Abstract
Biological systems form complex networks of interaction on several scales, ranging from the molecular to the ecosystem level. On the subcellular scale, interaction between genes and gene products (mRNAs, proteins) forms the basis of essential processes like signal transduction, cell metabolism or embryonic development. Recent experimental advances helped uncover the qualitative structure of many gene control networks, creating a surge of interest in the quantitative description of gene regulation. We give a brief description of the main frameworks and methods used in modeling gene regulatory networks, then focus on a recent model of the segment polarity genes of the fruit fly Drosophila melanogaster.
The basis of this model is the known interactions between the products of the segment polarity genes, and the network topology these interactions form. The interactions between mRNAs and proteins are described as logical (Boolean) functions. The success in reproducing both wild type and mutant gene expression patterns suggests that the kinetic details of the interactions are not essential as long as the network of interactions is unperturbed. The model predicts the gene patterns for cases that were not yet studied experimentally, and implies a remarkable robustness toward changes in internal parameters, initial conditions and even some mutations.
The success of this approach also suggests a wide applicability of real-topology-based Boolean modeling for gene regulatory networks. In cases when the information about the system is incomplete, Boolean modeling can verify the sufficiency of interactions and can propose ways to complete the network. After a coherent picture is obtained, more realistic kinetic models can be used to gain additional insights into the functioning of the system.
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References
1. B. Alberts et al., Molecular Biology of the Cell, 4th edn. ( 2003).
2. L. Wolpert, R. Beddington, J. Brockes, T. Jessell, P. Lawrence and E. Meyerowitz, Principles of Development, (Current Biology Ltd., London 1998).
3. E.H. Davidson et al., Science 295, 1669 (2002).
4. S. A. Kauffman, J. Theor. Biol. 22, 437 (1969).
5. S. A. Kauffman, The origins of Order, (Oxford University Press, New York, 1993).
6. B. Derrida and Y. Pomeau, Europhys. Lett. 1, 45 (1986).
7. G. Weisbuch and D. Stauffer, J. Phys. (Paris) 48 11 (1987).
8. B. Luque and R. V. Solé, Phys. Rev. E 55, 257 (1997).
9. R. Albert and A.-L. BarabĂ¡si, Phys. Rev. Lett. 84, 5660 (2000).
10. R. Thomas, J. Theor. Biol. 42, 563 (1973).
11. R. Thomas and R. D’Ari, Biological Feedback (CRC Press, Boca Raton, Ann Arbor, Boston, 1990).
12. L. Mendoza, D. Thieffry and E. R. Alvarez-Buylla, Bioinformatics 15, 593 (1999).
13. L. SĂ¡nchez and D. Thieffry, J. Theor. Biol. 211, 115 (2001).
14. A. Ghysen and R. Thomas, BioEssays 25, 802 (2003).
15. J. W. Bodnar, J. Theor. Biol. 188, 391 (1997).
16. J. W. Bodnar and M. K. Bradley, Cell Biochem. and Biophys. 34, 153 (2001).
17. C.-H. Yuh, H. Bolouri and E. H. Davidson, Development 128, 617 (2001).
18. R. Albert and H. G. Othmer, J. Theor. Biol 223, 1 (2003).
19. J. Reinitz and D. H. Sharp, Mechanisms of Development 49, 133 (1995).
20. G. von Dassow, E. Meir., E. M. Munro and G. M. Odell, Nature 406, 188 (2000).
21. V. V. Gursky, J. Reinitz and A. M. Samsonov, Chaos 11, 132 (2001).
22. P. W. Ingham and A. P. McMahon, Genes Dev. 15, 3059 (2001).
23. B. Sanson, EMBO Reports 2, 1083 (2001).
24. V. Hatini and S. DiNardo, Trends in Genetics 17, 574 (2001).
25. J. E. Hooper and M. P. Scott, The Molecular Genetic Basis of Positional Information in Insect Segments. In: Early Embryonic Development of Animals, ed. by W. Hennig (Springer, Berlin 1992) pp. 1-49.
26. K. M. Cadigan, U. Grossniklaus and W. J. Gehring, Genes Dev. 8, 899 (1994).
27. S. Pfeiffer and J.-P. Vincent, Cell & Dev. Biol. 10, 303 (1999).
28. K. M. Cadigan and R. Nusse, Genes Dev. 11, 3286 (1997).
29. T. Tabata, S. Eaton and T. B. Kornberg, Genes Dev. 6, 2635 (1992).
30. S. Eaton and T. B. Kornberg, Genes. Dev. 4, 1068 (1990).
31. A. Hidalgo and P. Ingham, Development 110, 291-301 (1990).
32. A. M. Taylor, Y. Nakano, J. Mohler and P. W. Ingham, Mechanisms of Development 42, 89 (1993).
33. M. van den Heuvel and P. W. Ingham, Nature 382, 547 (1996).
34. P. W. Ingham, EMBO J. 17, 3505 (1998).
35. P. Aza-Blanc and T. B. Kornberg, Trends in Genetics 15, 458 (1999).
36. J. T. Ohlmeyer and D. Kalderon, Nature 396, 749 (1998).
37. N. MĂ©thot and K. Basler, Cell 96, 819 (1999).
38. C. Alexandre, A. Jacinto and P. W. Ingham, Genes Dev. 10, 2003 (1996).
39. T. von Ohlen and J. E. Hooper, Mechanisms of Development 68, 149 (1997).
40. P. W. Ingham, A. M. Taylor and Y. Nakano, Nature 353, 184 (1991).
41. J. Alcedo, Y. Zou and M. Noll, Molecular Cell 6, 457 (2000).
42. S. DiNardo, E. Sher, J. Heemskerk-Jongens, J. A. Kassis and P. H. O’Farrell, Nature 332, 45 (1988).
43. C. Schwartz, J. Locke, C. Nishida and T. B. Kornberg, Development 121, 1625 (1995).
44. A. Gallet, C. Angelats, S. Kerridge and P. P. Thérond, Development 127, 5509 (2000).
45. A. Martinez-Arias, N. Baker and P. W. Ingham, Development 103, 157 (1988).
46. A. Bejsovec and E. Wieschaus, Development 119 501 (1993).
47. J. Heemskerk, S. DiNardo, R. Kostriken and P. H. O’Farrell, Nature 352, 404 (1991).
48. A. Bejsovec and A. Martinez-Arias, Development 113, 471 (1991).
49. R. Laubenbacher and B. Stigler, Polynomial models for biochemical networks (preprint, 2003).
50. I. Shmulevich, E. Dougherty and W. Zhang, Proc. IEEE 90, 1778 (2002).
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Albert, R. Boolean Modelingof Genetic Regulatory Networks. In: Ben-Naim, E., Frauenfelder, H., Toroczkai, Z. (eds) Complex Networks. Lecture Notes in Physics, vol 650. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-44485-5_21
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DOI: https://doi.org/10.1007/978-3-540-44485-5_21
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