Screening of siRNA target sequences by using fragmentized DNA

Journal of Gene Medicine

Volumn 8, Issue 6, 2006, Pages 782-791

  Kasim, Vivi ^a,b   Taira, Kazunari ^a,b   Miyagishi, Makoto ^b,c  

^a UNIVERSITY OF TOKYO   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

Author keywords

Enzymatic; Fragmentized DNA; RNA interference; RNAi; Screening; SiRNA target sequences

Indexed keywords

DNA FRAGMENT; DOUBLE STRANDED RNA; GREEN FLUORESCENT PROTEIN; SMALL INTERFERING RNA;

ANIMAL CELL; ARTICLE; BACTERIAL CELL; CONTROLLED STUDY; CYTOTOXICITY; ESCHERICHIA COLI; EXPERIMENTAL MODEL; EXPRESSION VECTOR; GENE EXPRESSION; GENE SEQUENCE; GENE SILENCING; GENE TARGETING; GENETIC SCREENING; GENETIC SELECTION; HELA CELL; HUMAN; HUMAN CELL; MAMMAL CELL; MOLECULAR CLONING; MOLECULAR LIBRARY; NONHUMAN; PLASMID; PRIORITY JOURNAL; REPORTER GENE; RNA INTERFERENCE; SEQUENCE ANALYSIS;

BASE SEQUENCE; BLOTTING, NORTHERN; CELL DEATH; CLONE CELLS; DNA; GENE EXPRESSION; GENE LIBRARY; GENETIC VECTORS; HELA CELLS; HUMANS; PLASMIDS; RNA INTERFERENCE; RNA, MESSENGER; RNA, SMALL INTERFERING; SUBSTRATE SPECIFICITY;

MAMMALIA;

EID: 33745229691     PISSN: 1099498X     EISSN: 15212254     Source Type: Journal    
DOI: 10.1002/jgm.900     Document Type: Article

References (27)

1. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998; 391: 806-811.
2. Fire A. RNA-triggered gene silencing. Trends Genet 1999; 15: 358-363.
3. Sharp PA. RNA interference - 2001. Genes Dev 2001; 15: 485-490.
4. Hammond SM, Caudy AA, Hannon GJ. Post-transcriptional gene silencing by double-stranded RNA. Nat Rev Genet 2001; 2: 110-119.
5. Zamore PD. RNA interference: listening to the sound of silence. Nat Struct Biol 2001; 8: 746-750.
6. 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: 5875-5885.
7. 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: 5864-5874.
8. Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T. Duplexes of 21-nudeotide RNAs mediate RNA interference in cultured mammalian cells. Nature 2001; 411: 494-498.
9. Caplen NJ, Parrish S, Imani F, Fire A, Morgan RA. Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems. Proc Natl Acad Sci U S A 2001; 98: 9742-9747.
10. Akashi H, Miyagishi M, Yokota T, et al. Escape from the interferon response associated with RNA interference using vectors that encode long modified hairpin-RNA. Mol BioSyst 2005; 1: 382.
11. Miyagishi M, Taira K. Strategies for generation of an siRNA expression library directed against the human genome. Oligonucleotides 2003; 13: 325-333.
12. 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: 497-500.
13. Brummelkamp TR, Bernards R, Agami R. A system for stable expression of short interfering RNAs in mammalian cells. Science 2002; 296: 550-553.
14. Kawasaki H, Taira K. Short hairpin type of dsRNAs that are controlled by tRNA(Val) promoter significantly induce RNAi-mediated gene silencing in the cytoplasm of human cells. Nucleic Acids Res 2003; 31: 700-707.
15. 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: 948-958.
16. Lee NS, Dohjima T, Bauer G, et al. Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells. Nat Biotechnol 2002; 20: 500-505.
17. 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 U S A 2002; 99: 5515-5520.
18. Paul CP, Good PD, Winer I, Engelke DR. Effective expression of small interfering RNA in human cells. Nat Biotechnol 2002; 20: 505-508.
19. Yu JY, DeRuiter SL, Turner DL. RNA interference by expression of short-interfering RNAs and hairpin RNAs in mammalian cells. Proc Natl Acad Sci U S A 2002; 99: 6047-6052.
20. Shirane D, Sugao K, Namiki S, Tanabe M, Iino M, Hirose K. Enzymatic production of RNAi libraries from cDNAs. Nat Genet 2004; 36: 190-196.
21. Miyagishi M, Fujii R, Hatta M, et al. Regulation of Lef-mediated transcription and p53-dependent pathway by associating beta-catenin with CBP/p300. J Biol Chem 2000; 275: 35170-35175.
22. Luo B, Heard AD, Lodish HF. Small interfering RNA production by enzymatic engineering of DNA (SPEED). Proc Natl Acad Sci USA 2004; 101: 5494-5499.
23. 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: 715-723.
24. Judge AD, Sood V, Shaw JR, Fang D, McClintock K, MacLachlan I. Sequence-dependent stimulation of the mammalian innate immune response by synthetic siRNA. Nat Biotechnol 2005; 23: 457-462.
25. Hornung V, Guenthner-Biller M, Bourquin C, et al. Sequence-specific potent induction of IFN-alpha by short interfering RNA in plasmacytoid dendritic cells through TLR7. Nat Med 2005; 11: 263-270.
26. Miyagishi M, Taira K. siRNA becomes smart and intelligent. Nat Biotechnol 2005; 23: 946-947.
27. 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: 222-226.