Control of the interferon response in RNAi experiments

Methods in Molecular Biology

Volumn 820, Issue , 2012, Pages 133-161

  Nejepinska, Jana ^a   Flemr, Matyas ^a   Svoboda, Petr ^a  

^a INSTITUTE OF MOLECULAR GENETICS   (Czech Republic)

Author keywords

Double stranded RNA; Interferon; RNA interference; Short hairpin RNA; Small interfering RNA

Indexed keywords

DOUBLE STRANDED RNA; INTERFERON; PRIMER DNA; SMALL INTERFERING RNA;

AMINO ACID SEQUENCE; ARTICLE; CELL STRAIN HEK293; GENE EXPRESSION REGULATION; GENE SILENCING; GENETICS; HELA CELL; HUMAN; METABOLISM; MOLECULAR CLONING; MOLECULAR GENETICS; RNA INTERFERENCE;

AMINO ACID SEQUENCE; CLONING, MOLECULAR; DNA PRIMERS; GENE EXPRESSION REGULATION; GENE SILENCING; HEK293 CELLS; HELA CELLS; HUMANS; INTERFERONS; MOLECULAR SEQUENCE DATA; RNA INTERFERENCE; RNA, DOUBLE-STRANDED; RNA, SMALL INTERFERING;

MAMMALIA;

EID: 84555187756     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-439-1_9     Document Type: Article

References (68)

1. Sontheimer, E. J., Carthew, R. W. (2005) Silence from within: endogenous siRNAs and miRNAs. Cell 122: 9-12. (Pubitemid 40977934)
2. Zamore, P. D., Haley, B. (2005) Ribo-gnome: the big world of small RNAs. Science 309: 1519-1524. (Pubitemid 41266468)
3. Filipowicz, W. (2005) RNAi: the nuts and bolts of the RISC machine. Cell 122: 17-20. (Pubitemid 40977936)
4. Tolia, N. H., Joshua-Tor, L. (2007) Slicer and the argonautes. Nat. Chem. Biol. 3: 36-43. (Pubitemid 46005696)
5. Elbashir, S. M., Harborth, J., Lendeckel, W., Yalcin, A., Weber, K., Tuschl, T. (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411: 494-498. (Pubitemid 32494397)
6. Manche, L., Green, S. R., Schmedt, C., Mathews, M. B. (1992) Interactions between doublestranded RNA regulators and the protein kinase DAI. Mol. Cell. Biol. 12: 5238-5248.
7. Svoboda, P. (2008) RNA silencing in mammalian oocytes and early embryos. Curr. Top. Microbiol. Immunol. 320: 225-256.
8. Mineno, J., Okamoto, S., Ando, T., Sato, M., Chono, H., Izu, H., Takayama, M., Asada, K., Mirochnitchenko, O., Inouye, M., Kato, I. (2006) The expression profi le of microRNAs in mouse embryos. Nucleic Acids Res. 34: 1765-1771.
9. Cummins, J. M., He, Y., Leary, R. J., Pagliarini, R., Diaz, L. A., Jr., Sjoblom, T., Barad, O., Bentwich, Z., Szafranska, A. E., Labourier, E., Raymond, C. K., Roberts, B. S., Juhl, H., Kinzler, K. W., Vogelstein, B., Velculescu, V. E. (2006) The colorectal microRNAome. Proc. Natl. Acad. Sci. USA 103: 3687-3692. (Pubitemid 43376616)
10. Liu, J., Carmell, M. A., Rivas, F. V., Marsden, C. G., Thomson, J. M., Song, J. J., Hammond, S. M., Joshua-Tor, L., Hannon, G. J. (2004) Argonaute2 is the catalytic engine of mammalian RNAi. Science 305: 1437-1441. (Pubitemid 39167657)
11. Meister, G., Landthaler, M., Patkaniowska, A., Dorsett, Y., Teng, G., Tuschl, T. (2004) Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol. Cells 15: 185-197. (Pubitemid 38950966)
12. Pillai, R. S., Artus, C. G., Filipowicz, W. (2004) Tethering of human AGO proteins to mRNA mimics the miRNA-mediated repression of protein synthesis. RNA - Publ. RNA Soc. 10: 1518-1525. (Pubitemid 39288186)
13. Song, J. J., Smith, S. K., Hannon, G. J., Joshua- Tor, L. (2004) Crystal structure of Argonaute and its implications for RISC slicer activity. Science 305: 1434-1437. (Pubitemid 39167656)
14. Doench, J. G., Petersen, C. P., Sharp, P. A. (2003) siRNAs can function as miRNAs. Genes Dev. 17: 438-442. (Pubitemid 36258757)
15. Hutvagner, G., Zamore, P. D. (2002) A microRNA in a multiple-turnover RNAi enzyme complex. Science 297: 2056-2060.
16. Yekta, S., Shih, I. H., Bartel, D. P. (2004) MicroRNA-directed cleavage of HOXB8 mRNA. Science 304: 594-596. (Pubitemid 38541919)
17. Brummelkamp, T. R., Bernards, R., Agami, R. (2002) A system for stable expression of short interfering RNAs in mammalian cells. Science 296: 550-553. (Pubitemid 34408678)
18. McManus, M. T., Petersen, C. P., Haines, B. B., Chen, J., Sharp, P. A. (2002) Gene silencing using micro-RNA designed hairpins. RNA - Publ. RNA Soc. 8: 842-850. (Pubitemid 34620459)
19. Paddison, P. J., Caudy, A. A., Bernstein, E., Hannon, G. J., Conklin, D. S. (2002) Short hairpin RNAs (shRNAs) induce sequence-specifi c silencing in mammalian cells. Genes Dev. 16: 948-958. (Pubitemid 34408544)
20. van de Wetering, M., Oving, I., Muncan, V., Pon Fong, M. T., Brantjes, H., van Leenen, D., Holstege, F. C., Brummelkamp, T. R., Agami, R., Clevers, H. (2003) Specifi c inhibition of gene expression using a stably integrated, inducible small-interfering-RNA vector. EMBO Rep. 4: 609-615. (Pubitemid 36939953)
21. Chung, K. H., Hart, C. C., Al-Bassam, S., Avery, A., Taylor, J., Patel, P. D., Vojtek, A. B., Turner, D. L. (2006) Polycistronic RNA polymerase II expression vectors for RNA interference based on BIC/miR-155. Nucleic Acids Res. 34 : e53.
22. Zeng, Y., Wagner, E. J., Cullen, B. R. (2002) Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells. Mol. Cells 9: 1327-1333. (Pubitemid 34722311)
23. de Veer, M. J., Sledz, C. A., Williams, B. R. (2005) Detection of foreign RNA: implications for RNAi. Immunol. Cell Biol. 83: 224-228. (Pubitemid 40799550)
24. Geiss, G., Jin, G., Guo, J., Bumgarner, R., Katze, M. G., Sen, G. C. (2001) A comprehensive view of regulation of gene expression by double-stranded RNA-mediated cell signaling. J. Biol. Chem. 276: 30178-30182.
25. Schlee, M., Hornung, V., Hartmann, G. (2006) siRNA and isRNA: two edges of one sword. Mol. Ther. 14: 463-470. (Pubitemid 44296098)
26. Sledz, C. A., Holko, M., de Veer, M. J., Silverman, R. H., Williams, B. R. (2003) Activation of the interferon system by shortinterfering RNAs. Nat. Cell Biol. 5: 834-839. (Pubitemid 37087172)
27. Bridge, A. J., Pebernard, S., Ducraux, A., Nicoulaz, A. L., Iggo, R. (2003) Induction of an interferon response by RNAi vectors in mammalian cells. Nature Genet. 34: 263-264. (Pubitemid 36792856)
28. Svoboda, P. (2007) Off-targeting and other nonspecifi c effects of RNAi experiments in mammalian cells. Curr. Opin. Mol. Ther. 9: 248-257. (Pubitemid 46944316)
29. Marques, J. T., Devosse, T., Wang, D., Zamanian-Daryoush, M., Serbinowski, P., Hartmann, R., Fujita, T., Behlke, M. A., Williams, B. R. (2006) A structural basis for discriminating between self and nonself double- stranded RNAs in mammalian cells. Nat. Biotechnol. 24: 559-565.
30. Kim, D. H., Longo, M., Han, Y., Lundberg, P., Cantin, E., Rossi, J. J. (2004) Interferon induction by siRNAs and ssRNAs synthesized by phage polymerase. Nat. Biotechnol. 22: 321-325. (Pubitemid 38295765)
31. Hornung, V., Ellegast, J., Kim, S., Brzozka, K., Jung, A., Kato, H., Poeck, H., Akira, S., Conzelmann, K. K., Schlee, M., Endres, S., Hartmann, G. (2006) 5'-Triphosphate RNA is the ligand for RIG-I. Science 314: 994-997.
32. Pichlmair, A., Schulz, O., Tan, C. P., Naslund, T. I., Liljestrom, P., Weber, F., Reis e Sousa, C. (2006) RIG-I-mediated antiviral responses to single-stranded RNA bearing 5'-phosphates. Science 314: 997-1001. (Pubitemid 44749946)
33. Pebernard, S., Iggo, R. D. (2004) Determinants of interferon-stimulated gene induction by RNAi vectors. Differentiation 72: 103-111. (Pubitemid 41702145)
34. Judge, A. D., Sood, V., Shaw, J. R., Fang, D., McClintock, K., MacLachlan, I. (2005) Sequence-dependent stimulation of the mammalian innate immune response by synthetic siRNA. Nat. Biotechnol. 23: 457-462. (Pubitemid 41724921)
35. Hornung, V., Guenthner-Biller, M., Bourquin, C., Ablasser, A., Schlee, M., Uematsu, S., Noronha, A., Manoharan, M., Akira, S., de Fougerolles, A., Endres, S., Hartmann, G. (2005) Sequence-specifi c potent induction of IFN-alpha by short interfering RNA in plasmacytoid dendritic cells through TLR7. Nat. Med. 11: 263-270. (Pubitemid 40460553)
36. Sioud, M. (2005) Induction of infl ammatory cytokines and interferon responses by doublestranded and single-stranded siRNAs is sequence-dependent and requires endosomal localization. J. Mol. Biol. 348: 1079-1090. (Pubitemid 40602367)
37. Marques, J. T., Williams, B. R. (2005) Activation of the mammalian immune system by siRNAs. Nat. Biotechnol. 23: 1399-1405. (Pubitemid 41679392)
38. Jackson, A. L., Bartz, S. R., Schelter, J., Kobayashi, S. V., Burchard, J., Mao, M., Li, B., Cavet, G., Linsley, P. S. (2003) Expression profi ling reveals off-target gene regulation by RNAi. Nat. Biotechnol. 21: 635-637. (Pubitemid 36638089)
39. Jackson, A. L., Burchard, J., Schelter, J., Chau, B. N., Cleary, M., Lim, L., Linsley, P. S. (2006) Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity. RNA - Publ. RNA Soc. 12: 1179-1187. (Pubitemid 43990543)
40. Scacheri, P. C., Rozenblatt-Rosen, O., Caplen, N. J., Wolfsberg, T. G., Umayam, L., Lee, J. C., Hughes, C. M., Shanmugam, K. S., Bhattacharjee, A., Meyerson, M., Collins, F. S. (2004) Short interfering RNAs can induce unexpected and divergent changes in the levels of untargeted proteins in mammalian cells. Proc. Natl. Acad. Sci. USA 101: 1892-1897. (Pubitemid 38228987)
41. Brown, K., Samarsky, D. (2005) RNAi off-targeting: Light at the end of the tunnel. J. RNAi Gene Silencing 2: 175-177.
42. Echeverri, C. J., Beachy, P. A., Baum, B., Boutros, M., Buchholz, F., Chanda, S. K., Downward, J., Ellenberg, J., Fraser, A. G., Hacohen, N., Hahn, W. C., Jackson, A. L., Kiger, A., Linsley, P. S., Lum, L., Ma, Y., Mathey-Prevot, B., Root, D. E., Sabatini, D. M., Taipale, J., Perrimon, N., Bernards, R. (2006) Minimizing the risk of reporting false positives in large-scale RNAi screens. Nat. Methods 3: 777-779. (Pubitemid 44445821)
43. Snove, O., Jr., Holen, T. (2004) Many commonly used siRNAs risk off-target activity. Biochem. Biophys. Res. Commun. 319: 256-263. (Pubitemid 38670188)
44. Jackson, A. L., Burchard, J., Leake, D., Reynolds, A., Schelter, J., Guo, J., Johnson, J. M., Lim, L., Karpilow, J., Nichols, K., Marshall, W., Khvorova, A., Linsley, P. S. (2006) Positionspecifi c chemical modifi cation of siRNAs reduces "off-target" transcript silencing. RNA - Publ. RNA Soc. 12: 1197-1205. (Pubitemid 43990545)
45. Birmingham, A., Anderson, E., Sullivan, K., Reynolds, A., Boese, Q., Leake, D., Karpilow, J., Khvorova, A. (2007) A protocol for designing siRNAs with high functionality and specifi city. Nat. Protoc. 2: 2068-2078. (Pubitemid 351565844)
46. Peek, A. S., Behlke, M. A. (2007) Design of active small interfering RNAs. Curr. Opin. Mol. Ther. 9: 110-118. (Pubitemid 46623942)
47. Huesken, D., Lange, J., Mickanin, C., Weiler, J., Asselbergs, F., Warner, J., Meloon, B., Engel, S., Rosenberg, A., Cohen, D., Labow, M., Reinhardt, M., Natt, F., Hall, J. (2005) Design of a genome-wide siRNA library using an artifi cial neural network. Nat. Biotechnol. 23: 995-1001. (Pubitemid 41114034)
48. Tafer, H., Ameres, S. L., Obernosterer, G., Gebeshuber, C. A., Schroeder, R., Martinez, J., Hofacker, I. L. (2008) The impact of target site accessibility on the design of effective siRNAs. Nat. Biotechnol. 26: 578-583. (Pubitemid 351668044)
49. Chalk, A. M., Sonnhammer, E. L. L. (2008) siRNA specifi city searching incorporating mismatch tolerance data. Bioinformatics 24: 1316-1317. (Pubitemid 351659633)
50. Matveeva, O., Nechipurenko, Y., Rossi, L., Moore, B., Saetrom, P., Ogurtsov, A. Y., Atkins, J. F., Shabalina, S. A. (2007) Comparison of approaches for rational siRNA design leading to a new effi cient and transparent method. Nucleic Acids Res. 35: e63.
51. Ameres, S. L., Martinez, J., Schroeder, R. (2007) Molecular basis for target RNA recognition and cleavage by human RISC. Cell 130: 101-112. (Pubitemid 47031315)
52. Vert, J. P., Foveau, N., Lajaunie, C., Vandenbrouck, Y. (2006) An accurate and interpretable model for siRNA effi cacy prediction. BMC Bioinformatics 7: 520.
53. Sambrook, J., Fritsch, E. F., Maniatis, T. (1989) Molecular cloning 2nd ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
54. Reynolds, A., Anderson, E. M., Vermeulen, A., Fedorov, Y., Robinson, K., Leake, D., Karpilow, J., Marshall, W. S., Khvorova, A. (2006) Induction of the interferon response by siRNA is cell type- and duplex length-dependent. RNA - Publ. RNA Soc. 12: 988-993. (Pubitemid 43788117)
55. Schmitter, D., Filkowski, J., Sewer, A., Pillai, R. S., Oakeley, E. J., Zavolan, M., Svoboda, P., Filipowicz, W. (2006) Effects of Dicer and Argonaute down-regulation on mRNA levels in human HEK293 cells. Nucleic Acids Res. 34: 4801-4815. (Pubitemid 44605625)
56. Zeng, Y., Cai, X., Cullen, B. R. (2005) Use of RNA polymerase II to transcribe artifi cial microRNAs. Methods Enzymol. 392: 371-380. (Pubitemid 40092526)
57. Abe, Y., Sinozaki, H., Takagi, T., Minegishi, T., Kokame, K., Kangawa, K., Uesaka, M., Miyamoto, K. (2006) Identifi cation of 2,3,7,8- tetrachlorodibenzo-p-dioxin (TCDD)- inducible genes in human amniotic epithelial cells. Reprod. Biol. Endocrinol. 4: 27.
58. Hu, X., Herrero, C., Li, W. P., Antoniv, T. T., Falck-Pedersen, E., Koch, A. E., Woods, J. M., Haines, G. K., Ivashkiv, L. B. (2002) Sensitization of IFN-gamma Jak-STAT signaling during macrophage activation. Nat. Immunol. 3: 859-866.
59. Kato, A., Homma, T., Batchelor, J., Hashimoto, N., Imai, S., Wakiguchi, H., Saito, H., Matsumoto, K. (2003) Interferon-alpha/beta receptor-mediated selective induction of a gene cluster by CpG oligodeoxynucleotide 2006. BMC Immunol. 4: 8.
60. Kamezaki, K., Shimoda, K., Numata, A., Matsuda, T., Nakayama, K., Harada, M. (2004) The role of Tyk2, Stat1 and Stat4 in LPSinduced endotoxin signals. Int. Immunol. 16: 1173-1179. (Pubitemid 39136734)
61. Sakamoto, S., Qin, J., Navarro, A., Gamero, A., Potla, R., Yi, T., Zhu, W., Baker, D. P., Feldman, G., Larner, A. C. (2004) Cells Previously Desensitized to Type 1 Interferons Display Different Mechanisms of Activation of Stat-dependent Gene Expression from Naive Cells. J. Biol. Chem. 279: 3245-3253. (Pubitemid 38140558)
62. Wang, Z. W., Sarmento, L., Wang, Y., Li, X.-q., Dhingra, V., Tseggai, T., Jiang, B., Fu, Z. F. (2005) Attenuated Rabies Virus Activates, while Pathogenic Rabies Virus Evades, the Host Innate Immune Responses in the Central Nervous System. J. Virol. 79: 12554-12565. (Pubitemid 41346118)
63. Stewart, M. J., Smoak, K., Blum, M. A., Sherry, B. (2005) Basal and Reovirus-Induced Beta Interferon (IFN-{beta}) and IFN-{beta}- Stimulated Gene Expression Are Cell Type Specifi c in the Cardiac Protective Response. J. Virol. 79: 2979-2987. (Pubitemid 40270577)
64. Pauls, E., Senserrich, J., Bofi ll, M., Clotet, B., Este, J. A. (2007) Induction of interleukins IL-6 and IL-8 by siRNA. Clin. Exp. Immunol. 147: 189-196. (Pubitemid 44915571)
65. Yang, R., Murillo, F. M., Cui, H., Blosser, R., Uematsu, S., Takeda, K., Akira, S., Viscidi, R. P., Roden, R. B. S. (2004) Papillomavirus-Like Particles Stimulate Murine Bone Marrow- Derived Dendritic Cells To Produce Alpha Interferon and Th1 Immune Responses via MyD88. J. Virol. 78: 11152-11160. (Pubitemid 39299655)
66. Bolcato-Bellemin, A.-L., Bonnet, M.-E., Creusat, G., Erbacher, P., Behr, J.-P. (2007) Sticky overhangs enhance siRNA-mediated gene silencing. Proc. Natl. Acad. Sci. USA 104: 16050-16055. (Pubitemid 350099361)
67. Cekaite, L., Furset, G., Hovig, E., Sioud, M. (2007) Gene expression analysis in blood cells in response to unmodifi ed and 2'-modifi ed siRNAs reveals TLR-dependent and independent effects. J. Mol. Biol. 365: 90-108. (Pubitemid 44830036)
68. Persengiev, S. P., Zhu, X., Green, M. R. (2004) Nonspecifi c, concentration-dependent stimulation and repression of mammalian gene expression by small interfering RNAs (siRNAs). RNA - Publ. RNA Soc. 10: 12-18. (Pubitemid 38018731)