Phenotypic switching in gene regulatory networks

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 19, 2014, Pages 6994-6999

  Thomas, Philipp ^a,b   Popovic, Nikola ^a   Grima, Ramon ^a,b  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b SynthSys   (United Kingdom)

Author keywords

Chemical master equation; Gene expression noise

Indexed keywords

ALLOSTERISM; ARTICLE; GENE EXPRESSION; GENE REGULATORY NETWORK; GENE SWITCHING; HUMAN; HUMAN CELL; OSCILLATOR; PHENOTYPE; PRIORITY JOURNAL; PROMOTER REGION; SINGLE CELL ANALYSIS; STOCHASTIC MODEL; TRANSCRIPTION REGULATION; TRANSLATION REGULATION;

CHEMICAL MASTER EQUATION; GENE EXPRESSION NOISE;

ANIMALS; COMPUTER SIMULATION; EPIGENOMICS; FEEDBACK, PHYSIOLOGICAL; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; HUMANS; MODELS, GENETIC; PHENOTYPE; PROMOTER REGIONS, GENETIC; STOCHASTIC PROCESSES;

EID: 84900519810     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1400049111     Document Type: Article

References (25)

1. To T-L, Maheshri N (2010) Noise can induce bimodality in positive transcriptional feedback loops without bistability. Science 327(5969):1142-1145.
2. Pelet S, et al. (2011) Transient activation of the HOG MAPK pathway regulates bi-modal gene expression. Science 332(6030):732-735.
3. Shalek AK, et al. (2013) Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature 498(7453):236-240.
4. Choi PJ, Cai L, Frieda K, Xie XS (2008) A stochastic single-molecule event triggers phenotype switching of a bacterial cell. Science 322(5900):442-446.
5. Acar M, Becskei A, van Oudenaarden A (2005) Enhancement of cellular memory by reducing stochastic transitions. Nature 435(7039):228-232.
6. Gupta PB, et al. (2011) Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells. Cell 146(4):633-644.
7. Chang HH, Hemberg M, Barahona M, Ingber DE, Huang S (2008) Transcriptome-wide noise controls lineage choice in mammalian progenitor cells. Nature 453(7194):544-547.
8. Strasser M, Theis FJ, Marr C (2012) Stability and multiattractor dynamics of a toggle switch based on a two-stage model of stochastic gene expression. Biophys J 102(1):19-29.
9. Acar M, Mettetal JT, van Oudenaarden A (2008) Stochastic switching as a survival strategy in fluctuating environments. Nat Genet 40(4):471-475.
10. Blake WJ, et al. (2006) Phenotypic consequences of promoter-mediated transcrip-tional noise. Mol Cell 24(6):853-865.
11. Shahrezaei V, Swain PS (2008) Analytical distributions for stochastic gene expression. Proc Natl Acad Sci USA 105(45):17256-17261.
12. Qian H, Shi P-Z, Xing J (2009) Stochastic bifurcation, slow fluctuations, and bistability as an origin of biochemical complexity. Phys Chem Chem Phys 11(24):4861-4870.
13. Grima R, Schmidt DR, Newman TJ (2012) Steady-state fluctuations of a genetic feedback loop: An exact solution. J Chem Phys 137(3):035104.
14. Mariani L, et al. (2010) Short-term memory in gene induction reveals the regulatory principle behind stochastic IL-4 expression. Mol Syst Biol 6(1).
15. Paulsson J (2005) Models of stochastic gene expression. Phys Life Rev 2(2):157-175.
16. Perkins TJ, Weiße AY, Swain PS (2012) Chance and memory. Quantitative Biology: From Molecular to Cellular Systems, ed Wall ME (CRC, Boca Raton, FL), pp 51-72.
17. Goutsias J (2005) Quasiequilibrium approximation of fast reaction kinetics in stochastic biochemical systems. J Chem Phys 122(18):184102.
18. Song C, et al. (2010) Estimating the stochastic bifurcation structure of cellular networks. PLOS Comput Biol 6(3):e1000699.
19. Kaern M, Elston TC, Blake WJ, Collins JJ (2005) Stochasticity ingene expression: from theories to phenotypes. Nat Rev Genet 6(6):451-464.
20. Gardner TS, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403(6767):339-342.
21. Geva-Zatorsky N, et al. (2006) Oscillations and variability in the p53 system. Mol Syst Biol 2(1).
22. Balázsi G, van Oudenaarden A, Collins JJ (2011) Cellular decision making and biological noise: From microbes to mammals. Cell 144(6):910-925.
23. Innocentini GCP, Forger M, Ramos AF, Radulescu O, Hornos JEM (2013) Multimodality and flexibility of stochastic gene expression. Bull Math Biol 75(12):2600-2630.
24. Hasenauer J, Wolf V, Kazeroonian A, Theis FJ (2013) Method of conditional moments (MCM) for the Chemical Master Equation: A unified framework for the method of moments and hybrid stochastic-deterministic models. J Math Biol, 10.1007/s00285-013-0711-5.
25. Nevozhay D, Adams RM, Van Itallie E, Bennett MR, Balázsi G (2012) Mapping the environmental fitness landscape of a synthetic gene circuit. PLOS Comput Biol 8(4): e1002480.