SiSPOTR: A tool for designing highly specific and potent siRNAs for human and mouse

Nucleic Acids Research

Volumn 41, Issue 1, 2013, Pages

  Boudreau, Ryan L ^a   Spengler, Ryan M ^b   Hylock, Ray H ^b   Kusenda, Brandyn J ^b   Davis, Heather A ^b   Eichmann, David A ^b   Davidson, Beverly L ^a,b  

^a UNIVERSITY OF IOWA   (United States)

^b UNIVERSITY OF IOWA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SMALL INTERFERING RNA;

ARTICLE; BIOINFORMATICS; BRAIN; DRUG DESIGN; DRUG IDENTIFICATION; DRUG POTENCY; DRUG SPECIFICITY; DRUG TOLERANCE; GENE EXPRESSION; GENE IDENTIFICATION; GENE OFF TARGETING; GENE SILENCING; GENE TARGETING; GENETIC ALGORITHM; HUMAN; INTERMETHOD COMPARISON; MICROARRAY ANALYSIS; MOUSE; NONHUMAN; ONLINE SYSTEM; PRIORITY JOURNAL; RNA INTERFERENCE; RNA SEQUENCE; VALIDATION PROCESS;

ALGORITHMS; ANIMALS; CELL LINE; GENOME; HUMANS; MICE; RNA INTERFERENCE; RNA, SMALL INTERFERING; SOFTWARE; TRANSCRIPTOME;

EID: 84871768648     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks797     Document Type: Article

References (51)

1. Provost, P., Dishart, D., Doucet, J., Frendewey, D., Samuelsson, B. and Radmark, O. (2002) Ribonuclease activity and RNA binding of recombinant human Dicer. EMBO J., 21, 5864-5874.
2. Davidson, B.L. and McCray, P.B. Jr (2011) Current prospects for RNA interference-based therapies. Nat. Rev. Genet., 12, 329-340.
3. Chi, J.T., Chang, H.Y., Wang, N.N., Chang, D.S., Dunphy, N. and Brown, P.O. (2003) Genomewide view of gene silencing by small interfering RNAs. Proc. Natl. Acad. Sci. USA, 100, 6343-6346.
4. Semizarov, D., Frost, L., Sarthy, A., Kroeger, P., Halbert, D.N. and Fesik, S.W. (2003) Specificity of short interfering RNA determined through gene expression signatures. Proc. Natl. Acad. Sci. USA, 100, 6347-6352.
5. Jackson, A.L., Bartz, S.R., Schelter, J., Kobayashi, S.V., Burchard, J., Mao, M., Li, B., Cavet, G. and Linsley, P.S. (2003) Expression profiling reveals off-target gene regulation by RNAi. Nat. Biotechnol., 21, 635-637.
6. Jackson, A.L., Burchard, J., Schelter, J., Chau, B.N., Cleary, M., Lim, L. and Linsley, P.S. (2006) Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity. RNA, 12, 1179-1187.
7. Lewis, B.P., Burge, C.B. and Bartel, D.P. (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell, 120, 15-20.
8. Guo, H., Ingolia, N.T., Weissman, J.S. and Bartel, D.P. (2010) Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature, 466, 835-840.
9. Birmingham, A., Anderson, E.M., Reynolds, A., Ilsley-Tyree, D., Leake, D., Fedorov, Y., Baskerville, S., Maksimova, E., Robinson, K., Karpilow, J. et al. (2006) 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat. Methods, 3, 199-204.
10. Ma, Y., Creanga, A., Lum, L. and Beachy, P.A. (2006) Prevalence of off-target effects in Drosophila RNA interference screens. Nature, 443, 359-363.
11. Schultz, N., Marenstein, D.R., De Angelis, D.A., Wang, W.Q., Nelander, S., Jacobsen, A., Marks, D.S., Massague, J. and Sander, C. (2011) Off-target effects dominate a large-scale RNAi screen for modulators of the TGF-beta pathway and reveal microRNA regulation of TGFBR2. Silence, 2, 3.
12. Fedorov, Y., Anderson, E.M., Birmingham, A., Reynolds, A., Karpilow, J., Robinson, K., Leake, D., Marshall, W.S. and Khvorova, A. (2006) Off-target effects by siRNA can induce toxic phenotype. RNA, 12, 1188-1196.
13. Anderson, E.M., Birmingham, A., Baskerville, S., Reynolds, A., Maksimova, E., Leake, D., Fedorov, Y., Karpilow, J. and Khvorova, A. (2008) Experimental validation of the importance of seed complement frequency to siRNA specificity. RNA, 14, 853-861.
14. Birmingham, A., Anderson, E., Sullivan, K., Reynolds, A., Boese, Q., Leake, D., Karpilow, J. and Khvorova, A. (2007) A protocol for designing siRNAs with high functionality and specificity. Nat. Protoc., 2, 2068-2078.
15. Naito, Y., Yamada, T., Ui-Tei, K., Morishita, S. and Saigo, K. (2004) siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference. Nucleic Acids Res., 32, W124-129.
16. Jackson, A.L. and Linsley, P.S. (2010) Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application. Nat. Rev. Drug Discov., 9, 57-67.
17. Boudreau, R.L., Spengler, R.M. and Davidson, B.L. (2011) Rational design of therapeutic siRNAs: minimizing off-targeting potential to improve the safety of RNAi therapy for Huntington's disease. Mol. Ther., 19, 2169-2177.
18. Moffat, J., Grueneberg, D.A., Yang, X., Kim, S.Y., Kloepfer, A.M., Hinkle, G., Piqani, B., Eisenhaure, T.M., Luo, B., Grenier, J.K. et al. (2006) A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell, 124, 1283-1298.
19. McBride, J.L., Pitzer, M.R., Boudreau, R.L., Dufour, B., Hobbs, T., Ojeda, S.R. and Davidson, B.L. (2011) Preclinical safety of RNAi-mediated HTT suppression in the rhesus macaque as a potential therapy for Huntington's disease. Mol. Ther., 19, 2152-2162.
20. Garcia, D.M., Baek, D., Shin, C., Bell, G.W., Grimson, A. and Bartel, D.P. (2011) Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat. Struct. Mol. Biol., 18, 1139-1146.
21. Karolchik, D., Hinrichs, A.S., Furey, T.S., Roskin, K.M., Sugnet, C.W., Haussler, D. and Kent, W.J. (2004) The UCSC Table Browser data retrieval tool. Nucleic Acids Res., 32, D493-496.
22. Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M. and Haussler, D. (2002) The human genome browser at UCSC. Genome Res., 12, 996-1006.
23. Fujita, P.A., Rhead, B., Zweig, A.S., Hinrichs, A.S., Karolchik, D., Cline, M.S., Goldman, M., Barber, G.P., Clawson, H., Coelho, A. et al. (2011) The UCSC Genome Browser database: update 2011. Nucleic Acids Res., 39, D876-D882.
24. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W. et al. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
25. Pruitt, K.D., Tatusova, T. and Maglott, D.R. (2005) NCBI reference sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 33, D501-D504.
26. Wang, X., Wang, X., Varma, R.K., Beauchamp, L., Magdaleno, S. and Sendera, T.J. (2009) Selection of hyperfunctional siRNAs with improved potency and specificity. Nucleic Acids Res., 37, e152.
27. Wu, C., Orozco, C., Boyer, J., Leglise, M., Goodale, J., Batalov, S., Hodge, C.L., Haase, J., Janes, J., Huss, J.W. 3rd et al. (2009) BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol., 10, R130.
28. Su, A.I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K.A., Block, D., Zhang, J., Soden, R., Hayakawa, M., Kreiman, G. et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. USA, 101, 6062-6067.
29. Vert, J.P., Foveau, N., Lajaunie, C. and Vandenbrouck, Y. (2006) An accurate and interpretable model for siRNA efficacy prediction. BMC Bioinformatics, 7, 520.
30. Goecks, J., Nekrutenko, A. and Taylor, J. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, R86.
31. Blankenberg, D., Von Kuster, G., Coraor, N., Ananda, G., Lazarus, R., Mangan, M., Nekrutenko, A. and Taylor, J. (2010) Galaxy: a web-based genome analysis tool for experimentalists. Curr. Protoc. Mol. Biol., Chapter 19, Unit 19.10.1-21.
32. Giardine, B., Riemer, C., Hardison, R.C., Burhans, R., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J. et al. (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res., 15, 1451-1455.
33. Schwarz, D.S., Hutvagner, G., Du, T., Xu, Z., Aronin, N. and Zamore, P.D. (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell, 115, 199-208.
34. Khvorova, A., Reynolds, A. and Jayasena, S.D. (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell, 115, 209-216.
35. Matveeva, O., Nechipurenko, Y., Rossi, L., Moore, B., Saetrom, P., Ogurtsov, A.Y., Atkins, J.F. and Shabalina, S.A. (2007) Comparison of approaches for rational siRNA design leading to a new efficient and transparent method. Nucleic Acids Res., 35, e63.
36. Huesken, D., Lange, J., Mickanin, C., Weiler, J., Asselbergs, F., Warner, J., Meloon, B., Engel, S., Rosenberg, A., Cohen, D. et al. (2005) Design of a genome-wide siRNA library using an artificial neural network. Nat. Biotechnol., 23, 995-1001.
37. Miller, V., Gouvion, C., Davidson, B. and Paulson, H. (2004) Targeting Alzheimer's disease genes with RNA interference: an efficient strategy for silencing mutant allele. Nucleic Acids Res., 32, 661-668.
38. Nielsen, C.B., Shomron, N., Sandberg, R., Hornstein, E., Kitzman, J. and Burge, C.B. (2007) Determinants of targeting by endogenous and exogenous microRNAs and siRNAs. RNA, 13, 1894-1910.
39. Doench, J.G. and Sharp, P.A. (2004) Specificity of microRNA target selection in translational repression. Genes Dev., 18, 504-511.
40. Grimson, A., Farh, K.K., Johnston, W.K., Garrett-Engele, P., Lim, L.P. and Bartel, D.P. (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell., 27, 91-105.
41. Burchard, J., Jackson, A.L., Malkov, V., Needham, R.H., Tan, Y., Bartz, S.R., Dai, H., Sachs, A.B. and Linsley, P.S. (2009) MicroRNA-like off-target transcript regulation by siRNAs is species specific. RNA, 15, 308-315.
42. Jackson, A.L., Burchard, J., Leake, D., Reynolds, A., Schelter, J., Guo, J., Johnson, J.M., Lim, L., Karpilow, J., Nichols, K. et al. (2006) Position-specific chemical modification of siRNAs reduces "off-target" transcript silencing. RNA, 12, 1197-1205.
43. Bramsen, J.B., Pakula, M.M., Hansen, T.B., Bus, C., Langkjaer, N., Odadzic, D., Smicius, R., Wengel, S.L., Chattopadhyaya, J., Engels, J.W. et al. (2010) A screen of chemical modifications identifies position-specific modification by UNA to most potently reduce siRNA off-target effects. Nucleic Acids Res., 38, 5761-5773.
44. Vaish, N., Chen, F., Seth, S., Fosnaugh, K., Liu, Y., Adami, R., Brown, T., Chen, Y., Harvie, P., Johns, R. et al. (2011) Improved specificity of gene silencing by siRNAs containing unlocked nucleobase analogs. Nucleic Acids Res., 39, 1823-1832.
45. Sigoillot, F.D., Lyman, S., Huckins, J.F., Adamson, B., Chung, E., Quattrochi, B. and King, R.W. (2012) A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens. Nat. Methods, 9, 363-366.
46. Zhang, X.D., Santini, F., Lacson, R., Marine, S.D., Wu, Q., Benetti, L., Yang, R., McCampbell, A., Berger, J.P., Toolan, D.M. et al. (2011) cSSMD: assessing collective activity for addressing off-target effects in genome-scale RNA interference screens. Bioinformatics, 27, 2775-2781.
47. Caffrey, D.R., Zhao, J., Song, Z., Schaffer, M.E., Haney, S.A., Subramanian, R.R., Seymour, A.B. and Hughes, J.D. (2011) siRNA off-target effects can be reduced at concentrations that match their individual potency. PLoS One, 6, e21503.
48. Grimm, D., Streetz, K.L., Jopling, C.L., Storm, T.A., Pandey, K., Davis, C.R., Marion, P., Salazar, F. and Kay, M.A. (2006) Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways. Nature, 441, 537-541.
49. McBride, J.L., Boudreau, R.L., Harper, S.Q., Staber, P.D., Monteys, A.M., Martins, I., Gilmore, B.L., Burstein, H., Peluso, R.W., Polisky, B. et al. (2008) Artificial miRNAs mitigate shRNA-mediated toxicity in the brain: implications for the therapeutic development of RNAi. Proc. Natl. Acad. Sci. USA, 105, 5868-5873.
50. Boudreau, R.L., Martins, I. and Davidson, B.L. (2009) Artificial microRNAs as siRNA shuttles: improved safety as compared to shRNAs in vitro and in vivo. Mol. Ther., 17, 169-175.
51. Martin, J.N., Wolken, N., Brown, T., Dauer, W.T., Ehrlich, M.E. and Gonzalez-Alegre, P. (2011) Lethal toxicity caused by expression of shRNA in the mouse striatum: implications for therapeutic design. Gene Ther., 18, 666-673.