1887
banner image
No data available.
Please log in to see this content.
You have no subscription access to this content.
No metrics data to plot.
The attempt to load metrics for this article has failed.
The attempt to plot a graph for these metrics has failed.
The full text of this article is not currently available.
oa
A common repressor pool results in indeterminacy of extrinsic noise
Rent:
Rent this article for
Access full text Article
/content/aip/journal/chaos/21/4/10.1063/1.3658618
1.
1. H. C. Berg, Random Walks in Biology (Princeton University, Princeton, NJ, 1993).
2.
2. A. Einstein, Ann. Phys. 17, 549 (1905).
http://dx.doi.org/10.1002/andp.v322:8
3.
3. A. Pikovsky, M. Rosenblum, and J. Kurths, Synchronization: A Universal Concept in Nonlinear Sciences (Cambridge University Press, Cambridge, UK, 2003).
4.
4. S. H. Strogatz, Nonlinear Dynamics And Chaos: With Applications To Physics, Biology, Chemistry, And Engineering (Westview Press, Cambridge, MA, USA, 2001).
5.
5. V. S. Anishchenko, V. Astakhov, A. Neiman, T. Vadivasova, and L. Schimansky-Geier, Nonlinear Dynamics of Chaotic and Stochastic Systems: Tutorial and Modern Developments, 2nd ed. (Springer, New York, 2007).
6.
6. A.-L. Barabási, Linked: How Everything Is Connected to Everything Else and What It Means (Plume, New York, NY, USA, 2003).
7.
7. A. L. Barabási and Z. N. Oltvai, Nat. Rev. Genet. 5(2), 101 (2004).
http://dx.doi.org/10.1038/nrg1272
8.
8. K. Wiesenfeld and F. Moss, Nature (London) 373(6509), 33 (1995).
http://dx.doi.org/10.1038/373033a0
9.
9. G. Balázsi, A. van Oudenaarden, and J. J. Collins, Cell 144(6), 910 (2011).
http://dx.doi.org/10.1016/j.cell.2011.01.030
10.
10. A. Eldar and M. B. Elowitz, Nature (London) 467(7312), 167 (2010).
http://dx.doi.org/10.1038/nature09326
11.
11. M. Kaern, T. C. Elston, W. J. Blake, and J. J. Collins, Nat. Rev. Genet. 6(6), 451 (2005).
http://dx.doi.org/10.1038/nrg1615
12.
12. N. Maheshri and E. K. O’Shea, Annu. Rev. Biophys. Biomol. Struct. 36, 413 (2007).
http://dx.doi.org/10.1146/annurev.biophys.36.040306.132705
13.
13. A. Raj and A. van Oudenaarden, Cell 135(2), 216 (2008).
http://dx.doi.org/10.1016/j.cell.2008.09.050
14.
14. C.V. Rao, D. M. Wolf, and A. P. Arkin, Nature (London) 420(6912), 231 (2002).
http://dx.doi.org/10.1038/nature01258
15.
15. K. F. Murphy, G. Balázsi, and J. J. Collins, Proc. Natl Acad. Sci. U.S.A. 104(31), 12726 (2007).
http://dx.doi.org/10.1073/pnas.0608451104
16.
16. K. F. Murphy, R. M. Adams, X. Wang, G. Balázsi, and J. J. Collins, Nucleic. Acids Res. 38(8), 2712 (2010).
http://dx.doi.org/10.1093/nar/gkq091
17.
17. P. S. Swain, M. B. Elowitz, and E. D. Siggia, Proc. Natl Acad. Sci. U.S.A. 99(20), 12795 (2002).
http://dx.doi.org/10.1073/pnas.162041399
18.
18. M. B. Elowitz, A. J. Levine, E. D. Siggia, and P. S. Swain, Science 297(5584), 1183 (2002).
http://dx.doi.org/10.1126/science.1070919
19.
19. M. Thattai and A. van Oudenaarden, Proc. Natl. Acad. Sci. U. S. A. 98(15), 8614 (2001).
http://dx.doi.org/10.1073/pnas.151588598
20.
20. J. J. Tyson and H. G. Othmer, Prog.Theor. Biol., 5, 1 (1978).
21.
21. C. Tan, P. Marguet, and L. C. You,. Nat. Chem. Biol., 5(11), 842 (2009).
http://dx.doi.org/10.1038/nchembio.218
22.
22. F. J. Isaacs, J. Hasty, C. R. Cantor, and J. J. Collins, Proc. Natl Acad. Sci. U.S.A. 100(13), 7714 (2003).
http://dx.doi.org/10.1073/pnas.1332628100
23.
23. P. Guptasarma, BioEssays 17(11), 987 (1995).
http://dx.doi.org/10.1002/bies.v17:11
24.
24. D. Normanno, F. Vanzi, and F. S. Pavone,. Nucleic Acids Res. 36(8), 2505 (2008).
http://dx.doi.org/10.1093/nar/gkn071
25.
25. W. Bialek, F. Rieke, R. R. de Ruyter van Steveninck, and D. Warland, Science 252(5014), 1854 (1991).
http://dx.doi.org/10.1126/science.2063199
26.
26. J. K. Douglass et al., Nature (London) 365(6444), 337 (1993).
http://dx.doi.org/10.1038/365337a0
27.
27. Z. Gingl, L. B. Kiss, and F. Moss, Europhys. Lett. 29(3), 191 (1995).
http://dx.doi.org/10.1209/0295-5075/29/3/001
28.
28. K. Wiesenfeld, D. Pierson, E. Pantazelou, C. Dames, and F. Moss, Phys. Rev. Lett. 72(14), 2125 (1994).
http://dx.doi.org/10.1103/PhysRevLett.72.2125
29.
29. S. M. Bezrukov and I. Vodyanoy, Nature (London) 378(6555), 362 (1995).
http://dx.doi.org/10.1038/378362a0
30.
30. P. C. Gailey, A. Neiman, J. J. Collins, and F. M. Moss, Phys. Rev. Lett. 79(23), 4701 (1997).
http://dx.doi.org/10.1103/PhysRevLett.79.4701
31.
31. J. J. Collins, C. C. Chow, and T. T. Imhoff, Nature (London) 376(6537), 236 (1995).
http://dx.doi.org/10.1038/376236a0
32.
32. E. M. Ozbudak, M. Thattai, I. Kurtser, A. D. Grossman, and A. van Oudenaarden, Nat. Genet. 31(1), 69 (2002).
http://dx.doi.org/10.1038/ng869
33.
33. T. M. Neildez-Nguyen, A. Parisot, C. Vignal, P. Rameau, D. Stockholm, J. Picot, V. Allo, C. Le Bec, C. Laplace, and A. Paldi, Differentiation 76(1), 33 (2008).
34.
34. A. Raj, C. S. Peskin, D. Tranchina, D. Y. Vargas, and S. Tyagi, PLoS Biol. 4(10), e309 (2006).
http://dx.doi.org/10.1371/journal.pbio.0040309.sd001
35.
35. J. M. Raser and E. K. O’Shea,. Science 304(5678), 1811 (2004).
http://dx.doi.org/10.1126/science.1098641
36.
36. A. Becskei, B. B. Kaufmann, and A. van Oudenaarden,. Nat. Genet. 37(9), 937 (2005).
http://dx.doi.org/10.1038/ng1616
37.
37. D. Volfson, J. Marciniak, W. J. Blake, N. Ostroff, L. S. Tsimring, and J. Hasty, Nature (London) 439(7078), 861 (2006).
http://dx.doi.org/10.1038/nature04281
38.
38. W. J. Blake, G. Balazsi, M. A. Kohanski, F. J. Isaacs, K. F. Murphy, Y. Kuang, C. R. Cantor, D. R. Walt, and J. J. Collins, Mol. Cell 24(6), 853 (2006).
http://dx.doi.org/10.1016/j.molcel.2006.11.003
39.
39. W. J. Blake, M. Kærn, C. R. Cantor, and J. J. Collins, Nature 422(6932), 633 (2003).
http://dx.doi.org/10.1038/nature01546
40.
40. M. Stamatakis and N. V. Mantzaris, Biophys. J. 96(3), 887 (2009).
http://dx.doi.org/10.1016/j.bpj.2008.10.028
41.
41. D. T. Gillespie, J. Comput. Phys. 22(4), 403 (1976).
http://dx.doi.org/10.1016/0021-9991(76)90041-3
42.
42. D. T. Gillespie, J. Phys. Chem. 81(25), 2340 (1977).
http://dx.doi.org/10.1021/j100540a008
43.
43. N. G. van Kampen, Stochastic Processes in Physics and Chemistry (North-Holland-Personal-Library, New York, Amsterdam, 1992).
44.
44. C. V. Rao and A. P. Arkin, J. Chem. Phys. 118(11), 4999 (2003).
http://dx.doi.org/10.1063/1.1545446
45.
45. C. Z. Jiang and B. F. Pugh, Nat. Rev. Genet. 10(3), 161 (2009).
http://dx.doi.org/10.1038/Nrg2522
http://aip.metastore.ingenta.com/content/aip/journal/chaos/21/4/10.1063/1.3658618
Loading
/content/aip/journal/chaos/21/4/10.1063/1.3658618
Loading

Data & Media loading...

Loading

Article metrics loading...

/content/aip/journal/chaos/21/4/10.1063/1.3658618
2011-12-29
2014-12-28

Abstract

For just over a decade, stochastic gene expression has been the focus of many experimental and theoretical studies. It is now widely accepted that noise in gene expression can be decomposed into extrinsic and intrinsic components, which have orthogonal contributions to the total noise. Intrinsic noise stems from the random occurrence of biochemical reactions and is inherent to gene expression. Extrinsic noise originates from fluctuations in the concentrations of regulatory components or random transitions in the cell’s state and is imposed to the gene of interest by the intra- and extra-cellular environment. The basic assumption has been that extrinsic noise acts as a pure input on the gene of interest, which exerts no feedback on the extrinsic noise source. Thus, multiple copies of a gene would be uniformly influenced by an extrinsic noise source. Here, we report that this assumption falls short when multiple genes share a common pool of a regulatory molecule. Due to the competitive utilization of the molecules existing in this pool, genes are no longer uniformly influenced by the extrinsic noise source. Rather, they exert negative regulation on each other and thus extrinsic noise cannot be determined by the currently established method.

Loading

Full text loading...

/deliver/fulltext/aip/journal/chaos/21/4/1.3658618.html;jsessionid=89eg87qpo554m.x-aip-live-06?itemId=/content/aip/journal/chaos/21/4/10.1063/1.3658618&mimeType=html&fmt=ahah&containerItemId=content/aip/journal/chaos
true
true
This is a required field
Please enter a valid email address
752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: A common repressor pool results in indeterminacy of extrinsic noise
http://aip.metastore.ingenta.com/content/aip/journal/chaos/21/4/10.1063/1.3658618
10.1063/1.3658618
SEARCH_EXPAND_ITEM