| Ambion Technical Bulletin 503 Selected RNA Interference (RNAi) References We've grouped the references alphabetically in the following categories: - RNAi in Mammalian Cells
- RNAi Mechanism
- stRNA and miRNA, and Their Connections with RNAi
- RNAi Reviews
- The Use of RNAi in Gene Silencing Studies
- Posttranscriptional Gene Silencing in Plants
References of particular note are indicated by c* or **. This list will be updated frequently. 1. RNAi and the Use of siRNAs in Mammalian Cells **Brummelkamp, TR, Bernards, R, and Agami, R. (2002). A system for stable expression of short interfering RNAs in mammalian cells. Science 296:550-553.
**Elbashir, SM, 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. **Elbashir SM, Martinez J, Patkaniowska A, Lendeckel W, Tuschl T. (2001) Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J 20(23):6877-6888. *Gitlin L, Karelsky S, and Andino R. (2002). Short interfering RNA confers intracellular antiviral immunity in human cells. Nature 418:430-434. *Jacque J-M, Triques K, and Stevenson M. (2002). Modulation of HIV-1 replication by RNA interference. Nature 418:435-438. *Lee, NS, Dohjima, T, Bauer, G, Li, H, Li, M-J, Ehsani, A, Salvaterra, P, and Rossi, J. (2002). Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells. Nature Biotechnol 19:500-505. Li H, Li WX, and Ding SW. (2002). Induction and suppression of RNA silencing by an animal virus. Science 296:1319-1321. **McCaffrey AP, Meuse L, Pham T-T, Conklin DS, Hannon GJ, and Kay MA. (2002). RNA interference in adult mice. Nature 418:38-39. Miyagishi, M, and Taira, K. (2002). U6-promoter-driven siRNAs with four uridine 3' overhangs efficiently suppress targeted gene expression in mammalian cells. Nature Biotechnol 19:497-500. *Novina CD, Murray MF, Dykxhoorn D, Beresford PJ, Riess J, Lee S-K, Collman RG, Lieberman J, Shankar P, and Sharp PA. (2002). siRNA-directed inhibition of HIV-1 infection. Nature Med 8(7):681-686.
*Nykanen A, Haley B, Zamore PD. (2001) ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell. 107(3):309-321. **Paddison PJ, Caudy AA, Bernstein E, Hannon GJ and Conklin DS. (2002). Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes & Development 16:948-958. *Paddison PJ, Caudy AA, Hannon GJ. (2002) Stable suppression of gene expression by RNAi in mammalian cells. Proc Natl Acad Sci USA 99(3):1443-1448. Paul, CP, Good, PD, Winer, I, and Engelke, DR. (2002). Effective expression of small interfering RNA in human cells. Nature Biotechnol 19:505-508. Sui G, Soohoo C, Affar EB, Gay F, Shi Y, Forrester WC, and Shi Y. (2002) A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc Natl Acad Sci USA 99(8): 5515-5520. **Wianny F, Zernicka-Goetz M. (2000) Specific interference with gene function by double-stranded RNA in early mouse development. Nat Cell Biol 2:70-75. Yang D, Buchholz F, Huang Z, Goga A, Chen C-Y, Brodsky FM, and Bishop MJ. (2002). Short RNA duplexes produced by hydrolysis with Escherichia coli RNase III mediate effective RNA interference in mammalian cells. Proc Natl Acad Sci USA 99(15): 9942-9947. Yu J-Y, DeRuiter SL, and Turner DL. (2002). RNA interference by expression of short-interfering RNAs and hairpin RNAs in mammalian cells. Proc Nat Acad Sci USA 99(9):6047-6052.
2. RNAi Mechanism Dudley NR, Labbe J-C, and Goldstein B. (2002). Using RNA interference to identify genes required for RNA interference. Proc Natl Acad Sci USA 99:4191-4196. Ketting RF and Plasterk RHA. (2000). A genetic link between co-suppression and RNA interference in C. elegans. Nature 404:296-298.
Lipardi C, Wei Q, Paterson BM. (2001) RNAi as random degradative PCR: siRNA primers convert mRNA into dsRNAs that are degraded to generate new siRNAs. Cell 107(3):297-307. Sijen T, Fleenor J, Simmer F, Thijssen KL, Parrish S, Timmons L, Plasterk RH, Fire A. (2001) On the role of RNA amplification in dsRNA-triggered gene silencing. Cell 107(4):465-476. Tabara H, Yigit E, Siomi N, and Mello C. (2002). The dsRNA binding protein RDE-4 interacts with RDE-1, DCR-1, and a DexH-box helicase to direct RNAi in C. elegans. Cell 109:861-871. *Tijsterman M, Ketting RF, Okihara KL, Sijen T, Plasterk RH. (2002) RNA helicase MUT-14-dependent gene silencing triggered in C. elegans by short antisense RNAs. Science 295(5555):694-697. Tuchl T, Zamore PD, Lehmann R, Bartel DP, and Sharp PA. (1999). Targeted mRNA degradation by double-stranded RNA in vitro. Genes & Development 13:3191-3197. Winston WM, Molodowitch C, and Hunter CP. (2002). Systemic RNAi in C. elegans requires the putative transmembrane protein SID-1. Science 295:2456-2459. Zamore PD, Tuschl T, Sharp PA, and Bartel DP. (2000). RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101:25-33.
3. stRNA and miRNA, and Their Connections with RNAi Ambros V. (2001) MicroRNAs: tiny regulators with great potential. Cell 107(7):823-826. Ambros V. (2001) Development: Dicing up RNAs. Science 293(5531):811. Billy E, Brondani V, Zhang H, Muller U, Filipowicz W. (2001) Specific interference with gene expression induced by long, double-stranded RNA in mouse embryonal teratocarcinoma cell lines. Proc Natl Acad Sci USA 98(25):14428-14433. Dennis, C. (2002). The brave new world. Nature 418:122-124. Dzitoyeva S, Dimitrijevic N, Manev H. (2001) Intra-abdominal injection of double-stranded RNA into anesthetized adult Drosophila triggers RNA interference in the central nervous system. Mol Psychiatry 6(6):665-670. Hong Y, Lee RC, Ambros V. (2000) Structure and function analysis of LIN-14, a temporal regulator of postembryonic developmental events in Caenorhabditis elegans. Mol Cell Biol 20(6):2285-2295. *Hutvagner G, McLachlan J, Pasquinelli AE, Balint E, Tuschl T, Zamore PD (2001) A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293(5531):834-838. *Ketting RF, Fischer SE, Bernstein E, Sijen T, Hannon GJ, Plasterk RH. (2001) Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev 15(20):2654-2659. Lai EC. (2002). Micro RNAs are complementary to 3´ UTR sequence motifs that mediate negative post-transcriptional regulation. Nature Genet. 30:363-364. Lau NC, Lim LP, Weinstein EG, Bartel DP. (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294(5543):858-862. Lee RC, Ambros V. (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294(5543):862-864. *Montgomery MK, Xu S, Fire A. (1998) RNA as a target of double stranded RNA-mediated genetic interference in C. elegans. Proc. Natl. Acad. Sci. USA 95: 15502-15507. Nishikawa T, Natori S. (2001) Targeted disruption of a pupal hemocyte protein of Sarcophaga by RNA interference. Eur J Biochem 268(20):5295-5299. Olsen PH, Ambros V. (1999) The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev Biol 216(2):671-680. Pasquinelli AE. (2002). MicroRNAs: deviants no longer. Trends in Genet. 18(4):171-173. Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, and Bartel DP. (2002). MicroRNAs in plants. Genes & Dev. 16:1616-1626. Schwarz DS and Zamore PD. (2002). Why do miRNAs live in the miRNP? Genes & Dev. 16:1025-1031.
Tuschl T. (2001) RNA Interference and Small Interfering RNAs. Chembiochem Europ J Chem Biol 2(4):239-245. Yang S, Tutton S, Pierce E, Yoon K. (2001) Specific double-stranded RNA interference in undifferentiated mouse embryonic stem cells. Mol Cell Biol 21(22):7807-7816.
4. RNAi Reviews Ahlquist P. (2002). RNA-dependent RNA polymerases, viruses, and RNA silencing. Science 296:1270-1273. *Carmichael GG. (2002). Silencing viruses with RNA. Nature 418:379-380.
Chicas A and Macino G. (2001). Characteristics of post-transcriptional gene silencing. EMBO J 2(11):992-996.
Cogoni, C., and Macino, G. (2000) Post-transcriptional gene silencing across kingdoms. Genes Dev 10: 638-643. Fire, A. (1999) RNA-triggered gene silencing. Trends in Genetics, 15:358-363. Abstract. Ding, S.W. (2000) RNA silencing. Curr. Opin. Biotech. 11:152-156. Abstract. Gura, T. (2000) A silence that speaks volumes. Nature 404:804-808. Hammond, S.M., Caudy, A.A., and Hannon, G. J. (2001) Post-Transcriptional Gene Silencing by Double-stranded RNA. Nature Rev Genetics 2: 110-119. Hannon GJ. (2002). RNA interference. Nature 418:244-251. Hunter, C.P. (2000) Shrinking the black box of RNAi. Current Biology 10:R137-R140. Abstract. Hutvagner G, Zamore PD. (2002) RNAi: nature abhors a double-strand. Curr Opin Genet Dev 12:225-232. Plasterk RHA. (2002). RNA silencing: the genome's immune system. Science 296:1263-1265. Sharp, P.A. (2001) RNA interference—2001 Genes Devel 15: 485-490. Sharp, P.A., and P.D. Zamore. (2000) RNA Interference. Science 287:2431-2433. Sharp, P.A. (1999) RNAi and double-strand RNA. Genes Dev 13:139-141. Tuschl T. (2002). Expanding small RNA interference. Nature Biotechnol 20:446-448. *Zamore PD. (2002). Ancient pathways programmed by small RNAs. Science 296:1265-1269.
5. The Use of RNAi in Gene Silencing Studies Clemens JC, Worby CA, Simonson-Leff N, Muda M, Maehama T, Hemmings BA, and Dixon JE. (2000) Use of double-stranded RNA interference in Drosophila cell lines to dissect signal transduction pathways. PNAS 97: 6499-6503. Article. Colussi, PA, Quinn LM, Huang DCS, Coombe M, Read SH, Richardson H, and Kumar S. (2000) Debcl, a Proapoptotic Bcl-2 Homologue, Is a Component of the Drosophila melanogaster Cell Death Machinery. J. Cell Biol. 148: 703-714. Abstract. Cortez D, Guntuku S, Qin J, Elledge SJ. (2001). ATR and ATRIP: partners in checkpoint signaling. Science 294:1713-1716 **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. Giet R, and Glover DM. (2001) Drosophila Aurora B Kinase Is Required for Histone H3 Phosphorylation and Condensin Recruitment during Chromosome Condensation and to Organize the Central Spindle during Cytokinesis. J Cell Biol 152: 669-681. Gotta M, and Ahringer J. (2001) Distinct roles for G-alpha and G-beta-gamma in regulating spindle position and orientation in Caenorhabditis elegans embryos. Nature Cell Biol 3: 297-300. Haag E, and Kimble J. (2000) Regulatory Elements Required for Development of Caenorhabditis elegans Hermaphrodites Are Conserved in the tra-2 Homologue of C. remanei, a Male/Female Sister Species. Genetics 155: 105-116. Abstract. **Harborth J, Elbashir SM, Bechert K, Tuschl T, Weber K. (2001) Identification of essential genes in cultured mammalian cells using small interfering RNAs. J Cell Sci. 114(Pt 24):4557-4565. Marchler G, and Wu C. (2001) Modulation of Drosophila heat shock transcription factor activity by the molecular chaperone DROJ1. EMBO 20: 499-509. Misquitta L, and Paterson BM. (2000) Targeted Disruption of Gene Function in Drosophila by RNA Interference, in Drosophila Protocols, Sullivan, W., Ashburner, M., and Hawley, R.S., Eds. Cold Spring Harbor Laboratory Press. Moorthy S, Chen L, and Bennett V. (2000) Caenorhabditis elegans ß-G Spectrin Is Dispensable for Establishment of Epithelial Polarity, but Essential for Muscular and Neuronal Function. J. Cell Biol. 149: 915-930. Abstract. Peters JM, McKay RM, McKay JP, and Graff JM. (1999) Casein Kinase I Transduces Wnt Signals. Nature 401:345-350. Abstract. Rousset R, Mack JA, Wharton, Jr KA, Axelrod JD, Cadigan KM, Fish MP, Nusse R, and Scott MP. (2001) naked cuticle targets dishevelled to antagonize Wnt signal transduction. Genes Dev 15: 658-671. Rudel D, and Kimble J. (2001) Conservation of glp-1 Regulation and Function in Nematodes. Genetics 157: 639-654. Shippy TD, Guo J, Brown SJ, Beeman RW, and Denell RE. (2000) Analysis of maxillopedia Expression Pattern and Larval Cuticular Phenotype in Wild-Type and Mutant Tribolium. Genetics 155: 721-731. Abstract. Srayko M, Buster DW, Bazirgan OA, McNally FJ, and Mains PE. (2000) MEI-1/MEI-2 katanin-like microtubule severing activity is required for Caenorhabditis elegans meiosis. Genes & Dev. 14: 1072-1084. Abstract. Stansberry J, Baude EJ, Taylor MK, Chen P-J, Jin S-W, Ellis RE, and Uhler MD. (2001) A cGMP-dependent protein kinase is implicated in wild-type motility in C. elegans. J Neurochem 76: 1177-1187. 6. Posttranscriptional Gene Silencing in Plants Fagard M, Boutet S, Morel JB, Bellini C, Vaucheret H. (2000) AGO1, QDE-2, and RDE-1 are related proteins required for post-transcriptional gene silencing in plants, quelling in fungi, and RNA interference in animals. Proc Natl Acad Sci USA 97(21):11650-4.). Hamilton AJ, and Baulcombe DC. (1999) A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286(5441): 950-952. Matzje H, Matzje A, Pruss G, and Vance V. (2001) RNA-based silencing strategies in plants" Current Opinion in Genetics & Development. 11:221-227. *Silhavy D, Molnar A, Lucioli A, Szittya G, Hornyik C, Tavazza M, and Burgyan J. (2002). A viral protein suppresses RNA silencing and binds silencing-generated, 21- to 25-nucleotide double-stranded RNAs. EMBO J. 21(12):3070-3080. Vaucheret H, Beclin C, and Fagard M. (2001) Post-transcriptional gene silencing in plants J Cell Science 114: 3083-3091. Voinnet O and Baulcomb DC. (1997). Systemic signaling in gene silencing. Nature 389:553. Voinnet O, Lederer C, and Baulcomb DC. (2000). A viral movement protein prevents spread of the gene silencing signal in Nicotiana benthamiana. Cell 103:157-167. Voinnet O, Pinto YM, and Baulcombe DC. (1999). Suppression of gene silencing: a general strategy used by diverse DNA and RNA viruses of plants. Proc. Natl. Acad. Sci. USA 96(24):14147-14152.
Waterhouse PM, Wang M, and Lough T. (2001) Gene silencing as an adaptive defence against viruses Nature 411: 834-840. |