RNA interference: A practical approach

Journal of Surgical Research

Volumn 117, Issue 2, 2004, Pages 339-344

  Duxbury, Mark S ^a   Whang, Edward E ^a  

^a BRIGHAM AND WOMEN S HOSPITAL   (United States)

Author keywords

Design; Experiment; Gene; Mammalian; Practical; RNA interference; RNAi; Silencing; siRNA; Small interfering RNA

Indexed keywords

GENE EXPRESSION; GENE FUNCTION; GENE SILENCING; GENETIC TRANSFECTION; HUMAN; MAMMAL; NONHUMAN; NORTHERN BLOTTING; PRIORITY JOURNAL; REVIEW; RNA INTERFERENCE; RNA STRUCTURE; WESTERN BLOTTING;

ANIMALS; MOLECULAR STRUCTURE; RESEARCH DESIGN; RNA INTERFERENCE; RNA-INDUCED SILENCING COMPLEX; TRANSFECTION;

EID: 1642400103     PISSN: 00224804     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jss.2003.09.010     Document Type: Review

References (38)

1. Fire A., Xu S., Montgomery M.K., Kostas S.A., Driver S.E., Mello C.C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature. 391:1998;806.
2. Williams B.R. Role of the double-stranded RNA-activated protein kinase (PKR) in cell regulation. Biochem. Soc. Trans. 25:1997;509.
3. Williams B.R. PKR A sentinel kinase for cellular stress. Oncogene. 18:1999;6112.
4. Hamilton A.J., Baulcombe D.C. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science. 286:1999;950.
5. Elbashir S.M., Harborth J., Lendeckel W., Yalcin A., Weber K., Tuschl T. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature. 411:2001;494.
6. Elbashir S.M., Harborth J., Weber K., Tuschl T. Analysis of gene function in somatic mammalian cells using small interfering RNAs. Methods. 26:2002;199.
7. Maine E.M. A conserved mechanism for post-transcriptional gene silencing? Genome Biol. 1:2000;1018. REVIEWS.
8. Hannon G.J. RNA interference. Nature. 418:2002;244.
9. Knight S.W., Bass B.L. A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science. 293:2001;2269.
10. Bernstein E., Caudy A.A., Hammond S.M., Hannon G.J. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature. 409:2001;363.
11. Cerutti L., Mian N., Bateman A. Domains in gene silencing and cell differentiation proteins The novel PAZ domain and redefinition of the Piwi domain. Trends Biochem. Sci. 25:2000;481.
12. Doi N., Zenno S., Ueda R., Ohki-Hamazaki H., Ui-Tei K., Saigo K. Short-interfering-RNA-mediated gene silencing in mammalian cells requires Dicer and eIF2C translation initiation factors. Curr. Biol. 13:2003;41.
13. Tabara H., Yigit E., Siomi H., Mello C.C. The dsRNA binding protein RDE-4 interacts with RDE-1, DCR-1, and a DExH-box helicase to direct RNAi in C. elegans. Cell. 109:2002;861.
14. Tabara H., Sarkissian M., Kelly W.G., Fleenor J., Grishok A., Timmons L., Fire A., Mello C.C. The rde-1 gene, RNA interference, and transposon silencing in C. elegans. Cell. 99:1999;123.
15. Winston W.M., Molodowitch C., Hunter C.P. Systemic RNAi in C. elegans requires the putative transmembrane protein SID-1. Science. 295:2002;2456.
16. Elbashir S.M., Lendeckel W., Tuschl T. RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev. 15:2001;188.
17. Micura R. Small interfering RNAs and their chemical synthesis. Angew. Chem. Int. Ed. Engl. 41:2002;2265.
18. Donze O., Picard D. RNA interference in mammalian cells using siRNAs synthesized with T7 RNA polymerase. Nucleic Acids Res. 30:2002;e46.
19. Yang D., Buchholz F., Huang Z., Goga A., Chen C.Y., Brodsky F.M., Bishop J.M. Short RNA duplexes produced by hydrolysis with Escherichia coli RNase III mediate effective RNA interference in mammalian cells. Proc. Natl. Acad. Sci. USA. 99:2002;9942.
20. Sui G., Soohoo C., Affar E.B., Gay F., Shi Y., Forrester W.C., Shi Y. A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc. Natl. Acad. Sci. USA. 99:2002;5515.
21. Paddison P.J., Caudy A.A., Hannon G.J. Stable suppression of gene expression by RNAi in mammalian cells. Proc. Natl. Acad. Sci. USA. 99:2002;1443.
22. Bogenhagen D.F., Sakonju S., Brown D.D. A control region in the center of the 5S RNA gene directs specific initiation of transcription: II. The 3′ border of the region. Cell. 19:1980;27.
23. Elbashir S.M., Martinez J., Patkaniowska A., Lendeckel W., Tuschl T. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J. 20:2001;6877.
24. Yang S., Tutton S., Pierce E., Yoon K. Specific double-stranded RNA interference in undifferentiated mouse embryonic stem cells. Mol. Cell Biol. 21:2001;7807.
25. Brummelkamp T.R., Bernards R., Agami R. A system for stable expression of short interfering RNAs in mammalian cells. Science. 296:2002;550.
26. Shen C., Buck A.K., Liu X., Winkler M., Reske S.N. Gene silencing by adenovirus-delivered siRNA. FEBS Lett. 539:2003;111.
27. Stewart S.A., Dykxhoorn D.M., Palliser D., Mizuno H., Yu E.Y., An D.S., Sabatini D.M., Chen I.S., Hahn W.C., Sharp P.A., Weinberg R.A., Novina C.D. Lentivirus-delivered stable gene silencing by RNAi in primary cells. RNA. 9:2003;493.
28. Brummelkamp T.R., Bernards R., Agami R. Stable suppression of tumorigenicity by virus-mediated RNA interference. Cancer Cell. 2:2002;243.
29. Devroe E., Silver P.A. Retrovirus-delivered siRNA. BMC Biotechnol. 2:2002;15.
30. Barton G.M., Medzhitov R. Retroviral delivery of small interfering RNA into primary cells. Proc. Natl. Acad. Sci. USA. 99:2002;14943.
31. McManus M.T., Petersen C.P., Haines B.B., Chen J., Sharp P.A. Gene silencing using micro-RNA designed hairpins. RNA. 8:2002;842.
32. Elbashir S.M., Martinez J., Patkaniowska A., Lendeckel W., Tuschl T. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J. 20:2001;6877.
33. Benov L.C., Antonov P.A., Ribarov S.R. Oxidative damage of the membrane lipids after electroporation. Gen. Physiol. Biophys. 13:1994;85.
34. Whither RNAi? Nat. Cell Biol. 5:2003;489.
35. Lassus P., Rodriguez J., Lazebnik Y. Confirming specificity of RNAi in mammalian cells. Sci. STKE. 2002:2002;L13.
36. Yokota T., Sakamoto N., Enomoto N., Tanabe Y., Miyagishi M., Maekawa S., Yi L., Kurosaki M., Taira K., Watanabe M., Mizusawa H. Inhibition of intracellular hepatitis C virus replication by synthetic and vector-derived small interfering RNAs. EMBO Rep. 4:2003;602.
37. Wu R.Z., Bailey S.N., Sabatini D.M. Cell-biological applications of transfected-cell microarrays. Trends Cell Biol. 12:2002;485.
38. Ziauddin J., Sabatini D.M. Microarrays of cells expressing defined cDNAs. Nature. 411:2001;107.