Abstract
Stochastic phenomena in gene regulatory networks can be modelled by the chemical master equation for gene products such as mRNA and proteins. If some of these elements are present in significantly higher amounts than the rest, or if some of the reactions between these elements are substantially faster than others, it is often possible to reduce the master equation to a simpler problem using asymptotic methods. We present examples of such a procedure and analyse the relationship between the reduced models and the original.
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Abramowitz M, Stegun I (1972) Handbook of mathematical functions with formulas, graphs, and mathematical tables. National Bureau of Standards, Washington
Berg O (1978) A model for the statistical fluctuations of protein numbers in a microbial population. J Theor Biol 71: 587–603
Berg O, Blomberg C (1977) Mass action relations in vivo with application to the lac operon. J Theor Biol 67: 523–533
Bernstein J, Khodursky A, Lin P, Lin-Chao S, Cohen S (2002) Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc Natl Acad Sci USA 99: 9697–9702
Blake W, Kaern M, Cantor C, Collins J (2003) Noise in eukaryotic gene expression. Nature 422: 633–637
Bokes P, King J, Wood A, Loose M (2011) Exact and approximate distributions of protein and mRNA levels in the low-copy regime of gene expression. J Math Biol. doi:10.1007/s00285-011-0433-5
Breuer H, Petruccione F (2002) The theory of open quantum systems. Oxford University Press, New York
Cai L, Friedman N, Xie X (2006) Stochastic protein expression in individual cells at the single molecule level. Nature 440: 358–362
Cao Y, Gillespie D, Petzold L (2005) The slow-scale stochastic simulation algorithm. J Chem Phys 122: 014,116
Carrier G, Pearson C (1988) Partial differential equations: theory and technique, 2nd edn. Academic Press, London
Cooley J, Lewis P, Welch P (1970) The fast Fourier transform algorithm: programming considerations in the calculation of sine, cosine and Laplace transforms. J Sound Vib 12: 315–337
Davies B, Martin B (1979) Numerical inversion of the Laplace transform: a survey and comparison of methods. J Comput Phys 33: 1–32
Dubner H, Abate J (1968) Numerical inversion of Laplace transforms by relating them to the finite Fourier cosine transform. J Assoc Comput Mach 15: 115–123
E W, Liu D, Vanden-Eijnden E (2005a) Analysis of multiscale methods for stochastic differential equations. Commun Pure Appl Math 58: 1544–1585
E W, Liu D, Vanden-Eijnden E (2005b) Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates. J Chem Phys 123: 194,107
E W, Liu D, Vanden-Eijnden E (2007) Response to “Comment on ‘Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates’ [J Chem Phys 123:194107 (2005)]”. J Chem Phys 126:137,102
Elowitz M, Levine A, Siggia E, Swain P (2002) Stochastic gene expression in a single cell. Science 297: 1183–1186
Enver T, Heyworth C, Dexter T (1998) Do stem cells play dice?. Blood 92: 348–351
Feller W (1951) Two singular diffusion problems. Ann Math 54: 173–182
Friedman N, Cai L, Xie X (2006) Linking stochastic dynamics to population distribution: an analytical framework of gene expression. Phys Rev Lett 97: 168,302
Gardiner C (1985) Handbook of stochastic methods. Springer, New York
Gibbs A, Su F (2002) On choosing and bounding probability metrics. Int Stat Rev 70: 419–435
Gillespie D (2001) Approximate accelerated stochastic simulation of chemically reacting systems. J Chem Phys 115: 1716–1733
Golding I, Paulsson J, Zawilski S, Cox E (2005) Real-time kinetics of gene activity in individual bacteria. Cell 123: 1025–1036
Haseltine E, Rawlings J (2002) Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics. J Chem Phys 117: 6959–6969
Hume D (2000) Probability in transcriptional regulation and its implications for leukocyte differentiation and inducible gene expression. Blood 96: 2323–2328
Keener J, Sneyd J (2008) Mathematical physiology: cellular physiology. Springer, Berlin
Kevorkian J, Cole J (1981) Perturbation methods in applied mathematics. Springer, New York
Khasminskii R, Yin G (2005) Limit behavior of two-time-scale diffusions revisited. J Differ Equ 212: 85–113
Larson D, Singer R, Zenklusen D (2009) A single molecule view of gene expression. Trends Cell Biol 19: 630–637
Lipniacki T, Paszek P, Marciniak-Czochra A, Brasier A, Kimmel M (2006) Transcriptional stochasticity in gene expression. J Theor Biol 238: 348–367
Mastny E, Haseltine E, Rawlings J (2007) Two classes of quasi-steady-state model reductions for stochastic kinetics. J Chem Phys 127: 094,106
McAdams H, Arkin A (1997) Stochastic mechanisms in gene expression. Proc Natl Acad Sci USA 94: 814–819
McAdams H, Arkin A (1998) Simulation of prokaryotic genetic circuits. Annu Rev Biophys Biomol Struct 27: 199–224
Munsky B, Khammash M (2006) The finite state projection algorithm for the solution of the chemical master equation. J Chem Phys 124: 044,104
Murray J (2003) Mathematical biology. Springer, Berlin
Ozbudak E, Thattai M, Kurtser I, Grossman A, van Oudenaarden A (2002) Regulation of noise in the expression of a single gene. Nat Genet 31: 69–73
Pahlajani C, Atzberger P, Khammash M (2010) Stochastic reduction method for biological chemical kinetics using time-scale separation. J Theor Biol 272: 96–112
Paszek P (2007) Modeling stochasticity in gene regulation: characterization in the terms of the underlying distribution function. B Math Biol 69: 1567–1601
Paulsson J, Ehrenberg M (2000) Random signal fluctuations can reduce random fluctuations in regulated components of chemical regulatory networks. Phys Rev Lett 84: 5447–5450
Paulsson J, Berg O, Ehrenberg M (2000) Stochastic focusing: fluctuation-enhanced sensitivity of intracellular regulation. Proc Natl Acad Sci USA 97: 7148–7153
Peccoud J, Ycart B (1995) Markovian modeling of gene-product synthesis. Theor Popul Biol 48: 222–234
Peleš S, Munsky B, Khammash M (2006) Reduction and solution of the chemical master equation using time scale separation and finite state projection. J Chem Phys 125: 204,104caron;
Raj A, van Oudenaarden A (2009) Single-molecule approaches to stochastic gene expression. Annu Rev Biophys 38: 255–270
Raj A, Peskin C, Tranchina D, Vargas D, Tyagi S (2006) Stochastic mRNA synthesis in mammalian cells. PLoS Biol 4: e309
Rao C, Wolf D, Arkin A (2002) Control, exploitation and tolerance of intracellular noise. Nature 420: 231–237
Raser J, O’Shea E (2004) Control of stochasticity in eukaryotic gene expression. Science 304: 1811–1814
Shahrezaei V, Swain P (2008) Analytical distributions for stochastic gene expression. Proc Natl Acad Sci USA 105: 17,256
Shea M, Ackers G (1985) The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation. J Mol Biol 181: 211–230
Sinitsyn N, Hengartner N, Nemenman I (2009) Adiabatic coarse-graining and simulations of stochastic biochemical networks. Proc Natl Acad Sci USA 106:10546–10551
Srivastava R, Haseltine E, Mastny E, Rawlings J (2011) The stochastic quasi-steady-state assumption: reducing the model but not the noise. J Chem Phys 134(154): 109
Taniguchi Y, Choi P, Li G, Chen H, Babu M, Hearn J, Emili A, Xie X (2010) Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329: 533–538
Thattai M, van Oudenaarden A (2001) Intrinsic noise in gene regulatory networks. Proc Natl Acad Sci USA 98: 151588–151598
van Kampen N (2006) Stochastic processes in physics and chemistry. Elsevier, Amsterdam
Vanden-Eijnden E (2003) Numerical techniques for multi-scale dynamical systems with stochastic effects. Commun Math Sci 1: 385–391
Wang Y, Liu C, Storey J, Tibshirani R, Herschlag D, Brown P (2002) Precision and functional specificity in mRNA decay. Proc Natl Acad Sci USA 99: 5860–5865
Yin G, Zhang Q (1998) Continuous-time Markov chains and applications: a singular perturbation approach. Springer, Berlin
Yu J, Xiao J, Ren X, Lao K, Xie X (2006) Probing gene expression in live cells, one protein molecule at a time. Science 311: 1600–1603
Zeiser S, Franz U, Wittich O, Liebscher V (2008) Simulation of genetic networks modelled by piecewise deterministic Markov processes. IET Syst Biol 2: 113–135
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Bokes, P., King, J.R., Wood, A.T.A. et al. Multiscale stochastic modelling of gene expression. J. Math. Biol. 65, 493–520 (2012). https://doi.org/10.1007/s00285-011-0468-7
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DOI: https://doi.org/10.1007/s00285-011-0468-7