Signatures of gene expression noise in cellular systems

Progress in Biophysics and Molecular Biology

Volumn 100, Issue 1-3, 2009, Pages 57-66

  Rausenberger, Julia ^a   Fleck, Christian ^a   Timmer, Jens ^a   Kollmann, Markus ^b  

^a UNIVERSITY OF FREIBURG   (Germany)

^b HUMBOLDT UNIVERSITY   (Germany)

Author keywords

Gene expression noise; Population distribution; Stochastic modeling; Transcription factor

Indexed keywords

TRANSCRIPTION FACTOR;

ANIMAL; BIOLOGICAL MODEL; CELL; CYTOLOGY; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; GENETICS; HUMAN; METABOLISM; REVIEW; STATISTICS; TIME;

ANIMALS; CELLS; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; HUMANS; MODELS, GENETIC; STOCHASTIC PROCESSES; TIME FACTORS; TRANSCRIPTION FACTORS;

EID: 71549130710     PISSN: 00796107     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbiomolbio.2009.06.003     Document Type: Review

References (53)

1. Alon U. An Introduction to Systems Biology: Design Principles of Biological Circuits (2006), Chapman & Hall/CRC
2. Austin D.W., Allen M.S., McCollum J.M., Dar R.D., Wilgus J.R., Sayler G.S., Samatova N.F., Cox C.D., and Simpson M.L. Gene network shaping of inherent noise spectra. Nature 439 (2006) 608-611
3. Avery S.V. Microbial cell individuality and the underlying sources of heterogeneity. Nat. Rev. Microbiol. 4 (2006) 577-587
4. Balaban N.Q., Merrin J., Chait R., Kowalik L., and Leibler S. Bacterial persistence as a phenotypic switch. Science 305 (2004) 1622-1625
5. Bar-Even A., Paulsson J., Maheshri N., Carmi M., O'Shea E., Pilpel Y., and Barkai N. Noise in protein expression scales with natural protein abundance. Nat. Genet. 38 6 (2006) 636-643
6. Becskei A., Kaufmann B.B., and van Oudenaarden A. Contributions of low molecule number and chromosomal positioning to stochastic gene expression. Nat. Genet. 37 9 (2005) 937-944
7. Becskei A., and Serrano L. Engineering stability in gene networks by autoregulation. Nature 405 (2000) 590-593
8. Berg O.G. A model for statistical fluctuations of protein numbers in a microbial population. J. Theor. Biol. 71 (1978) 587-603
9. Bintu L., Buchler N.E., Garcia H.G., Gerland U., Hwa T., Kondev J., and Phillips R. Transcriptional regulation by numbers: models. Curr. Opin. Genet. Dev. 15 (2005) 116-124
10. Blake W.J., Kœrn M., Cantor C.R., and Collins J.J. Noise in eukaryotic gene expression. Nature 422 (2003) 633-637
11. Buchler N.E., Gerland U., and Hwa T. On schemes of combinatorial transcription logic. Proc. Natl. Acad. Sci. U.S.A. 100 9 (2003) 5136-5141
12. Cai L., Friedman N., and Xie X.S. Stochastic protein expression in individual cells at the single molecule level. Nature 440 (2006) 358-362
13. Colman-Lerner A., Gordon A., Serra E., Chin T., Resnekov O., Endy D., Pesce C.G., and Brent R. Regulated cell-to-cell variation in a cell-fate decision system. Nature 437 (2005) 695-706
14. Dublanche Y., Michalodimitrakis K., Kummerer N., Foglierini M., and Serrano L. Noise in transcription negative feedback loops: simulation and experimental analysis. Mol. Sys. Biol. 2 (2006) 41
15. Elf J., Li G.W., and Xie X.S. Probing transcription factor dynamics at the single-molecule level in a living cell. Science 316 (2007) 1191-1194
16. Elowitz M.B., Levine A.J., Siggia E.D., and Swain P.S. Stochastic gene expression in a single cell. Science 297 (2002) 1183-1186
17. Friedman N., Cai L., and Xie X.S. Linking stochastic dynamics to population distribution: an analytical framework to gene expression. Phys. Rev. Lett. 97 (2006) 168302
18. Gardiner C.W. Handbook of Stochastic Methods for Physics, Chemistry, and the Natural Sciences. second ed. (1990), Springer-Verlag
19. Gerstung M., Timmer J., and Fleck C. Noisy signaling through promoter logic gates. Phys. Rev. E 79 (2009) 011923
20. Gillespie D.T. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81 25 (1977) 2340-2361
21. Gillespie D.T. Stochastic simulation of chemical kinetics. Annu. Rev. Phys. Chem. 58 (2007) 35-55
22. Gillespie D.T., and Petzold L.R. Numerical simulation for biochemical kinetics. In: Szallasi Z., Stelling J., and Periwal V. (Eds). Systems Modelling in Cellular Biology: From Concepts to Nuts and Bolts (2006), MIT Press 125-147
23. Golding I., Paulsson J., Zawilski S.M., and Cox E.C. Real-time kinetics of gene activity in individual bacteria. Cell 123 (2005) 1025-1036
24. Kaufmann B.B., and van Oudenaarden A. Stochastic gene expression: from single molecules to the proteome. Curr. Opin. Genet. Dev. 17 2 (2007) 107-112
25. Ko M.S., Nakauchi H., and Takahashi N. The dose dependence of glucocorticoid-inducible gene expression results from changes in the number of transcriptionally active templates. EMBO J. 9 (1990) 2835-2842
26. Kœrn M., Elston T.C., Blake W.J., and Collins J.J. Stochasticity in gene expression: from theories to phenotypes. Nat. Rev. Genet. 6 (2005) 451-464
27. Kollmann M., Løvdok L., Bartolome K., Timmer J., and Sourjik V. Design principles of a bacterial signalling network. Nature 438 (2005) 504-507
28. Lu T., Volfson D., Tsimring L., and Hasty J. Cellular growth and division in the Gillespie algorithm. Syst. Biol. 1 1 (2004) 121-128
29. McAdams H.H., and Arkin A. Stochastic mechanisms in gene expression. Proc. Natl. Acad. Sci. U.S.A. 94 (1997) 814-819
30. Mettetal J.T., Muzzey D., Pedraza J.M., Ozbudak E.M., and van Oudenaarden A. Predicting stochastic gene expression dynamics in single cells. Proc. Natl. Acad. Sci. U.S.A. 103 19 (2006) 7304-7309
31. Newman J.R.S., Ghaemmaghami S., Ihmels J., Breslow D., Noble M., DeRisi J.L., and Weissmann J.S. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441 (2006) 840-846
32. Ozbudak E.M., Thattai M., Kurtser I., Grossman A.D., and van Oudenaarden A. Regulation of noise in the expression of a single gene. Nat. Genet. 31 (2002) 69-73
33. Paulsson J. Summing up the noise in gene networks. Nature 427 (2004) 415-418
34. Paulsson J. Models of stochastic gene expression. Phys. Life Rev. 2 (2005) 157-175
35. Pedraza J., and Paulsson J. Effects of molecular memory and bursting on fluctuations in gene expression. Science 319 (2008) 339-343
36. Pedraza J., and van Oudenaarden A. Noise propagation in gene networks. Science 307 (2005) 1965-1969
37. Pulkkinen, O., Berg, J., 2008. Dynamics of gene expression under feedback. arXiv:0807.3521v1.
38. Raj A., Peskin C.S., Tranchina D., Vargas D.Y., and Tyagi S. Stochastic mRNA synthesis in mammalian cells. PLoS Biol. 4 10 (2006) 1707-1719
39. Raj A., and van Oudenaarden A. Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 135 (2008) 216-262
40. Raser J.M., and O'Shea E.K. Control of stochasticity in eukaryotic gene expression. Science 304 (2004) 1811-1814
41. Raser J.M., and O'Shea E.K. Noise in gene expression: origins, consequences, and control. Science 309 (2005) 2010-2013
42. Rausenberger J., and Kollmann M. Quantifying origins of cell-to-cell variations in gene expression. Biophys. J. 95 (2008) 4523-4528
43. Rosenfeld N., Young J.W., Alon U., Swain P.S., and Elowitz M.B. Gene regulation at the single-cell level. Science 307 (2005) 1962-1965
44. Shahrezaei V., and Swain P.S. Analytical distributions for stochastic gene expression. Proc. Natl. Acad. Sci. U.S.A. 105 (2008) 17256-17261
45. Sigal A., Milo R., Cohen A., Geva-Zatorsky N., Klein Y., Liron Y., Rosenfeld N., Danon T., Perzov N., and Alon U. Variability and memory of protein levels in human cells. Nature 444 (2006) 643-646
46. Spudich J.L., and Koshland D.E.J. Non-genetic individuality: chance in the single cell. Nature 262 (1976) 467-471
47. Suel G.M., Garcia-Ojalvo J., Liberman L.M., and Elowitz M.B. An excitable gene regulatory circuit induces transient cellular differentiation. Nature 440 (2006) 545-550
48. Swain P.S. Efficient attenuation of stochasticity in gene expression through post-transcriptional control. J. Mol. Biol. 344 (2004) 965-976
49. Swain P.S., Elowitz M.B., and Siggia E.D. Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc. Natl. Acad. Sci. U.S.A. 99 20 (2002) 12795-12800
50. Thattai M., and van Oudenaarden A. Intrinsic noise in gene regulatory networks. Proc. Natl. Acad. Sci. U.S.A. 98 15 (2001) 8614-8619
51. Tǎnase-Nicola S., Warren P.B., and ten Wolde P.R. Signal detection, modularity and the correlation between extrinsic and intrinsic noise in biochemical networks. Phys. Rev. Lett. 97 6 (2006) 068102
52. van Kampen, N.G., 1992. Stochastic Processes in Physics and Chemistry, rev. and enlarged Edition. North Holland.
53. Volfson D., Marciniak J., Blake W.J., Ostroff N., Tsimring L.S., and Hasty J. Origins of extrinsic variability in eukaryotic gene expression. Nature 439 (2006) 861-864