Synthetic feedback control using an RNAi-based gene-regulatory device

Journal of Biological Engineering

Volumn 9, Issue 1, 2015, Pages

  Bloom, Ryan J ^a   Winkler, Sally M ^a   Smolke, Christina D ^a  

^a Stanford University   (United States)

Author keywords

Feedback control; MicroRNA; Ribozyme; Synthetic biology

Indexed keywords

CELL PROTEIN; DNA FRAGMENT; HAMMERHEAD RIBOZYME; LIGAND; MICRORNA; TRANSCRIPTION FACTOR E2F1;

ANALYTICAL PARAMETERS; ARTICLE; CELL ENGINEERING; DNA TEMPLATE; ENZYMATIC DEGRADATION; FLOW CYTOMETRY; FUSION GENE; GENERAL MEDICAL DEVICE; GENETIC REGULATION; HUMAN; HUMAN CELL; MATHEMATICAL MODEL; MICHAELIS MENTEN KINETICS; NEGATIVE FEEDBACK; NONHUMAN; OFF GENETIC CONTROL DEVICE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; RNA INTERFERENCE; RNA PROBE; STEADY STATE; SYNTHETIC BIOLOGY;

MAMMALIA;

EID: 84928040343     PISSN: None     EISSN: 17541611     Source Type: Journal    
DOI: 10.1186/s13036-015-0002-3     Document Type: Article

References (43)

1. Lienert F, Lohmueller JJ, Garg A, Silver PA. Synthetic biology in mammalian cells: next generation research tools and therapeutics. Nat Rev Mol Cell Biol. 2014;15(2):95-107.
2. Jaenisch R, Young R. Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell. 2008;132(4):567-82.
3. Hahn WC, Weinberg RA. Modelling the molecular circuitry of cancer. Nat Rev Cancer. 2002;2(5):331-41.
4. Slusarczyk AL, Lin A, Weiss R. Foundations for the design and implementation of synthetic genetic circuits. Nat Rev Genet. 2012;13(6):406-20.
5. Win MN, Liang JC, Smolke CD. Frameworks for programming biological function through RNA parts and devices. Chem Biol. 2009;16(3):298-310.
6. Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell. 2009;136(2):215-33.
7. Shukla GC, Singh J, Barik S. MicroRNAs: Processing, Maturation, Target Recognition and Regulatory Functions. Mol Cell Pharmacol. 2011;3(3):83-92.
8. Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 2005;120(1):15-20.
9. Culler SJ, Hoff KG, Smolke CD. Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science. 2010;330(6008):1251-5.
10. Tigges M, Marquez-Lago TT, Stelling J, Fussenegger M. A tunable synthetic mammalian oscillator. Nature. 2009;457(7227):309-12.
11. Deans TL, Cantor CR, Collins JJ. A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells. Cell. 2007;130(2):363-72.
12. Leisner M, Bleris L, Lohmueller J, Xie Z, Benenson Y. Rationally designed logic integration of regulatory signals in mammalian cells. Nat Nanotechnol. 2010;5(9):666-70.
13. Beisel CL, Chen YY, Culler SJ, Hoff KG, Smolke CD. Design of small molecule-responsive microRNAs based on structural requirements for Drosha processing. Nucleic Acids Res. 2011;39(7):2981-94.
14. Beisel CL, Bayer TS, Hoff KG, Smolke CD. Model-guided design of ligand-regulated RNAi for programmable control of gene expression. Mol Syst Biol. 2008;4:224.
15. An CI, Trinh VB, Yokobayashi Y. Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction. RNA. 2006;12(5):710-6.
16. Bloom RJ, Winkler SM, Smolke CD. A quantitative framework for the forward design of synthetic miRNA circuits. Nat Methods. 2014;11(11):1147-53.
17. Yi TM, Huang Y, Simon MI, Doyle J. Robust perfect adaptation in bacterial chemotaxis through integral feedback control. Proc Natl Acad Sci U S A. 2000;97(9):4649-53.
18. Ang J, McMillen DR. Physical constraints on biological integral control design for homeostasis and sensory adaptation. Biophys J. 2013;104(2):505-15.
19. Ballarino M, Pagano F, Girardi E, Morlando M, Cacchiarelli D, Marchioni M, et al. Coupled RNA processing and transcription of intergenic primary microRNAs. Mol Cell Biol. 2009;29(20):5632-8.
20. Win MN, Smolke CD. A modular and extensible RNA-based gene-regulatory platform for engineering cellular function. Proc Natl Acad Sci U S A. 2007;104(36):14283-8.
21. Wei KY, Chen YY, Smolke CD. A yeast-based rapid prototype platform for gene control elements in mammalian cells. Biotechnol Bioeng. 2013;110(4):1201-10.
22. Bloom RJ, WInkler SM, Smolke CD. A quantitative framework for the forward design of synthetic miRNA circuits. Nat Methods. 2014; in press.
23. Kennedy AB, Liang JC, Smolke CD. A versatile cis-blocking and trans-activation strategy for ribozyme characterization. Nucleic Acids Res. 2013;41(2):e41.
24. Chang AL, McKeague M, Liang JC, Smolke CD. Kinetic and equilibrium binding characterization of aptamers to small molecules using a label-free, sensitive, and scalable platform. Anal Chem. 2014;86(7):3273-8.
25. Liang JC, Chang AL, Kennedy AB, Smolke CD. A high-throughput, quantitative cell-based screen for efficient tailoring of RNA device activity. Nucleic Acids Res. 2012;40(20):e154.
26. Mukherji S, Ebert MS, Zheng GX, Tsang JS, Sharp PA, van Oudenaarden A. MicroRNAs can generate thresholds in target gene expression. Nat Genet. 2011;43(9):854-9.
27. Kim DH, Saetrom P, Snove Jr O, Rossi JJ. MicroRNA-directed transcriptional gene silencing in mammalian cells. Proc Natl Acad Sci U S A. 2008;105(42):16230-5.
28. Hirao I, Spingola M, Peabody D, Ellington AD. The limits of specificity: an experimental analysis with RNA aptamers to MS2 coat protein variants. Mol Divers. 1998;4(2):75-89.
29. Ishizaki J, Nevins JR, Sullenger BA. Inhibition of cell proliferation by an RNA ligand that selectively blocks E2F function. Nat Med. 1996;2(12):1386-9.
30. Kennedy AB, Vowles JV, d'Espaux L, Smolke CD. Protein-responsive ribozyme switches in eukaryotic cells. Nucleic Acids Res. 2014;42(19):12306-21.
31. Purnick PE, Weiss R. The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol. 2009;10(6):410-22.
32. Shimoga V, White JT, Li Y, Sontag E, Bleris L. Synthetic mammalian transgene negative autoregulation. Mol Syst Biol. 2013;9:670.
33. Elowitz MB, Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature. 2000;403(6767):335-8.
34. Stapleton JA, Endo K, Fujita Y, Hayashi K, Takinoue M, Saito H, et al. Feedback control of protein expression in mammalian cells by tunable synthetic translational inhibition. ACS Synth Biol. 2012;1(3):83-8.
35. Rosenfeld N, Young JW, Alon U, Swain PS, Elowitz MB. Accurate prediction of gene feedback circuit behavior from component properties. Mol Syst Biol. 2007;3:143.
36. Corish P, Tyler-Smith C. Attenuation of green fluorescent protein half-life in mammalian cells. Protein Eng. 1999;12(12):1035-40.
37. pDsRed-Express-DR Vector Information [Brochure]. 2005. Mountain View, CA: Clontech Laboratories, Inc.
38. Becskei A, Serrano L. Engineering stability in gene networks by autoregulation. Nature. 2000;405(6786):590-3.
39. Gardner TS, Cantor CR, Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature. 2000;403(6767):339-42.
40. Kumar D, An CI, Yokobayashi Y. Conditional RNA interference mediated by allosteric ribozyme. J Am Chem Soc. 2009;131(39):13906-7.
41. Zhao S, Fernald RD. Comprehensive algorithm for quantitative real-time polymerase chain reaction. J Comput Biol. 2005;12(8):1047-64.
42. Katsamba PS, Park S, Laird-Offringa IA. Kinetic studies of RNA-protein interactions using surface plasmon resonance. Methods. 2002;26(2):95-104.
43. Myszka DG. Improving biosensor analysis. J Mol Recognit. 1999;12(5):279-84.