Parameter asymmetry and time-scale separation in core genetic commitment circuits

Quantitative Biology

Volumn 3, Issue 1, 2015, Pages 19-45

  Xi, Hongguang ^a   Turcotte, Marc ^a,b  

^a UNIVERSITY OF TEXAS AT ARLINGTON   (United States)

^b UNIVERSITY OF TEXAS AT DALLAS   (United States)

Author keywords

gene regulation; nonlinear dynamics; stochasticity; systems biology; theoretical biology

Indexed keywords

EID: 85018467768     PISSN: 20954689     EISSN: 20954697     Source Type: Journal    
DOI: 10.1007/s40484-015-0042-1     Document Type: Article

References (38)

1. Waddington, C. H. (1957) The Strategy of the Genes. London: Routledge
2. Ferrell, J. E. Jr. (2012) Bistability, bifurcations, and Waddington’s epigenetic landscape. Curr. Biol., 22, R458–R466
3. Strogatz, S. H. (1994) Nonlinear Dynamics and Chaos. Cambridge: Perseus Books Publishing
4. Jaeger, J., Monk, N. (2014) Bioattractors: Dynamical systems theory and the evolution of regulatory processes. J. Physiol., 592, 2267–2281
5. Çağatay, T., Turcotte, M., Elowitz, M. B., Garcia-Ojalvo, J. and Süel, G. M. (2009) Architecture-dependent noise discriminates functionally analogous differentiation circuits. Cell, 139, 512–522
6. Elowitz, M. B., Levine, A. J., Siggia, E. D. and Swain, P. S. (2002) Stochastic gene expression in a single cell. Science, 297, 1183–1186
7. Süel, G. M., Garcia-Ojalvo, J., Liberman, L. M. and Elowitz, M. B. (2006) An excitable gene regulatory circuit induces transient cellular differentiation. Nature, 440, 545–550
8. Süel, G. M., Kulkarni, R. P., Dworkin, J., Garcia-Ojalvo, J. and Elowitz, M. B. (2007) Tunability and noise dependence in differentiation dynamics. Science, 315, 1716–1719
9. Thattai, M. and van Oudenaarden, A. (2004) Stochastic gene expression in fluctuating environments. Genetics, 167, 523–530
10. Turcotte, M., Garcia-Ojalvo, J. and Süel, G. M. (2008) A genetic timer through noise-induced stabilization of an unstable state. Proc. Natl. Acad. Sci. USA, 105, 15732–15737
11. Xi, H., Duan, L. and Turcotte, M. (2013) Point-cycle bistability and stochasticity in a regulatory circuit for Bacillus subtilis competence. Math. Biosci., 244, 135–147
12. Xi, H., Yang, Z. and Turcotte, M. (2013) Subtle interplay of stochasticity and deterministic dynamics pervades an evolutionary plausible genetic circuit for Bacillus subtilis competence. Math. Biosci., 246, 148–163
13. Li, C., Wang, E. and Wang, J. (2011) Landscape and flux decomposition for exploring global natures of non-equilibrium dynamical systems under intrinsic statistical fluctuations. Chem. Phys. Lett., 505, 75–80.
14. Li, C., Wang, E. and Wang, J. (2011) Landscape, flux, correlation, resonance, coherence, stability, and key network wirings of stochastic circadian oscillation. Biophys. J., 101, 1335–1344
15. Li, C., Wang, E. and Wang, J. (2012) Landscape topography determines global stability and robustness of a metabolic network. ACS Synth Biol, 1, 229–239
16. Li, C. and Wang, J. (2013) Quantifying Waddington landscapes and paths of non-adiabatic cell fate decisions for differentiation, reprogramming and transdifferentiation. J. R. Soc. Interface, 10, 20130787
17. Li, C. and Wang, J. (2014) Landscape and flux reveal a new global view and physical quantification of mammalian cell cycle. Proc. Natl. Acad. Sci. USA, 111, 14130–14135
18. Li, C. and Wang, J. (2014) Quantifying the underlying landscape and paths of cancer. J. R. Soc. Interface, 11, 20140774
19. Wang, J., Zhang, K., Xu, L. and Wang, E. (2011) Quantifying the Waddington landscape and biological paths for development and differentiation. Proc. Natl. Acad. Sci. USA, 108, 8257–8262
20. Wu, W. and Wang, J. (2013) Landscape framework and global stability for stochastic reaction diffusion and general spatially extended systems with intrinsic fluctuations. J. Phys. Chem. B, 117, 12908–12934
21. Wu, W. and Wang, J. (2013) Potential and flux field landscape theory. I. Global stability and dynamics of spatially dependent non-equilibrium systems. J. Chem. Phys., 139, 121920
22. Xu, L., Zhang, F., Zhang, K., Wang, E. and Wang, J. (2014) The potential and flux landscape theory of ecology. PLoS One, 9, e86746
23. Zhang F., Xu L., Zhang K., Wang E., Wang J., (2012) The potential and flux landscape theory of evolution. J. Chem. Phys., 137, 065102
24. Beard, D. A. D., Babson, E., Curtis, E. and Qian, H. (2004) Thermodynamic constraints for biochemical networks. J. Theor. Biol., 228, 327–333
25. Beard, D. A. and Qian H. (2008) Chemical Biophysics, Cambridge: Cambridge University Press
26. Qian, H. and Cooper, J. A. (2008) Temporal cooperativity and sensitivity amplification in biological signal transduction. Biochemistry, 47, 2211–2220
27. Qian, H. (2007) Phosphorylation energy hypothesis: open chemical systems and their biological functions. Annu. Rev. Phys. Chem., 58, 113–142
28. Qian, H. and Beard, D. A. (2005) Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium. Biophys. Chem., 114, 213–220
29. Qian, H., Beard, D. A. and Liang, S. D. (2003) Stoichiometric network theory for nonequilibrium biochemical systems. Eur. J. Biochem., 270, 415–421
30. Ma, W., Trusina, A., El-Samad, H., Lim, W. A. and Tang, C. (2009) Defining network topologies that can achieve biochemical adaptation. Cell, 138, 760–773
31. Zhang, J., Yuan, Z., Li, H. X. and Zhou, T. (2010) Architecturedependent robustness and bistability in a class of genetic circuits. Biophys. J., 99, 1034–1042
32. Snoussi, E. H. (1998) Necessary Conditions for Multistationarity and Stable Periodicity. J. Biol. Syst., 06, 3–9
33. Gardner, T. S. and Faith, J. J. (2005) Reverse-engineering transcription control networks. Phys. Life Rev., 2, 65–88
34. Chickarmane, V., Troein, C., Nuber, U. A., Sauro, H. M. and Peterson, C. (2006) Transcriptional dynamics of the embryonic stem cell switch. PLoS Comput. Biol., 2, e123
35. Gillespie, D. T. (1976) A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions. J. Comput. Phys., 22, 403–434
36. Gillespie, D. T. (1977) Exact Stochastic Simulation of Coupled Chemical Reactions. J. Phys. Chem., 81, 2340–2361
37. Gillespie Markov Processes, D. T. An Introduction for Physical Scientists, Academic Press, 1991
38. Gillespie, D. T. (2007) Stochastic simulation of chemical kinetics. Annu. Rev. Phys. Chem., 58, 35–55