Non-coding RNAs and complex distributed genetic networks
Tóm tắt
In eukaryotic cells, the mRNA-protein interplay can be dramatically influenced by non-coding RNAs (ncRNAs). Although this new paradigm is now widely accepted, an understanding of the effect of ncRNAs on complex genetic networks is lacking. To clarify what may happen in this case, we propose a mean-field kinetic model describing the influence of ncRNA on a complex genetic network with a distributed architecture including mutual protein-mediated regulation of many genes transcribed into mRNAs. ncRNA is considered to associate with mRNAs and inhibit their translation and/or facilitate degradation. Our results are indicative of the richness of the kinetics under consideration. The main complex features are found to be bistability and oscillations. One could expect to find kinetic chaos as well. The latter feature has however not been observed in our calculations. In addition, we illustrate the difference in the regulation of distributed networks by mRNA and ncRNA.
Tài liệu tham khảo
S. Bornholdt, Science 310, 449 (2005)
G. Karlebach, R. Shamir, Nat. Rev. Mol. Cell Bio. 9, 771 (2008)
Y. Bar-Yam, D. Harmon, B. de Bivort, Science 323, 1016 (2009)
M.C. Lagomarsino, B. Bassetti, G. Castellani, D. Remondini, Mol. Biosyst. 5, 335 (2009)
D.F.T. Veiga, B. Dutta, G. Balazsi, Mol. Biosyst. 6, 469 (2010)
T.R. Mercer, M.E. Dinger, J.S. Mattick, Nat. Rev. Genet. 10, 155 (2009)
J. Whitehead, G.K. Pandey, C. Kanduri, Biochim. Biophys. Acta 1790, 936 (2009)
J.E. Wilusz, H. Sunwoo, D.L. Spector, Gene. Dev. 23, 1494 (2009)
D.P. Bartel, Cell 136, 215 (2009)
M. Ghildiyal, P.D. Zamore, Nat. Rev. Genet. 10, 94 (2009)
V. N. Kim, J. Han, M.C. Siomi, Nat. Rev. Mol. Cell Bio. 10, 126 (2009)
K.K.H. Farh et al., Science 310, 1817 (2005)
J. Gao et al., Nature 466, 1105 (2010)
E. Barbarotto, T.G. Schmittgen, G.A. Calin, Int. J. Cancer 122, 969 (2008)
F.C. Lynn, Trends Endocrin. Met. 20, 452 (2009)
D.H. Lenz et al., Cell 118, 69 (2004)
S. Semsey et al., Nucleic Acids Res. 34, 4960 (2006)
E. Levine, E.B. Jacob, H. Levine, Biophys. J. 93, L52 (2007)
E. Levine, P. McHale, H. Levine, PLOS Comput. Biol. 3, e233 (2007)
E. Levine, Z. Zhang, T. Kuhlman, T. Hwa, PLOS Biol. 5, e229 (2007)
N. Mitarai, A.M.C. Andersson, S. Krishna, S. Semsey, K. Sneppen, Phys. Biol. 4, 164 (2007)
Y. Shimoni et al., Mol. Syst. Biol. 3, 138 (2007)
S. Legewie, D. Dienst, A. Wilde, H. Herzel, I.M. Axmann, Biophys. J. 95, 3232 (2008)
E. Levine, T. Hwa, Curr. Opin. Microbiol. 11, 574 (2008)
P. Mehta, S. Goyal, N.S. Wingreen, Mol. Syst. Biol. 4, 221 (2008)
N. Mitarai et al., P. Natl Acad. Sci. USA 106, 10655 (2009)
Y. Jia, W.H. Liu, A.B. Li, L.J. Yang, X. Zhan, Biophys. Chem. 143, 60 (2009)
V.P. Zhdanov, Mol. Biosyst. 5, 638 (2009)
V.P. Zhdanov, Biophys. Rev. Lett. 4, 267 (2009)
V. Elgart, T. Jia, R. Kulkarni, Biophys. J. 98, 2780 (2010)
V. Elgart, T. Jia, R.V. Kulkarni, Phys. Rev. E 82, 021901 (2010)
V.P. Zhdanov, JETP Lett. 92, 410 (2010)
Z.-R. Xie, H.-T. Yang, W.-C. Liu, M.-J. Hwang, Biochem. Bioph. Res. Co. 358, 722 (2007)
V.P. Zhdanov, Chem. Phys. Lett. 458, 359 (2008)
V.P. Zhdanov, J. Phys. A-Math. Theor. 41, 285101 (2008)
V.P. Zhdanov, JETP Lett. 88, 466 (2008)
J.W. Shen, Z.R. Liu, W.X. Zheng, F.D. Xu, L.N. Chen, Physica A 388, 2995 (2009)
A. Nandi, C. Vaz, A. Bhattacharya, R. Ramaswamy, BMC Syst. Biol. 3, 45 (2009)
V.P. Zhdanov, Biosystems 95, 75 (2009)
L.P. Xiong, Y.-Q. Ma, L.H. Tang, Chinese Phys. Lett. 27, 098701 (2010)
V.P. Zhdanov, Biophys. Rev. Lett. 5, 89 (2010)
V.P. Zhdanov, Physica A 389, 887 (2010)
B.D. Aguda, Y. Kim, M.G. Piper-Hunter, A. Friedman, C.B. Marsh, P. Natl Acad. Sci. USA 105, 19678 (2008)
R.S. Wang, G. Jin, X.S. Zhang, L.N. Chen, BMC Bioinformatics 10, S6 (2009)
V.P. Zhdanov, Cent. Eur. J. Phys. 8, 864 (2010)
V.P. Zhdanov, Chaos (in press)
J.C. Nacher, N. Araki, Biosystems 101, 10 (2010)
H.H. Chang, M. Hemberg, M. Barahona, D.E. Ingber, S. Huang, Nature 453, 544 (2008)
N. Bhardwaj, K.K. Yan, M.B. Gerstein, P. Natl Acad. Sci. USA 107, 6841 (2010)
B.D. MacArthur, A. Ma’ayan, I.R. Lemischka, Nat. Rev. Mol. Cell Bio. 10, 672 (2009)
T. Gedeon, K. Mischaikow, K. Patterson, E. Traldid, B. Math. Biol. 70, 1660 (2008)
D. Müller, J. Stelling, PLOS Comput. Biol. 5, e1000279 (2009)
A. Coulon, O. Gandrillon, G. Beslon, BMC Syst. Biol. 4, 2 (2010)
D. Michel, Prog. Biophys. Mol. Bio. 102, 16 (2010)
E. Yang et al., Genome Res. 13, 1863 (2003)
A. Beyer, J. Hollunder, H.-P. Nasheuer, T. Wilhelm, Mol. Cell. Proteomics 3, 1083 (2004)
R. de Sousa Abreu, L.O. Penalva, E.M. Marcotte, C. Vogel, Mol. Biosyst. 5, 1512 (2009)
B. Derrida, Y. Pomeau, Europhys. Lett. 1, 45 (1986)
M. Andrecut, S.A. Kauffman, Phys. Lett. A 372, 4757 (2008)
V.P. Zhdanov, JETP Lett. (in press)