Dynamics of gene silencing by RNA interference

Biotechnology and Bioengineering

Volumn 88, Issue 1, 2004, Pages 121-132

  Raab, R Michael ^a   Stephanopoulos, Gregory ^a  

^a Massachusetts Institute of Technology Cambridge   (United States)

Author keywords

Cellular modeling; Gene silencing; GFP; RNA interference

Indexed keywords

BIOMEDICAL ENGINEERING; GENES; MATHEMATICAL MODELS; PROTEINS; RNA; THROUGHPUT;

GENE INDUCTION; GENE SILENCING; GREEN FLUORESCENT PROTEINS; RNA INTERFERENCE (RNAI);

GENETIC ENGINEERING;

GREEN FLUORESCENT PROTEIN; RNA; RNA INDUCED SILENCING COMPLEX;

ANIMAL CELL; ARTICLE; CONTROLLED STUDY; DOSE RESPONSE; GENE IDENTIFICATION; GENE INDUCTION; GENE SILENCING; HIGH THROUGHPUT SCREENING; KNOCKOUT GENE; MOUSE; NONHUMAN; PHENOTYPE; QUANTITATIVE ANALYSIS; REPORTER GENE; RNA INTERFERENCE; TECHNOLOGY;

ANIMALS; GENE SILENCING; GREEN FLUORESCENT PROTEINS; LUMINESCENT PROTEINS; MICE; MICE, KNOCKOUT; MODELS, ANIMAL; MODELS, GENETIC; PHENOTYPE; RNA INTERFERENCE; TRANSFECTION;

EID: 6344249316     PISSN: 00063592     EISSN: None     Source Type: Journal    
DOI: 10.1002/bit.20216     Document Type: Article

References (51)

1. Appel M, Couderc E, Feger J. 1992. Comparative studies of protein biosynthesis: the main experimental parameters in pulse and pulse-chase experiments must be standardized. Biol Cell 74:235-238.
2. Ashrafi K, Chang FY, Watts JL, Fraser AG, Kamath RS, Ahringer J, Ruvkun G. 2003. Genome-wide RNAi analysis of caenorhabditis elegans fat regulatory genes. Nature 421:268-272.
3. Boutros M, Kiger AA, Armknecht S, Kerr K, Hild M, Koch B, Haas SA, Consortium HF, Paro R, Perrimon N. 2004. Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science 303:832-835.
4. Boshart M, Weber F, Jahn G, Dorsch-Hasler K, Fleckenstein B, Schaffner W. 1985. A very strong enhancer is located upstream of an immediate early gene of human cytomegalovirus. Cell 41:521-530.
5. Collins FS, Patrinos A, Jordan E, Chakravarti A, Gesteland R, Walters L. 1998. New goals for the, U.S. human genome project: 1998-2003. Science 282:682-689.
6. Davis S, Watson JC. 1996. In vitro activation of the interferon-induced, double-stranded RNA-dependent protein kinase PKR by RNA from the 3′ untranslated regions of human alpha-tropomyosin. Proc Natl Acad USA 93:508-513.
7. Donze O, Picard D. 2002. RNA inteference in mammalian cells using siRNAs synthesized with T7 RNA polymerase. Nucl Acids Res 30:E46.
8. Elbashir SM, Harboth J, Lendeckel W, Yalcin A, Weber K, Tuschl T. 2001a. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411:494-498.
9. Elbashir SM, Martinez J, Patkaniowska A, Lendeckel W, Tuschl T. 2001b. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogasrer embryo lysate. EMBO J 20:6877-6888.
10. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. 1998. Potent and specific genetic interference by double-stranded RNA in C. elegans. Nature 391:806-811.
11. Ganguly S, Skoultchi AI. 1985. Absolute rates of globin gene transcription and mRNA formation during differentiation of cultured mouse erythroleukemia cells. J Biol Chem 260:12167-12173.
12. Galas DJ, McCormack SJ. 2003. An historical perspective on genomic technologies. Curr Issues Mol Biol 5:123-127.
13. Goldberg AL, Akopian TN, Kisselev AF, Lee DH, Rohrwild M. 1997. New insights into the mechansims and importance of the proteasome in intracellular protein degradation. Biol Chem 378:131-140.
14. Grosshans H, Slack FJ. 2002. Micro-RNAs: small is plentiful. J Cell Biol 156:17-21.
15. Hamada M, Ohtsuka T, Kawaida R, Koizumi M, Morita K, Furukawa H, Imanishi T, Miyagishi M, Taira K. 2002. Effects on RNA interference in gene expression (RNAi) in cultured mammalian cells of mismatches and the introduction of chemical modifications at the 3′-ends of siRNAs. Antisense Nucl Acid Drug Dev 12:301-309.
16. Hammond SM, Bernstein E, Beach D, Hannon GJ. 2000. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404:293-296.
17. Hannon GJ. 2002. RNA interference. Nature 418:244-251.
18. Hatzimanikatis V, Lee KH. 1999. Dynamical analysis of gene networks requires both mRNA and protein expression information. Met Eng 1:275-281.
19. Hemann MT, Fridman JS, Zilfou JT, Hernando E, Paddison PJ, Cordon-Cardo C, Hannon GJ, Lowe SW. 2003. An epi-allelic series of p53 hypomorphs created by stable RNAi produces distinct tumor phenotypes in vivo. Nat Genet 33:396-400.
20. Himber C, Dunoyer P, Moissiard G, Ritzenthaler C, Voinnet O. 2003. Transitivity-dependent and -independent cell-to-cell movement of RNA silencing. EMBO J 22:4523-4533.
21. Hoffmann A, Levchenko A, Scott ML, Baltimore D. 2002. The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation. Science 298:1241-1245.
22. Jackson AL, Bartz SR, Schelter J, Kobayashi SV, Burchard J, Mao M, Li B, Cavet G, Linsley PS. 2003. Expression profiling reveals off-target gene regulation by RNAi. Nat Biotechnol 21:635-637.
23. Jacque JM, Triques K, Stevenson M. 2002. Modulation of HlV-1 replication by RNA interference. Nature 418:379-380.
24. Krichesvky AM, Kosik KS. 2002. RNAi functions in cultured mammalian neurons. Proc Natl Acad Sci USA 99:11926-11929.
25. Maeda I, Kohara Y, Yamamoto M, Sugimoto A. 2001. Large-scale analysis of gene function in caenorhabditis elegans by high-throughput RNAi. Curr Biol 11:171-176.
26. Matsuda T, Cepko CL. 2004. Electroporation and RNA interference in the rodent retina in vivo and in vitro. Proc Natl Acad Sci 101:16-22.
27. Maxwell MM, Pasinelli P, Kazantsev AG, Brown RH Jr. 2004. RNA interference-mediated silencing of mutant Superoxide dismutase rescues cyclosporin A-induced death in cultured neuroblastoma cells. Proc Natl Acad Sci USA 101:3178-3183.
28. McCaffrey AP, Meuse L, Pham T-TT, Conklin DS, Hannon GJ, Kay MA. 2002. RNA interference in adult mice. Nature 418:38-39.
29. McManus MT, Sharp PA. 2002. Gene silencing in mammals by small interfering RNAs. Nat Rev Genet 3:737-747.
30. Meldrum D. 2000. Automation for genomics: II, sequencers, microarrays, and future trends. Genome Res 10:1288-1303.
31. Mohmmed A, Dasaradhi PV, Bhatnagar RK, Chauhan VS, Malhotra P. 2003. In vivo gene silencing in plasmodium berghei: a mouse malaria model. Biochem Biophsy Res Commun 309:506-511.
32. Myers JW, Jones JT, Meyer T, Ferrell JE Jr. 2003. Recombinant dicer efficiently converts large dsRNAs into siRNAs suitable for gene silencing. Nat Biotechnol 21:324-328.
33. Nicholson RH, Nicholson AW. 2002. Molecular characterization of a mouse cDNA encoding dicer, a ribonuclease III ortholog involved in RNA interferences. Mamm Genome 13:67-73.
34. Paddison PJ, Caudy AA, Hannon GJ. 2002. Stable suppression of gene expression by RNAi in mammalian cells. Proc Natl Acad Sci 99:1443-1448.
35. Pal-Bhadra M, Bhadra U, Birchler JA. 2002. RNAi related mechanisms affect both transcriptional and posttranscriptional transgene silencing in Drosophila. Mol Cell 9:315-327.
36. Pesole G, Mignone F, Gissi C, Grillo G, Licciulli F, Liuni S. 2001. Structural and functional features of eukaryotic mRNA untranslated regions. Gene 276:73-81.
37. Provost P, Dishart D, Doucet J, Frendewey D, Samuelsson B, Radmark O. 2002. Ribonuclease activity and RNA binding of recombinant human dicer. EMBO J 21:5864-5874.
38. Raghavan A, Ogilvie RL, Reilly C, Abelson ML, Raghavan S, Vasdewani J, Krathwohl M, Bohjanen PR. 2002. Genome-wide analysis of mRNA decay in resting and activated primary human t lymphocytes. Nucl Acids Res 30:5529-5538.
39. Reynolds A, Leake D, Boese Q, Scaringe S, Marshall WS, Khvorova A. 2004. Rational siRNA design for RNA interference. Nat Biotechnol 22:326-330.
40. Rubinson DA, Dillon CP, Kwiatkowski AV, Sievers C, Yang L, Kopinja J, Rooney DL, Ihrig MM, McManus MT, Gertler FB, Scott ML, Van Parijs L. 2003. A lentivirus-based system to functionally silence genes in primary mammalian cells, stem cells and transgenic mice by RNA interference. Nat Genet 33:401-406.
41. Sacchetti A, El Sewedy T, Nasr AF, Alberti S. 2001. Efficient GFP mutations profoundly affect mRNA transcription and translation rates. FEES Lett 492:151-155.
42. Scacheri PC, Rozenblatt-Rosen O, Caplen NJ, Wolfsberg TG, Umayam L, Lee JC, Hughs CM, Shanmugam KS, Bhattacharjee A, Meyerson M, Collins FS. 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.
43. Scherr M, Battmer K, Ganser A, Eder M. 2003. Modulation of gene expression by lentiviral-mediated delivery of small interfering RNA. Cell Cycle 2:251-257.
44. Shi Y. 2003. Mammalian RNAi for the masses. Trends Genet 19:9-12.
45. Smolen P, Baxter DA, Byrne JH. 2003. Reduced models of the circadian oscillators in neurospora crassa and Drosophila melanogaster illustrate mechanistic similarities. Omics 7:337-354.
46. Tenenbaum SA, Carson CC, Atasoy U, Keene JD. 2003. Genome-wide regulatory analysis using en masse nuclear run-ons and ribonomic profiling with autoimmune sera. Gene 317:79-87.
47. Torchia J, Glass C, Rosenfeld MG. 1998. Co-activators and co-repressors in the integration of transcriptional responses. Curr Opin Cell Biol 10:373-383.
48. Ui-Tei K, Naito Y, Takahashi F, Haraguchi T, Ohki-Hamazaki H, Juni A, Ueda R, Saigo K. 2004. Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. Nucl Acids Res 32:936-948.
49. Vaucheret H, Beclin C, Fagard M. 2001. Post-transcriptional gene silencing in plants. J Cell Sci 114:3083-3091.
50. Wilusz CJ, Wormington M, Peltz SW. 2001. The cap-to-tail guide to mRNA turnover. Nat Rev Mol Cell Biol 2:237-246.
51. Zeng Y, Cullen BR. 2003. Sequence requirements for microRNA processing and function in human cells. RNA 9:112-123.