Modeling RNA interference in mammalian cells

BMC Systems Biology

Volumn 5, Issue , 2011, Pages

  Cuccato, Giulia ^a   Polynikis, Athanasios ^b   Siciliano, Velia ^a   Graziano, Mafalda ^a   di Bernardo, Mario ^b,c   di Bernardo, Diego ^a,c  

^a TELETHON INSTITUTE OF GENETICS AND MEDICINE TIGEM   (Italy)

^b UNIVERSITY OF BRISTOL   (United Kingdom)

^c UNIVERSITY OF NAPLES FEDERICO II   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

CRICETINAE; MAMMALIA;

ENZYME; SMALL INTERFERING RNA;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CELL STRAIN HEK293; CHO CELL; CRICETULUS; GENETICS; HAMSTER; HUMAN; METABOLISM; RNA INTERFERENCE;

ANIMALS; CHO CELLS; CRICETINAE; CRICETULUS; ENZYMES; HEK293 CELLS; HUMANS; MODELS, GENETIC; RNA INTERFERENCE; RNA, SMALL INTERFERING;

EID: 79251538918     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-19     Document Type: Article

References (37)

1. Carthew R, Sontheimer E. Origins and Mechanisms of miRNAs and siRNAs. Cell 2009, 136:642-655. 10.1016/j.cell.2009.01.035, 2675692, 19239886.
2. Bartel D. MicroRNAs: Genomics, Biogenesis, Mechanism, and Function. Cell 2004, 116:281-297. 10.1016/S0092-8674(04)00045-5, 14744438.
3. Cullen BR. RNAi the natural way. Nat Genet 2005, 37:1163-1165. 10.1038/ng1105-1163, 16254559.
4. 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., http://www.sciencemag.org/cgi/content/abstract/296/5567/550
5. Elbashir S, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 2001, 411:494-498. 10.1038/35078107, 11373684.
6. Deans TL, Cantor CR, J CJ. A Tunable Genetic Switch Based on RNAi and Repressor Proteins for Regulating Gene Expression in Mammalian Cells. Cell 2007, 130:363-372. 10.1016/j.cell.2007.05.045, 17662949.
7. Tigges M, Marquez-Lago T, Stelling J, Fussenegger M. A tunable synthetic mammalian oscillator. Nature 2009, 457:309-312. 10.1038/nature07616, 19148099.
8. Barik S, Bitko V. Prospects of RNA interference therapy in respiratory viral diseases: update 2006. Expert Opin Biol Ther 2006, 6:115-160.
9. Fulton A, Peters S, Perkins G, Jarosinski KAD. Effective Treatment of Respiratory Alphaherpesvirus Infection Using RNA Interference. PLoS ONE 2009, 4:e4118. 10.1371/journal.pone.0004118, 2606062, 19122813.
10. Takeshita F, Ochiya T. Therapeutic potential of RNA interference against cancer. Cancer Sci 2006, 97:689-96. 10.1111/j.1349-7006.2006.00234.x, 16863503.
11. Leung R, Whittaker P. RNA interference: from gene silencing to gene-specific therapeutics. Pharmacol Ther 2005, 107:222-39. 10.1016/j.pharmthera.2005.03.004, 15908010.
12. Aagaarda L, JJ R. RNAi therapeutics: Principles, prospects and challenges. Adv Drug Del Rev 2007, 59:75-86.
13. Shrey K, Suchita A, Nishanta M, Vibha R. RNA interference: Emerging diagnostics and therapeutics tool. Bioch and Bioph Res Commun 2009, 386:273-277.
14. Filipowicz W. RNAi: the nuts and bolts of the RISC machine. Cell 2005, 122:17-20. 10.1016/j.cell.2005.06.023, 16009129.
15. Malphettes L, Fussenegger M. Impact of RNA interference on gene networks. Metab Eng 2006, 8:672-683. 10.1016/j.ymben.2006.07.005, 16996764.
16. Levine E, Zhang Z, Kuhlman T, Hwa T. Quantitative characteristics of gene regulation by small RNA. PLoS Biol 2007, 5:e229. 10.1371/journal.pbio.0050229, 1994261, 17713988.
17. Khanin R, Vinciotti V. Computational Modeling of Post-Transcriptional Gene Regulation by MicroRNAs. J Comput Biol 2008, 15:305-316. 10.1089/cmb.2007.0184, 18333757.
18. Shimoni Y, Friedlander G, Hetzroni G, Niv G, Altuvia S, Biham O, Margalit H. Regulation of gene expression by small non-coding RNAs: a quantitative view. Mol Syst Biol 2007, 3:138. 10.1038/msb4100181, 2013925, 17893699.
19. Mehta P, Goyal S, Wingreen S. A quantitative comparison of sRNA-based and protein-based gene regulation. Mol Syst Biol 2008, 4:221. 10.1038/msb.2008.58, 2583084, 18854820.
20. Mitarai N, Andersson AMC, Krishna S, Semsey S, Sneppen K. Efficient degradation and expression prioritization with small RNAs. Phys Biol 2007, 4:164-171. 10.1088/1478-3975/4/3/003, 17928655.
21. Massé E, Escorcia FE, Gottesman S. Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli. Genes Dev 2003, 17:2374-2383. 218075, 12975324.
22. Hutvagner G, Zamore P. A microRNA in a Multiple-Turnover RNAi Enzyme Complex. Science 2002, 297:2056-2060. 10.1126/science.1073827, 12154197.
23. Haley B, Zamore P. Kinetic analysis of the RNAi enzyme complex. Nat Struct & Mol Biol 2004, 11:7.
24. Meister G, Tuschl T. Mechanisms of gene silencing by double-stranded RNA. Nature 2004, 431:338-342. 10.1038/nature02873, 15372040.
25. Rajewsky N. microRNA target predictions in animals. Nat Rev Genet 2006, 38:S8-S13.
26. Martinez J, Tuschl T. RISC is a 5' phosphomonoester-producing RNA endonuclease. Genes Dev 2004, 18:975-980. 10.1101/gad.1187904, 406288, 15105377.
27. Overhoff M, Wünsche W, Sczakiel G. Quantitative detection of siRNA and single-stranded oligonucleotides: relationship between uptake and biological activity of siRNA. Nucleic Acids Res 2004, 32:e170. 10.1093/nar/gnh168, 535697, 15576677.
28. Doench J, Petersen C, Sharp P. siRNAs can function as miRNAs. Genes Dev 2003, 17:438-442. 10.1101/gad.1064703, 195999, 12600936.
29. Zeng Y, Yi R, Cullen B. MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms. Proc Natl Acad Sci 2003, 100:9779-9784. 10.1073/pnas.1630797100, 187842, 12902540.
30. Hastie T, Tibshirani R, Friedman J. The elements of statistical learning: data mining, inference, and prediction 2009, New York: Springer.
31. Khan AA, Betel D, Miller ML, Sander C, Leslie CS, Marks DS. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol 2009, 27:549-555. 10.1038/nbt0709-671a, 2782465, 19465925.
32. Brown KM, Chu C, Rana TM. Target accessibility dictates the potency of human RISC. Nat Struct Mol Biol 2005, 12:469-470. 10.1038/nsmb931, 15852021.
33. Arvey A, Larsson E, Sander C, Leslie C, Marks D. Target mRNA abundance dilutes microRNA and siRNA activity. Molecular systems biology 2010, 6. 10.1038/msb.2010.24, 2872614, 20404830.
34. Larsson E, Sander C, Marks D. mRNA turnover rate limits siRNA and microRNA efficacy. Molecular Systems Biology 2010, 6.
35. Hemann M, Fridman J, Zilfou J, Hernando E, Paddison P, Cordon-Cardo C, Hannon G, Lowe S. An epi-allelic series of p53 hypomorphs created by stable RNAi produces distinct tumor phenotypes in vivo. Nature Genetics 2003, 33:396-400. 10.1038/ng1091, 12567186.
36. Chen Y, Jensen M, Smolke C. Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems. Proc Natl Acad Sci 2010, 1-6.
37. Chiu Y, Rana T. RNAi in human cells: basic structural and functional features of small interfering RNA. Mol Cell 2002, 10:549-561. 10.1016/S1097-2765(02)00652-4, 12408823.