Intronically encoded siRNAs improve dynamic range of mammalian gene regulation systems and toggle switch

Nucleic Acids Research

Volumn 36, Issue 16, 2008, Pages

  Greber, David ^a   El Baba, Marie Daoud ^b   Fussenegger, Martin ^a  

^a ETH ZURICH   (Switzerland)

^b Institut Universitaire de Technologie   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DOXYCYCLINE; ERYTHROMYCIN; PRISTINAMYCIN; SMALL INTERFERING RNA; TETRACYCLINE; TRANSACTIVATOR PROTEIN; BETA GLUCOSIDASE; CRADD PROTEIN; CYANOGENIC BETA GLUCOSIDASE; CYANOGENIC BETA-GLUCOSIDASE;

ANIMAL CELL; ANIMAL EXPERIMENT; ARTICLE; CONTROLLED STUDY; EPIGENETICS; FEMALE; GENE CONTROL; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENE SILENCING; HUMAN; HUMAN CELL; IN VITRO STUDY; IN VIVO STUDY; INTRON; MOUSE; NONHUMAN; PRIORITY JOURNAL; REPRESSOR GENE; RNA VECTOR; TRANSCRIPTION REGULATION; TRANSGENE; ANIMAL; BIOSYNTHESIS; CELL LINE; CHO CELL; CRICETULUS; GENE VECTOR; GENETIC ENGINEERING; GENETIC EPIGENESIS; GENETICS; HAMSTER; HELA CELL; METHODOLOGY; REPORTER GENE; RNA INTERFERENCE;

MAMMALIA; MUS;

ANIMALS; BETA-GLUCOSIDASE; CELL LINE; CHO CELLS; CRADD SIGNALING ADAPTOR PROTEIN; CRICETINAE; CRICETULUS; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION; GENES, REPORTER; GENETIC ENGINEERING; GENETIC VECTORS; HELA CELLS; HUMANS; INTRONS; MICE; RNA INTERFERENCE; RNA, SMALL INTERFERING; TRANS-ACTIVATORS; TRANSGENES;

EID: 52649173346     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn443     Document Type: Article

References (64)

1. Greber,D. and Fussenegger,M. (2007) Mammalian synthetic biology: engineering of sophisticated gene networks. J. Biotechnol., 130 329-345.
2. Kramer,B.P., Viretta,A.U., Daoud-El-Baba,M., Aubel,D., Weber,W. and Fussenegger,M. (2004) An engineered epigenetic transgene switch in mammalian cells. Nat. Biotechnol., 22, 867-870.
3. Kramer,B.P. and Fussenegger,M. (2005) Hysteresis in a synthetic mammalian gene network. Proc. Natl Acad. Sci. USA, 102, 9517-9522.
4. Kramer,B.P., Fischer,C. and Fussenegger,M. (2004) BioLogic gates enable logical transcription control in mammalian cells. Biotechnol. Bioeng. 87, 478-484.
5. Rinaudo,K., Bleris,L., Maddamsetti,R., Subramanian,S., Weiss,R. and Benenson,Y. (2007) A universal RNAi-based logic evaluator that operates in mammalian cells. Nat. Biotechnol., 25, 795-801.
6. Weber,W., Kramer,B.P. and Fussenegger,M. (2007) A genetic time-delay circuitry in mammalian cells. Biotechnol. Bioeng., 98, 894-902.
7. Weber,W., Stelling,J., Rimann,M., Keller,B., Daoud-El Baba,M., Weber,C.C., Aubel,D. and Fussenegger,M. (2007) A synthetic time-delay circuit in mammalian cells and mice. Proc. Natl Acad. Sci. USA, 104, 2643-2648.
8. Bellefroid,E.J., Poncelet,D.A., Lecoeq,P.J., Revelant,O. and Martial,J.A. (1991) The evolutionarily conserved Kruppel-associated box domain defines a subfamily of eukaryotic multifingered proteins. Proc. Narl Acad. Sci. USA, 88, 3608-3612.
9. Gossen,M. and Bujard,H. (1992) Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. Proc. Natl Acad. Sci. USA, 89, 5547-5551.
10. Triezenberg,S.J., Kingsbury,R.C. and McKnight,S.L. (1988) Functional dissection of VP16, the trans-activator of herpes simplex virus immediate early gene expression. Genes Dev., 2, 718-729.
11. Fussenegger,M., Morris,R.P., Fux,C., Rimann,M., von Stockar,B., Thompson,C.J. and Bailey,J.E. (2000) Streptogramin-based gene regulation systems for mammalian cells. Nat. Biotechnol., 18, 1203-1208.
12. Weber,W., Fux,C., Daoud-el Baba,M., Keller,B., Weber,C.C., Kramer,B.P., Heinzen,C., Aubel,D., Bailey,J.E. and Fussenegger,M. (2002) Macrolide-based transgene control in mammalian cells and mice. Nat. Biotechnol., 20, 901-907.
13. Kramer,B.P. and Fussenegger,M. (2005) Transgene control engineering in mammalian cells. Methods Mol. Biol., 308, 123-143.
14. Weber,W. and Fussenegger,M. (2006) Pharmacologic transgene control systems for gene therapy. J. Gene Med., 8, 535-556.
15. Zhao,H.F., Boyd,J., Jolicoeur,N. and Shen,S.H. (2003) A coumermycin/ novobiocin-regulated gene expression system. Hum. Gene Ther., 14, 1619-1629.
16. Rivera,V.M., Clackson,T., Natesan,S., Pollock,R., Amara,J.F., Keenan,T., Magari,S.R., Phillips,T., Courage,N.L., Cerasoli,F. Jr. et al. (1996) A humanized system for pharmacologic control of gene expression. Nat. Med., 2, 1028-1032.
17. Braselmann,S., Graninger,P. and Busslinger,M. (1993) A selective transcriptional induction system for mammalian cells based on Gal4-estrogen receptor fusion proteins. Proc. Natl Acad. Sci. USA, 90, 1657-1661.
18. Weber,W., Malphettes,L., de Jesus,M., Schoenmakers,R., El-Baba,M.D., Spielmann,M., Keller,B., Weber,C.C., van de Wetering,P., Aubel,D. et al. (2005) Engineered Streptomyces quorum-sensing components enable inducible siRNA-mediated translation control in mammalian cells and adjustable transcription control in mice. J. Gene Med., 7, 518-525.
19. Kramer,B.P., Fischer,M. and Fussenegger,M. (2005) Semi-synthetic mammalian gene regulatory networks. Metab. Eng., 7, 241-250.
20. Semenza,G.L. (2003) Targeting HIF-1 for cancer therapy. Nat. Rev. Cancer, 3, 721-732.
21. Hartenbach,S., Daoud-El Baba,M., Weber,W. and Fussenegger,M. (2007) An engineered L-arginine sensor of Chlamydia pneumoniae enables arginine-adjustable transcription control in mammalian cells and mice. Nucleic Acids Res., 35, e135.
22. Malphettes,L., Weber,C.C., El-Baba,M.D., Schoenmakers,R.G., Aubel,D., Weber,W. and Fussenegger,M. (2005) A novel mammalian expression system derived from components coordinating nicotine degradation in arthrobacter nicotinovorans pAO1. Nucleic Acids Res., 33, e107.
23. Weber,W., Rimann,M., Spielmann,M., Keller,B., Daoud-El Baba,M., Aubel,D., Weber,C.C. and Fussenegger,M. (2004) Gas-inducible transgene expression in mammalian cells and mice. Nat. Biotechnol., 22 1440-1444.
24. Weber,W., Bacchus,W., Gruber,F., Hamberger,M. and Fussenegger,M. (2007) A novel vector platform for vitamin H-inducible transgene expression in mammalian cells. J. Biotechnol., 131, 150-158.
25. Boorsma,M., Nieba,L., Koller,D., Bachmann,M.F., Bailey,J.E. and Renner,W.A. (2000) A temperature-regulated replicon-based DNA expression system. Nat. Biotechnol., 18, 429-432.
26. Stanger,B.Z., Leder,P., Lee,T.H., Kim,E. and Seed,B. (1995) RIP: A novel protein containing a death domain that interacts with Fas/APO-1 (CD95) in yeast and causes cell death. Cell, 81, 513-523.
27. Link,N., Aubel,C., Kelm,J.M., Marty,R.R., Greber,D., Djonov,V., Bourhis,J., Weber,W. and Fussenegger,M. (2006) Therapeutic protein transduction of mammalian cells and mice by nucleic acid-free lentiviral nanoparticles. Nucleic Acids Res., 34, e16.
28. Prabhakaran,K., Li,L., Borowitz,J.L. and Isom,G.E. (2004) Caspase inhibition switches the mode of cell death induced by cyanide by enhancing reactive oxygen species generation and PARP-1 activation. Toxicol. Appl. Pharmacol., 195, 194-202.
29. Greber,D. and Fussenegger,M. (2007) Multi-gene engineering: Simultaneous expression and knockdown of six genes off a single platform. Biotechnol. Bioeng., 96, 821-834.
30. Mitta,B., Rimann,M., Ehrengruber,M.U., Ehrbar,M., Djonov,V., Kelm,J. and Fussenegger,M. (2002) Advanced modular self-inactivating lentiviral expression vectors for multigene interventions in mammalian cells and in vivo transduction. Nucleic Acids Res., 30, e113.
31. Weber,W., Schoenmakers,R., Spielmann,M., El-Baba,M.D., Folcher,M., Keller,B., Weber,C.C., Link,N., van de Wetering,P., Heinzen,C. et al. (2003) Streptomyces-derived quorum-sensing systems engineered for adjustable transgene expression in mammalian cells and mice. Nucleic Acids Res., 31, e71.
32. Berger,J., Hauber,J., Hauber,R., Geiger,R. and Cullen,BR. (1988) Secreted placental alkaline phosphatase: A powerful new quantitative indicator of gene expression in eukaryotic cells. Gene, 66, 1-10.
33. Schlatter,S., Rimann,M., Kelm,J. and Fussenegger,M. (2002) SAMY, a novel mammalian reporter gene derived from Bacillus stearothermophilus alpha-amylase. Gene, 282, 19-31.
34. Xia,H., Mao,Q., Paulson,H.L. and Davidson,B.L. (2002) siRNA-mediated gene silencing in vitro and in vivo. Nat. Biotechnol., 20, 1006-1010.
35. Malphettes,L. and Fussenegger,M. (2006) Improved transgene expression fine-tuning in mammalian cells using a novel transcription-translation network. J. Biotechnol., 124, 732-746.
36. Weber,W., Marty,R.R., Keller,B., Rimann,M., Kramer,B.P. and Fussenegger,M. (2002) Versatile macrolide-responsive mammalian expression vectors for multiregulated multigene metabolic engineering. Biotechnol. Bioeng., 80, 691-705.
37. Malphettes,L. and Fussenegger,M. (2006) Impact of RNA interference on gene networks. Metab. Eng., 8, 672-683.
38. Koponen,J.K., Kankkonen,H., Kannasto,J., Wirth,T., Hillen,W., Bujard,H. and Yla-Herttuala,S. (2003) Doxycycline-regulated lentiviral vector system with a novel reverse transactivator rtTA2S-M2 shows a tight control of gene expression in vitro and in vivo. Gene Ther., 10 459-466.
39. Urlinger,S., Baron,U., Thellmann,M., Hasan,M.T., Bujard,H. and Hillen,W. (2000) Exploring the sequence space for tetracycline-dependent transcriptional activators: Novel mutations yield expanded range and sensitivity. Proc. Natl Acad. Sci. USA, 97, 7963-7968.
40. Zhou,X., Symons,J., Hoppes,R., Krueger,C., Berens,C., Hillen,W., Berkhout,B. and Das,A.T. (2007) Improved single-chain transactivators of the Tet-On gene expression system. BMC Biotechnol., 7, 6.
41. Bockamp,E., Christel,C., Hameyer,D., Khobta,A., Maringer,M., Reis,M., Heck,R., Cabezas-Wallseheid,N., Epe,B., Oesch-Bartlomowiez,B. et al. (2007) Generation and characterization of tTS-H4: A novel transcriptional repressor that is compatible with the reverse tetracycline-controlled TET-ON system. J. Gene Med., 9, 308-318.
42. Sipo,I., Hurtado Pico,A., Wang,X., Eberle,J., Petersen,I., Weger,S., Poller,W. and Fechner,H. (2006) An improved Tet-On regulatable FasL-adenovirus vector system for lung cancer therapy. J. Mol. Med. 84, 215-225.
43. Bornkamm,G.W., Berens,C., Kuklik-Roos,C., Bechet,J.M., Laux,G., Bachl,J., Korndoerfer,M., Schlee,M., Holzel,M., Malamoussi,A. et al. (2005) Stringent doxycycline-dependent control of gene activities using an episomal one-vector system. Nucleic Acids Res., 33, e137.
44. Freundlieb,S., Schirra-Muller,C. and Bujard,H. (1999) A tetracycline controlled activation/repression system with increased potential for gene transfer into mammalian cells. J. Gene Med., 1, 4-12.
45. Lamartina,S., Silvi,L., Roscilli,G., Casimiro,D., Simon,A.J., Davies,M.E., Shiver,J.W., Rinaudo,C.D., Zampaglione,I., Fattori,E. et al. (2003) Construction of an rtTA2(s)-m2/tts(kid)-based transcription regulatory switch that displays no basal activity, good inducibility, and high responsiveness to doxycycline in mice and non-human primates. Mol. Ther., 7, 271-280.
46. Rossi,F.M., Kringstein,A.M., Spicher,A., Guicherit,O.M. and Blau,H.M. (2000) Transcriptional control: Rheostat converted to on/off switch. Mol. Cell, 6, 723-728.
47. Salucci,V., Scarito,A., Aurisicchio,L., Lamartina,S., Nicolaus,G., Giampaoli,S., Gonzalez-Paz,O., Toniatti,C., Bujard,H., Hillen,W. et al. (2002) Tight control of gene expression by a helper-dependent adenovirus vector carrying the rtTA2(s)-M2 tetracycline transactivator and repressor system. Gene Ther., 9, 1415-1421.
48. Baron,U., Gossen,M. and Bujard,H. (1997) Tetracycline-controlled transcription in eukaryotes: Novel transactivators with graded transactivation potential. Nucleic Acids Res., 25, 2723-2729.
49. Malphettes,L., Schoenmakers,R.G. and Fussenegger,M. (2006) 6-hydroxy-nicotine-inducible multilevel transgene control in mammalian cells. Metab. Eng., 8, 543-553.
50. Urlinger,S., Helbl,V., Guthmann,J., Pook,E., Grimm,S. and Hillen,W. (2000) The p65 domain from NF-kappaB is an efficient human activator in the tetracycline-regulatable gene expression system. Gene, 247 103-110.
51. Weber,W., Kramer,B.P., Fux,C., Keller,B. and Fussenegger,M. (2002) Novel promoter/transactivator configurations for macrolide-and streptogramin-responsive transgene expression in mammalian cells. J. Gene Med., 4, 676-686.
52. Aubrecht,J., Manivasakam,P. and Schiestl,R.H. (1996) Controlled gene expression in mammalian cells via a regulatory cascade involving the tetracycline transactivator and lac repressor. Gene, 172, 227-231.
53. ImhofM.O., Chatellard,P. and Mermod,N. (2000) A regulatory network for the efficient control of transgene expression. J. Gene Med., 2 107-116.
54. Deans,T.L., Cantor,C.R. and Collins,J.J. (2007) A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells. Cell, 130, 363-372.
55. Malphettes,L. and Fussenegger,M. (2004) Macrolide- and tetracycline-adjustable siRNA-mediated gene silencing in mammalian cells using polymerase II-dependent promoter derivatives. Biotechnol. Bioeng., 88, 417-425.
56. Pluta,K., Diehl,W., Zhang,X.Y., Kutner,R., Bialkowska,A. and Reiser,J. (2007) Lentiviral vectors encoding tetracycline-dependent repressors and transactivators for reversible knockdown of gene expression: A comparative study. BMC Biotechnol., 7, 41.
57. Stegmeier,F., Hu,G., Rickles,R.J., Hannon,G.J. and Elledge,S.J. (2005) A lentiviral microRNA-based system for single-copy polymerase II-regulated RNA interference in mammalian cells. Proc. Natl Acad. Sci. USA, 102, 13212-13217.
58. Szulc,J., Wiznerowicz,M., Sauvain,M.O., Trono,D. and Aebischer,P. (2006) A versatile tool for conditional gene expression and knockdown. Nat. Methods, 3, 109-116.
59. van de Wetering,M., Oving,I., Muncan,V., Pon Fong,M.T., Brantjes,H., van Leenen,D., Holstege,F.C., Brummelkamp,T.R., Agami,R. and Clevers,H. (2003) Specific inhibition of gene expression using a stably integrated, inducible small-interfering-RNA vector. EMBO Rep., 4, 609-615.
60. Fussenegger,M., Moser,S., Mazur,X. and Bailey,J.E. (1997) Autoregulated multicistronic expression vectors provide one-step cloning of regulated product gene expression in mammalian cells. Biotechnol. Prog., 13, 733-740.
61. Fussenegger,M., Mazur,X. and Bailey,J.E. (1997) A novel cytostatic process enhances the productivity of chinese hamster ovary cells. Biotechnol. Bioeng., 55, 927-939.
62. Moser,S., Rimann,M., Fux,C., Schlatter,S., Bailey,J.E. and Fussenegger,M. (2001) Dual-regulated expression technology: A new era in the adjustment of heterologous gene expression in mammalian cells. J. Gene Med., 3, 529-549.
63. Moser,S., Schlatter,S., Fux,C., Rimann,M., Bailey,J.E. and Fussenegger,M. (2000) An update of pTRIDENT multicistronic expression vectors: PTRIDENTs containing novel streptogramin-responsive promoters. Biotechnol. Prog., 16, 724-735.
64. Weber,W., Marty,R.R., Link,N., Ehrbar,M., Keller,B., Weber,C.C., Zisch,A.H., Heinzen,C., Djonov,V. and Fussenegger,M. (2003) Conditional human VEGF-mediated vascularization in chicken embryos using a novel temperature-inducible gene regulation (TIGR) system. Nucleic Acids Res., 31, e69.