Signatures of combinatorial regulation in intrinsic biological noise

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

Volumn 105, Issue 45, 2008, Pages 17262-17267

  Warmflash, Aryeh ^a   Dinner, Aaron R ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

Flow cytometry; Gene expression; Mathematical modeling; Noise analysis inference

Indexed keywords

PROTEIN CRIF; REGULATOR PROTEIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ARTICLE; CHEMICAL REACTION; DNA BINDING; GENE CONTROL; GENE EXPRESSION; GENE NUMBER; MATHEMATICAL MODEL; PRIORITY JOURNAL; REGULATORY MECHANISM; STOCHASTIC MODEL;

COMPUTER SIMULATION; DNA; GENE EXPRESSION REGULATION; MODELS, GENETIC; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS);

EID: 56249093501     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0809314105     Document Type: Article

References (48)

1. Glass L, Kauffman SA (1973) The logical analysis of continuous, non-linear biochemical control networks. J Theor Biol 39:103-129.
2. Arkin A, Ross J (1994) Computational functions in biochemical reaction networks. Biophys J 67:560-578.
3. Milo R, et al. (2002) Network motifs: Simple building blocks of complex networks. Science 298:824-827.
4. Mangan S, Zaslaver A, Alon U (2003) The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks. J Mol Biol 334:197-204.
5. Alon U (2007) Network motifs: Theory and experimental approaches. Nat Rev Genet 8:450-461.
6. Setty Y, Mayo AE, Surette MG, Alon U (2003) Detailed map of a cis-regulatory input function. Proc Natl Acad Sci USA 100:7702-7707.
7. Kuhlman T, Zhang Z, Saier MH, Hwa T (2007) Combinatorial transcriptional control of the lactose operon of Escherichia coli. Proc Natl Acad Sci USA 104:6043-6048.
8. Mayo AE, Setty Y, Shavit S, Zaslaver A, Alon U (2006) Plasticity of the cis-regulatory input function of a gene. PLoS Biol 4:555-561.
9. Yuh CH, Bolouri H, Davidson EH (1998) Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene. Science 279:1896-1902.
10. Davidson EH, et al. (2002) A genomic regulatory network for development. Science 295:1669-1678.
11. Hermsen R, Tans S, ten Wolde PR (2006) Transcriptional regulation by competing transcription factor modules. PLoS Comp Biol 2:1552-1560.
12. McKenna NJ, O'Malley BW (2002) Combinatorial control of gene expression by nuclear receptors and coregulators. Cell 108:465-474.
13. Remenyi A, Scholer HR, Wilmanns M (2004) Combinatorial control of gene expression. Nat Struct Mol Biol 11:812-815.
14. Buchler NE, Gerland U, Hwa T (2003) On schemes of combinatorial transcription logic. Proc Natl Acad Sci USA 100:5136-5141.
15. So CW, Cleary ML (2004) Dimerization: A versatile switch for oncogenesis. Blood 104:919-922.
16. Kato M, Hata N, Banerjee N, Futcher B, Zhang MQ (2004) Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol 5:R56.
17. Rothenberg EV, Taghon T (2005) Molecular genetics of T cell development. Annu Rev Immunol 23:601-649.
18. Lemaire V, Lee CF, Lei J, Métivier R, Glass L (2006) Sequential recruitment and combinatorial assembling of multiprotein complexes in transcriptional activation. Phys Rev Lett 96:198102.
19. Tuch BB, Galgoczy DJ, Hernday AD, Li H, Johnson AD (2008) The evolution of combinatorial gene regulation in fungi. PLoS Biol 6:e38.
20. Elowitz MB, Levine AJ, Siggia ED, Swain PS (2002) Stochastic gene expression in a single cell. Science 297:1183-1186.
21. Vilar JM, Kueh HY, Barkai N, Leibler S (2002) Mechanisms of noise resistance in genetic oscillators. Proc Natl Acad Sci USA 99:5988-5992.
22. Rosenfeld N, Young JW, Alon U, Swain PS, Elowitz MB (2005) Gene regulation at the single-cell level. Science 307:1962-1965.
23. Pedraza J, van Oudenaarden A (2005) Noise propagation in genetic networks. Science 307:1965-1969.
24. Acar M, Becskei A, van Oudenaarden A (2005) Enhancement of cellular memory by reducing stochastic transitions. Nature 435:228-232.
25. Suel GM, Garcia-Ojalvo J, Liberman LM, Elowitz MB (2006) An excitable gene regulatory circuit induces transient cellular differentiation. Nature 440:545-550.
26. Ozbudak EM, Thattai M, Kurtser I, Grossman AD, van Oudenaarden A (2002) Regulation of noise in the expression of a single gene. Nat Genet 31:69-73.
27. Pedraza JM, Paulsson J (2008) Effects of molecular memory and bursting on fluctuations in gene expression. Science 319:339-343.
28. Thattai M, van Oudenaarden A (2002) Attenuation of noise in ultrasensitive signaling cascades. Biophys J 82:2943-2950.
29. Paulsson J (2004) Summing up the noise in genetic networks. Nature 427:415-418.
30. Chandler D (1987) Introduction to Modern Statistical Mechanics (Oxford Univ Press, New York).
31. van Kampen NG (1992) Stochastic Processes in Physics and Chemistry (Elsevier Science, London).
32. Thattai M, van Oudenaarden A (2001) Intrinsic noise in gene regulatory networks. Proc Natl Acad Sci USA 98:8614-8619.
33. Guido NJ, et al. (2006) A bottom-up approach to gene regulation. Nature 439:856-860.
34. Bintu L, et al. (2005) Transcriptional regulation by the numbers: Applications. Curr Opin Gen Dev 15:125-135.
35. Gillespie DT (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81:2340-2361.
36. Swain PS, Elowitz MB, Siggia ED (2002) Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc Natl Acad Sci USA 99:12795-12800.
37. Joung JK, Koepp DM, Hochschild D (1994) Synergistic activation of transcription by bacteriophage λ cI protein and E. coli cAMP receptor protein. Science 265:1863-1866.
38. Aurell E, Brown S, Johanson J, Sneppen K (2002) Stability puzzles in phage λ. Phys Rev E 65:051914.
39. Santillan M, Mackey MC (2004) Why the lysogenic state of phage λ is so stable: a mathematical modeling approach. Biophys J 86:75-84.
40. Santillan M, Mackey MC, Zeron ES (2007) Origin of bistability in the lac operon. Biophys J 92:3830-3842.
41. Mettetal JT, Muzzey D, Pedraza JM, Ozbudak EM, van Oudenaarden A (2006) Predicting stochastic gene expression dynamics in single cells. Proc Natl Acad Sci USA 103:7304-7309.
42. Shibata T, Fujimoto K (2005) Noisy signal amplification in ultrasensitive signal transduction. Proc Natl Acad Sci USA 102:331-336.
43. Tanase-Nicola S, Warren PB, ten Wolde PR (2006) Signal detection, modularity, and the correlation between extrinsic and intrinsic noise in biochemical networks. Phys Rev Lett 97:068102.
44. Sanchez A, Kondev J (2008) Transcriptional control of noise in gene expression. Proc Natl Acad Sci USA 105:5081-5086.
45. Cox CD, McCollum JM, Allen MS, Dar RD, Simpson ML (2008) Using noise to probe and characterize gene circuits. Proc Natl Acad Sci USA 105:10809-10814.
46. Anderson LM, Yang H (2008) DNA looping can enhance lysogenic cI transcription in phage lambda. Proc Natl Acad Sci USA 105:5827-5832.
47. Sachs K, Perez O, Pe'er D, Lauffenburger DA, Nolan GP (2005) Causal protein-signaling networks derived from multiparameter single-cell data. Science 308:523-529.
48. Sigal A, et al. (2006) Variability and memory of protein levels in human cells. Nature 444:643-646.