RNA Interference (siRNA, shRNA)

Alternative pre-mRNA Splicing: Theory and Protocols

Volumn , Issue , 2012, Pages 164-173

  Cabianca, Daphne S ^a,b   Gabellini, Davide ^a,c  

^a SAN RAFFAELE HOSPITAL   (Italy)

^b VITA SALUTE SAN RAFFAELE UNIVERSITY   (Italy)

^c DULBECCO TELETHON INSTITUTE   (Italy)

Author keywords

Lentiviruses; RNAi; ShRNA; SiRNA

Indexed keywords

EID: 84885547137     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527636778.ch15     Document Type: Chapter

References (30)

1. Fire, A., Xu, S., Montgomery, M.K., Kostas, S.A., Driver, S.E., and Mello, C.C. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature, 391, 806-811.
2. Elbashir, S.M., Harborth, J., Lendeckel, W., Yalcin, A., Weber, K., and Tuschl, T. (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature, 411, 494-498.
3. Elbashir, S.M., Lendeckel,W., and Tuschl, T. (2001) RNA interference is mediated by 21-and 22-nucleotide RNAs. Genes Dev., 15, 188-200.
4. Ambros, V., Lee, R.C., Lavanway, A., Williams, P.T., and Jewell, D. (2003) MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr. Biol., 13, 807-818.
5. Aravin, A.A., Lagos-Quintana, M., Yalcin, A., Zavolan, M., Marks, D., Snyder, B., Gaasterland, T., Meyer, J., and Tuschl, T. (2003) The small RNA profile during Drosophila melanogaster development. Dev. Cell, 5, 337-350.
6. Xie, Z., Johansen, L.K., Gustafson, A.M., Kasschau, K.D., Lellis, A.D., Zilberman, D., Jacobsen, S.E., and Carrington, J.C. (2004) Genetic and functional diversification of small RNApathways in plants. PLoS Biol., 2, E104.
7. Ghildiyal, M., Seitz, H., Horwich, M.D., Li, C., Du, T., Lee, S., Xu, J., Kittler, E.L., Zapp, M.L., Weng, Z., and Zamore, P.D. (2008) Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science, 320, 1077-1081.
8. Watanabe, T., Totoki, Y., Toyoda, A., Kaneda, M., Kuramochi-Miyagawa, S., Obata, Y., Chiba, H., Kohara, Y., Kono, T., Nakano, T. et al. (2008) Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature, 453, 539-543.
9. Okamura, K., Chung,W.J., Ruby, J.G., Guo, H., Bartel, D.P., and Lai, E.C. (2008) The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs. Nature, 453, 803-806.
10. Babiarz, J.E., Ruby, J.G., Wang, Y., Bartel, D.P., and Blelloch, R. (2008) Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicerdependent small RNAs. Genes Dev., 22, 2773-2785.
11. Held, M.A., Penning, B., Brandt, A.S., Kessans, S.A., Yong, W., Scofield, S.R., and Carpita, N.C. (2008) Small-interfering RNAs from natural antisense transcripts derived from a cellulose synthase gene modulate cell wall biosynthesis in barley. Proc. Natl Acad. Sci. USA 105 20534-20539.
12. Chung, W.J., Okamura, K., Martin, R., and Lai, E.C. (2008) Endogenous RNA interference provides a somatic defense against Drosophila transposons. Curr. Biol., 18, 795-802.
13. Verdel, A., Jia, S., Gerber, S., Sugiyama, T., Gygi, S.,Grewal, S.I., and Moazed, D. (2004) RNAi-mediated targeting of heterochromatin by the RITS complex. Science, 303, 672-676.
14. Pal-Bhadra, M., Leibovitch, B.A., Gandhi, S.G., Rao, M., Bhadra, U., Birchler, J.A., and Elgin, S.C. (2004) Heterochromatic silencing and HP1 localization in Drosophila are dependent on the RNAi machinery. Science, 303, 669-672.
15. Mette, M.F.,Aufsatz,W., van der Winden, J., Matzke, M.A., and Matzke, A.J. (2000) Transcriptional silencing and promoter methylation triggered by double-stranded RNA. EMBO J., 19, 5194-5201.
16. Sijen, T., Vijn, I., Rebocho, A., van Blokland, R., Roelofs, D., Mol, J.N., and Kooter, J.M. (2001) Transcriptional and posttranscriptional gene silencing aremechanistically related. Curr. Biol., 11, 436-440.
17. 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. USA, 103, 17337-17342.
18. Allo, M., Buggiano, V., Fededa, J.P., Petrillo, E., Schor, I., de la Mata, M., Agirre, E., Plass, M., Eyras, E., Elela, S.A. et al. (2009) Control of alternative splicing through siRNA-mediated transcriptional gene silencing. Nat. Struct. Mol. Biol., 16, 717-724.
19. Tuschl, T. (2002) Expanding small RNA interference. Nat. Biotechnol., 20, 446-448.
20. Kawasaki, H. and Taira, K. (2003) Short hairpin type of dsRNAs that are controlled by tRNA(Val) promoter significantly induce RNAi-mediated gene silencing in the cytoplasm of human cells.NucleicAcids Res., 31, 700-707.
21. Gupta, S., Schoer, R.A., Egan, J.E.,Hannon, G.J., and Mittal, V. (2004) Inducible, reversible, and stable RNA interference in mammalian cells. Proc. Natl Acad. Sci. USA, 101, 1927-1932.
22. Dickins, R.A., Hemann, M.T., Zilfou, J.T., Simpson, D.R., Ibarra, I.,Hannon, G.J., and Lowe, S.W. (2005) Probing tumor phenotypes using stable and regulated synthetic microRNA precursors. Nat. Genet., 37, 1289-1295.
23. Dykxhoorn, D.M., Novina, C.D., and Sharp, P.A. (2003) Killing the messenger: short RNAs that silence gene expression. Nat. Rev. Mol. Cell Biol., 4, 457-467.
24. Brummelkamp, T.R., Bernards, R., and Agami, R. (2002) Stable suppression of tumorigenicity by virus-mediated RNA interference. Cancer Cell, 2, 243-247.
25. Rubinson, D.A., Dillon, C.P., Kwiatkowski, A.V., Sievers, C., Yang, L., Kopinja, J., Rooney, D.L., Zhang, M., Ihrig, M.M., McManus, M.T. et al. (2003) A lentivirusbased system to functionally silence genes in primary mammalian cells, stem cells and transgenic mice by RNA interference. Nat. Genet., 33, 401-406.
26. Arts, G.J., Langemeijer, E., Tissingh, R., Ma, L., Pavliska, H., Dokic, K., Dooijes, R., Mesic, E., Clasen, R., Michiels, F. et al. (2003) Adenoviral vectors expressing siRNAs for discovery and validation of gene function.Genome Res., 13, 2325-2332.
27. Blomer, U., Naldini, L., Kafri, T., Trono, D., Verma, I.M., and Gage, F.H. (1997) Highly efficient and sustained gene transfer in adult neurons with a lentivirus vector. J. Virol., 71, 6641-6649.
28. Fenner, F. (1976) The classification and nomenclature of viruses. Summary of results of meetings of the International Committee on Taxonomy of Viruses in Madrid, September 1975. Virology, 71, 371-378.
29. Ailles, L.E. and Naldini, L. (2002) HIV-1-derived lentiviral vectors. Curr. Top. Microbiol. Immunol., 261, 31-52.
30. Abbas-Terki, T., Blanco-Bose, W., Deglon, N., Pralong, W., and Aebischer, P. (2002) Lentiviral-mediated RNA interference. Hum. Gene Ther., 13, 2197-2201.