008. The antisense transcriptomes of human cells. Science 322:1855-1857.
53. Preker, P., J. Nielsen, S. Kammler, S. Lykke-Andersen, M.S. Christensen, C.K. Mapendano, M.H. Schierup, and T.H. Jensen. 2008. RNA exosome depletion reveals transcription upstream of active human promoters. Science 322:1851-1854.
54. Seila, A.C., J.M. Calabrese, S.S. Levine, G.W. Yeo, P.B. Rahl, R.A. Flynn, R.A. Young, and P.A. Sharp. 2008. Divergent transcription from active promoters. Science 322:1849-1851.
55. Guttman, M., I. Amit, M. Garber, C. French, M.F. Lin, D. Feldser, M. Huarte, O. Zuk, et al. 2009. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458:223-227.
56. Khalil, A.M., M. Guttman, M. Huarte, M. Garber, A. Raj, D. Rivea Morales, K. Thomas, A. Presser, 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.
57. Feinberg, A.P. and B. Tycko. 2004. The history of cancer epigenetics. Nat. Rev. Cancer 4:143-153.
58. Jones, P.A. and S.B. Baylin. 2002. The fundamental role of epigenetic events in cancer. Nat. Rev. Genet. 3:415-428.
59. Marks, P.A. and W.-S. Xu. 2009. Histone deacetylase inhibitors: potential in cancer therapy. J. Cell. Biochem. 107:600-608.
60. Behlke, M.A. 2008. Chemical modification of siRNAs for in vivo use. Oligonucleotides 18:305-320.
61. De Rosa, G. and M.I. La Rotonda. 2009. Nano and microtechnologies for the delivery of oligonucleotides with gene silencing properties. Molecules 14:2801-2823.
62. Fattal, E. and A. Bochot. 2008. State of the art and perspectives for the delivery of antisense oligonucleotides and siRNA by polymeric nanocarriers. Int. J. Pharm. 364:237-248.
63. Rossi, J.J., C.H. June, and D.B. Kohn. 2007. Genetic therapies against HIV. Nat. Biotechnol. 25:1444-1454.
64. Matrai, J., M.K.L. Chuah, and T. Vanden-Driessche. 2010. Recent advances in lentiviral vector development and applications. Mol. Ther. 18:477-490.