The effects of stem length and core placement on shRNA activity

BMC Molecular Biology

Volumn 12, Issue , 2011, Pages

  Mcintyre, Glen J ^a,b   Yu, Yi Hsin ^a,b   Lomas, Mehnaaz ^a   Fanning, Gregory C ^a,c  

^a JOHNSON AND JOHNSON   (United States)

^b UNIVERSITY OF NEW SOUTH WALES   (Australia)

^c TIBOTEC BVBA   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

DICER; SHORT HAIRPIN RNA; TRANSACTIVATOR PROTEIN; VPU PROTEIN; SMALL INTERFERING RNA;

ARTICLE; CONTROLLED STUDY; CORE PLACEMENT; GENE ACTIVITY; GENE REPRESSION; GENE SILENCING; GENETIC ALGORITHM; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS 1; LENGTH OF STAY; NUCLEOTIDE SEQUENCE; PROTEIN PROCESSING; RNA INTERFERENCE; RNA PROCESSING; RNA SEQUENCE; RNA STRUCTURE; RNA TRANSCRIPTION; STEM LENGTH; TERMINAL SEQUENCE; CELL STRAIN HEK293; CHEMISTRY; GENE VECTOR; GENETICS; METABOLISM; MOLECULAR GENETICS;

HUMAN IMMUNODEFICIENCY VIRUS 1; MAMMALIA;

BASE SEQUENCE; GENETIC VECTORS; HEK293 CELLS; HUMANS; MOLECULAR SEQUENCE DATA; RNA INTERFERENCE; RNA, SMALL INTERFERING;

EID: 79961102375     PISSN: None     EISSN: 14712199     Source Type: Journal    
DOI: 10.1186/1471-2199-12-34     Document Type: Article

References (58)

1. Zeng Y, Cullen BR. Efficient processing of primary microRNA hairpins by Drosha requires flanking non-structured RNA sequences. J Biol Chem 2005, 280(30):27595-27603. 10.1074/jbc.M504714200, 15932881.
2. Kim VN. MicroRNA precursors in motion: exportin-5 mediates their nuclear export. Trends Cell Biol 2004, 14(4):156-159. 10.1016/j.tcb.2004.02.006, 15134074.
3. Zeng Y, Cullen BR. Structural requirements for pre-microRNA binding and nuclear export by Exportin 5. Nucleic Acids Res 2004, 32(16):4776-4785. 10.1093/nar/gkh824, 519115, 15356295.
4. Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD. Asymmetry in the assembly of the RNAi enzyme complex. Cell 2003, 115(2):199-208. 10.1016/S0092-8674(03)00759-1, 14567917.
5. Elbashir SM, Lendeckel W, Tuschl T. RNA interference is mediated by 21-and 22-nucleotide RNAs. Genes Dev 2001, 15(2):188-200. 10.1101/gad.862301, 312613, 11157775.
6. Provost P, Dishart D, Doucet J, Frendewey D, Samuelsson B, Radmark O. Ribonuclease activity and RNA binding of recombinant human Dicer. EMBO J 2002, 21(21):5864-5874. 10.1093/emboj/cdf578, 131075, 12411504.
7. Brummelkamp TR, Bernards R, Agami R. A system for stable expression of short interfering RNAs in mammalian cells. Science 2002, 296(5567):550-553. 10.1126/science.1068999, 11910072.
8. Lee NS, Dohjima T, Bauer G, Li H, Li MJ, Ehsani A, Salvaterra PM, Rossi JJ. Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells. Nat Biotechnol 2002, 20(5):500-505.
9. McManus M, Petersen CP, Haines BB, Chen J, Sharp PA. Gene silencing using micro-RNA designed hairpins. Rna 2002, 8(6):842-850. 10.1017/S1355838202024032, 1370301, 12088155.
10. Miyagishi M, Taira K. U6 promoter-driven siRNAs with four uridine 3' overhangs efficiently suppress targeted gene expression in mammalian cells. Nat Biotechnol 2002, 20(5):497-500. 10.1038/nbt0502-497, 11981564.
11. Paddison PJ, Caudy AA, Hannon GJ. Stable suppression of gene expression by RNAi in mammalian cells. Proc Natl Acad Sci USA 2002, 99(3):1443-1448. 10.1073/pnas.032652399, 122210, 11818553.
12. Paul CP, Good PD, Winer I, Engelke DR. Effective expression of small interfering RNA in human cells. Nat Biotechnol 2002, 20(5):505-508. 10.1038/nbt0502-505, 11981566.
13. Sui G, Soohoo C, Affar el B, Gay F, Shi Y, Forrester WC. A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc Natl Acad Sci USA 2002, 99(8):5515-5520. 10.1073/pnas.082117599, 122801, 11960009.
14. Yu JY, DeRuiter SL, Turner DL. RNA interference by expression of short-interfering RNAs and hairpin RNAs in mammalian cells. Proc Natl Acad Sci USA 2002, 99(9):6047-6052. 10.1073/pnas.092143499, 122899, 11972060.
15. Reynolds A, Leake D, Boese Q, Scaringe S, Marshall WS, Khvorova A. Rational siRNA design for RNA interference. Nat Biotechnol 2004, 22(3):326-330. 10.1038/nbt936, 14758366.
16. Yu JY, Taylor J, DeRuiter SL, Vojtek AB, Turner DL. Simultaneous inhibition of GSK3alpha and GSK3beta using hairpin siRNA expression vectors. Mol Ther 2003, 7(2):228-236. 10.1016/S1525-0016(02)00037-0, 12597911.
17. Paddison PJ, Caudy AA, Bernstein E, Hannon GJ, Conklin DS. Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev 2002, 16(8):948-958. 10.1101/gad.981002, 152352, 11959843.
18. Miyagishi M, Sumimoto H, Miyoshi H, Kawakami Y, Taira K. Optimization of an siRNA-expression system with an improved hairpin and its significant suppressive effects in mammalian cells. J Gene Med 2004, 6(7):715-723. 10.1002/jgm.556, 15241778.
19. Jeanson-Leh L, Blondeau J, Galy A. Optimization of short hairpin RNA for lentiviral-mediated RNAi against WAS. Biochemical and Biophysical Research Communications 2007, 362(2):498-503. 10.1016/j.bbrc.2007.08.013, 17719003.
20. Rose SD, Kim D, Amarzguioui M, Heidel JD, Collingwood MA, Davis ME, Rossi JJ, Behlke MA. Functional polarity is introduced by Dicer processing of short substrate RNAs. Nucleic Acids Res 2005, 33(13):4140-4156. 10.1093/nar/gki732, 1180746, 16049023.
21. Kim DH, Behlke MA, Rose SD, Chang MS, Choi S, Rossi JJ. Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy. Nat Biotechnol 2005, 23(2):222-226. 10.1038/nbt1051, 15619617.
22. Siolas D, Lerner C, Burchard J, Ge W, Linsley PS, Paddison PJ, Hannon GJ, Cleary MA. Synthetic shRNAs as potent RNAi triggers. Nat Biotechnol 2005, 23(2):227-231. 10.1038/nbt1052, 15619616.
23. Cullen BR. Derivation and function of small interfering RNAs and microRNAs. Virus Res 2004, 102(1):3-9. 10.1016/j.virusres.2004.01.009, 15068874.
24. Castanotto D, Scherer L. Targeting Cellular Genes with PCR Cassettes Expressing Short Interfering RNAs. Methods Enzymol 2005, 392:173-185.
25. Li L, Lin X, Khvorova A, Fesik S, Shen Y. Defining the optimal parameters for hairpin-based knockdown constructs. RNA 2007, 13(10):1765-1774. 10.1261/rna.599107, 1986814, 17698642.
26. Zhang H, Kolb FA, Brondani V, Billy E, Filipowicz W. Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J 2002, 21(21):5875-5885. 10.1093/emboj/cdf582, 131079, 12411505.
27. Vermeulen A, Behlen L, Reynolds A, Wolfson A, Marshall WS, Karpilow J, Khvorova A. The contributions of dsRNA structure to Dicer specificity and efficiency. Rna 2005, 11(5):674-682. 10.1261/rna.7272305, 1370754, 15811921.
28. Zhang H, Kolb FA, Jaskiewicz L, Westhof E, Filipowicz W. Single processing center models for human Dicer and bacterial RNase III. Cell 2004, 118(1):57-68. 10.1016/j.cell.2004.06.017, 15242644.
29. Lee MT, Coburn GA, McClure MO, Cullen BR. Inhibition of human immunodeficiency virus type 1 replication in primary macrophages by using Tat- or CCR5-specific small interfering RNAs expressed from a lentivirus vector. J Virol 2003, 77(22):11964-11972. 10.1128/JVI.77.22.11964-11972.2003, 254276, 14581533.
30. Paddison PJ, Silva JM, Conklin DS, Schlabach M, Li M, Aruleba S, Balija V, O'Shaughnessy A, Gnoj L, Scobie K, et al. A resource for large-scale RNA-interference-based screens in mammals. Nature 2004, 428:427-431. 10.1038/nature02370, 15042091.
31. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003, 31(13):3406-3415. 10.1093/nar/gkg595, 169194, 12824337.
32. Dykxhoorn DM, Novina CD, Sharp PA. Killing the messenger: short RNAs that silence gene expression. Nat Rev Mol Cell Biol 2003, 4(6):457-467.
33. McIntyre GJ, Fanning GC. Design and cloning strategies for constructing shRNA expression vectors. BMC Biotechnol 2006, 6:1. 10.1186/1472-6750-6-1, 1343552, 16396676.
34. Williams BR. Dicing with siRNA. Nat Biotechnol 2005, 23(2):181-182. 10.1038/nbt0205-181, 15696144.
35. Lau NC, Lim LP, Weinstein EG, Bartel DP. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 2001, 294(5543):858-862. 10.1126/science.1065062, 11679671.
36. Chu C-Y, Rana TM. Potent RNAi by short RNA triggers. RNA 2008, 14(9):1714-1719. 10.1261/rna.1161908, 2525957, 18658119.
37. Lee Y, Jeon K, Lee JT, Kim S, Kim VN. MicroRNA maturation: stepwise processing and subcellular localization. EMBO J 2002, 21(17):4663-4670. 10.1093/emboj/cdf476, 126204, 12198168.
38. Paddison PJ, Cleary M, Silva JM, Chang K, Sheth N, Sachidanandam R, Hannon GJ. Cloning of short hairpin RNAs for gene knockdown in mammalian cells. Nat Methods 2004, 1(2):163-167. 10.1038/nmeth1104-163, 16144086.
39. Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark O, Kim S, Kim VN. The nuclear RNase III Drosha initiates microRNA processing. Nature 2003, 425:415-419. 10.1038/nature01957, 14508493.
40. Bridge AJ, Pebernard S, Ducraux A, Nicoulaz AL, Iggo RD. Induction of an interferon response by RNAi vectors in mammalian cells. Nat Genet 2003, 34:263-264. 10.1038/ng1173, 12796781.
41. Fish RJ, Kruithof EK. Short-term cytotoxic effects and long-term instability of RNAi delivered using lentiviral vectors. BMC Mol Biol 2004, 5:9. 10.1186/1471-2199-5-9, 514603, 15291968.
42. Hannon GJ, Rossi JJ. Unlocking the potential of the human genome with RNA interference. Nature 2004, 431:371-378. 10.1038/nature02870, 15372045.
43. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297. 10.1016/S0092-8674(04)00045-5, 14744438.
44. Zeng Y, Wagner EJ, Cullen BR. Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells. Mol Cell 2002, 9:1327-1333. 10.1016/S1097-2765(02)00541-5, 12086629.
45. Boden D, Pusch O, Silbermann R, Lee F, Tucker L, Ramratnam B. Enhanced gene silencing of HIV-1 specific siRNA using microRNA designed hairpins. Nucleic Acids Res 2004, 32:1154-1158. 10.1093/nar/gkh278, 373410, 14966264.
46. Dickins RA, Hemann MT, Zilfou JT, Simpson DR, Ibarra I, Hannon GJ, Lowe SW. Probing tumor phenotypes using stable and regulated synthetic microRNA precursors. Nat Genet 2005, 37(11):1289-1295.
47. Silva JM, Li MZ, Chang K, Ge W, Golding MC, Rickles RJ, Siolas D, Hu G, Paddison PJ, Schlabach MR, et al. Second-generation shRNA libraries covering the mouse and human genomes. Nat Genet 2005, 37(11):1281-1288.
48. Zeng Y, Cai X, Cullen BR. Use of RNA Polymerase II to Transcribe Artificial MicroRNAs. Methods Enzymol 2005, 392:371-380.
49. Boudreau RL, Monteys AM, Davidson BL. Minimizing variables among hairpin-based RNAi vectors reveals the potency of shRNAs. RNA 2008, 14(9):1834-1844. 10.1261/rna.1062908, 2525944, 18697922.
50. Kim VN. MicroRNA biogenesis: coordinated cropping and dicing. Nat Rev Mol Cell Biol 2005, 6(5):376-385.
51. Lee NS, Rossi JJ. Control of HIV-1 replication by RNA interference. Virus Res 2004, 102:53-58. 10.1016/j.virusres.2004.01.015, 15068880.
52. Yi R, Doehle BP, Qin Y, Macara IG, Cullen BR. Overexpression of exportin 5 enhances RNA interference mediated by short hairpin RNAs and microRNAs. Rna 2005, 11:220-226. 10.1261/rna.7233305, 1370710, 15613540.
53. Pusch O, Boden D, Silbermann R, Lee F, Tucker L, Ramratnam B. Nucleotide sequence homology requirements of HIV-1-specific short hairpin RNA. Nucleic Acids Res 2003, 31:6444-6449. 10.1093/nar/gkg876, 275570, 14602902.
54. Holen T, Amarzguioui M, Wiiger MT, Babaie E, Prydz H. Positional effects of short interfering RNAs targeting the human coagulation trigger Tissue Factor. Nucleic Acids Res 2002, 30:1757-1766. 10.1093/nar/30.8.1757, 113209, 11937629.
55. Vlassov AV, Korba B, Farrar K, Mukerjee S, Seyhan AA, Ilves H, Kaspar RL, Leake D, Kazakov SA, Johnston BH. shRNAs Targeting Hepatitis C: Effects of Sequence and Structural Features, and Comparision with siRNA. Oligonucleotides 2007, 17(2):223-236. 10.1089/oli.2006.0069, 17638526.
56. Ding H, Liao G, Wang H, Zhou Y. Asymmetrically designed siRNAs and shRNAs enhance the strand specificity and efficacy in RNAi. J RNAi Gene Silencing 2008, 4(1):269-280.
57. Boden D, Pusch O, Lee F, Tucker L, Shank PR, Ramratnam B. Promoter choice affects the potency of HIV-1 specific RNA interference. Nucleic Acids Res 2003, 31:5033-5038. 10.1093/nar/gkg704, 212804, 12930953.
58. Coburn GA, Cullen BR. Potent and specific inhibition of human immunodeficiency virus type 1 replication by RNA interference. Journal of Virology 2002, 76(18):9225-9231. 10.1128/JVI.76.18.9225-9231.2002, 136455, 12186906.