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Open Physics

formerly Central European Journal of Physics

Editor-in-Chief: Seidel, Sally

Managing Editor: Lesna-Szreter, Paulina

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Volume 9, Issue 4

Issues

Volume 13 (2015)

Non-coding RNAs and complex distributed genetic networks

Vladimir Zhdanov
Published Online: 2011-04-30 | DOI: https://doi.org/10.2478/s11534-010-0104-y

Abstract

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.

Keywords: gene transcription; mRNA translation; association of mRNA and ncRNA; mean-field kinetic equations; bistability and scillations

  • [1] S. Bornholdt, Science 310, 449 (2005) http://dx.doi.org/10.1126/science.1119959CrossrefGoogle Scholar

  • [2] G. Karlebach, R. Shamir, Nat. Rev. Mol. Cell Bio. 9, 771 (2008) http://dx.doi.org/10.1038/nrm2503CrossrefGoogle Scholar

  • [3] Y. Bar-Yam, D. Harmon, B. de Bivort, Science 323, 1016 (2009) http://dx.doi.org/10.1126/science.1163225CrossrefGoogle Scholar

  • [4] M.C. Lagomarsino, B. Bassetti, G. Castellani, D. Remondini, Mol. Biosyst. 5, 335 (2009) http://dx.doi.org/10.1039/b816841pCrossrefGoogle Scholar

  • [5] D.F.T. Veiga, B. Dutta, G. Balazsi, Mol. Biosyst. 6, 469 (2010) http://dx.doi.org/10.1039/b916989jCrossrefGoogle Scholar

  • [6] T.R. Mercer, M.E. Dinger, J.S. Mattick, Nat. Rev. Genet. 10, 155 (2009) http://dx.doi.org/10.1038/nrg2521CrossrefGoogle Scholar

  • [7] J. Whitehead, G.K. Pandey, C. Kanduri, Biochim. Biophys. Acta 1790, 936 (2009) http://dx.doi.org/10.1016/j.bbagen.2008.10.007CrossrefGoogle Scholar

  • [8] J.E. Wilusz, H. Sunwoo, D.L. Spector, Gene. Dev. 23, 1494 (2009) http://dx.doi.org/10.1101/gad.1800909CrossrefGoogle Scholar

  • [9] D.P. Bartel, Cell 136, 215 (2009) http://dx.doi.org/10.1016/j.cell.2009.01.002CrossrefGoogle Scholar

  • [10] M. Ghildiyal, P.D. Zamore, Nat. Rev. Genet. 10, 94 (2009) http://dx.doi.org/10.1038/nrg2504CrossrefGoogle Scholar

  • [11] V. N. Kim, J. Han, M.C. Siomi, Nat. Rev. Mol. Cell Bio. 10, 126 (2009) http://dx.doi.org/10.1038/nrm2632CrossrefGoogle Scholar

  • [12] K.K.H. Farh et al., Science 310, 1817 (2005) http://dx.doi.org/10.1126/science.1121158CrossrefGoogle Scholar

  • [13] J. Gao et al., Nature 466, 1105 (2010) http://dx.doi.org/10.1038/nature09271CrossrefGoogle Scholar

  • [14] E. Barbarotto, T.G. Schmittgen, G.A. Calin, Int. J. Cancer 122, 969 (2008) http://dx.doi.org/10.1002/ijc.23343CrossrefGoogle Scholar

  • [15] F.C. Lynn, Trends Endocrin. Met. 20, 452 (2009) http://dx.doi.org/10.1016/j.tem.2009.05.007CrossrefGoogle Scholar

  • [16] D.H. Lenz et al., Cell 118, 69 (2004) http://dx.doi.org/10.1016/j.cell.2004.06.009CrossrefGoogle Scholar

  • [17] S. Semsey et al., Nucleic Acids Res. 34, 4960 (2006) http://dx.doi.org/10.1093/nar/gkl627CrossrefGoogle Scholar

  • [18] E. Levine, E.B. Jacob, H. Levine, Biophys. J. 93, L52 (2007) http://dx.doi.org/10.1529/biophysj.107.118448CrossrefGoogle Scholar

  • [19] E. Levine, P. McHale, H. Levine, PLOS Comput. Biol. 3, e233 (2007) http://dx.doi.org/10.1371/journal.pcbi.0030233CrossrefGoogle Scholar

  • [20] E. Levine, Z. Zhang, T. Kuhlman, T. Hwa, PLOS Biol. 5, e229 (2007) http://dx.doi.org/10.1371/journal.pbio.0050229CrossrefGoogle Scholar

  • [21] N. Mitarai, A.M.C. Andersson, S. Krishna, S. Semsey, K. Sneppen, Phys. Biol. 4, 164 (2007) http://dx.doi.org/10.1088/1478-3975/4/3/003CrossrefGoogle Scholar

  • [22] Y. Shimoni et al., Mol. Syst. Biol. 3, 138 (2007) http://dx.doi.org/10.1038/msb4100181CrossrefGoogle Scholar

  • [23] S. Legewie, D. Dienst, A. Wilde, H. Herzel, I.M. Axmann, Biophys. J. 95, 3232 (2008) http://dx.doi.org/10.1529/biophysj.108.133819CrossrefGoogle Scholar

  • [24] E. Levine, T. Hwa, Curr. Opin. Microbiol. 11, 574 (2008) http://dx.doi.org/10.1016/j.mib.2008.09.016CrossrefGoogle Scholar

  • [25] P. Mehta, S. Goyal, N.S. Wingreen, Mol. Syst. Biol. 4, 221 (2008) http://dx.doi.org/10.1038/msb.2008.58CrossrefGoogle Scholar

  • [26] N. Mitarai et al., P. Natl Acad. Sci. USA 106, 10655 (2009) http://dx.doi.org/10.1073/pnas.0901466106CrossrefGoogle Scholar

  • [27] Y. Jia, W.H. Liu, A.B. Li, L.J. Yang, X. Zhan, Biophys. Chem. 143, 60 (2009) http://dx.doi.org/10.1016/j.bpc.2009.04.001CrossrefGoogle Scholar

  • [28] V.P. Zhdanov, Mol. Biosyst. 5, 638 (2009) http://dx.doi.org/10.1039/b808095jCrossrefGoogle Scholar

  • [29] V.P. Zhdanov, Biophys. Rev. Lett. 4, 267 (2009) http://dx.doi.org/10.1142/S1793048009001034CrossrefGoogle Scholar

  • [30] V. Elgart, T. Jia, R. Kulkarni, Biophys. J. 98, 2780 (2010) http://dx.doi.org/10.1016/j.bpj.2010.03.022CrossrefGoogle Scholar

  • [31] V. Elgart, T. Jia, R.V. Kulkarni, Phys. Rev. E 82, 021901 (2010) http://dx.doi.org/10.1103/PhysRevE.82.021901CrossrefGoogle Scholar

  • [32] V.P. Zhdanov, JETP Lett. 92, 410 (2010) http://dx.doi.org/10.1134/S0021364010180104CrossrefGoogle Scholar

  • [33] Z.-R. Xie, H.-T. Yang, W.-C. Liu, M.-J. Hwang, Biochem. Bioph. Res. Co. 358, 722 (2007) http://dx.doi.org/10.1016/j.bbrc.2007.04.207CrossrefGoogle Scholar

  • [34] V.P. Zhdanov, Chem. Phys. Lett. 458, 359 (2008) http://dx.doi.org/10.1016/j.cplett.2008.04.111CrossrefGoogle Scholar

  • [35] V.P. Zhdanov, J. Phys. A-Math. Theor. 41, 285101 (2008) http://dx.doi.org/10.1088/1751-8113/41/28/285101CrossrefGoogle Scholar

  • [36] V.P. Zhdanov, JETP Lett. 88, 466 (2008) http://dx.doi.org/10.1134/S0021364008190120CrossrefGoogle Scholar

  • [37] J.W. Shen, Z.R. Liu, W.X. Zheng, F.D. Xu, L.N. Chen, Physica A 388, 2995 (2009) http://dx.doi.org/10.1016/j.physa.2009.03.032CrossrefGoogle Scholar

  • [38] A. Nandi, C. Vaz, A. Bhattacharya, R. Ramaswamy, BMC Syst. Biol. 3, 45 (2009) http://dx.doi.org/10.1186/1752-0509-3-45CrossrefGoogle Scholar

  • [39] V.P. Zhdanov, Biosystems 95, 75 (2009) http://dx.doi.org/10.1016/j.biosystems.2008.07.002CrossrefGoogle Scholar

  • [40] L.P. Xiong, Y.-Q. Ma, L.H. Tang, Chinese Phys. Lett. 27, 098701 (2010) http://dx.doi.org/10.1088/0256-307X/27/9/098701CrossrefGoogle Scholar

  • [41] V.P. Zhdanov, Biophys. Rev. Lett. 5, 89 (2010) http://dx.doi.org/10.1142/S1793048010001159CrossrefGoogle Scholar

  • [42] V.P. Zhdanov, Physica A 389, 887 (2010) http://dx.doi.org/10.1016/j.physa.2009.11.028CrossrefGoogle Scholar

  • [43] B.D. Aguda, Y. Kim, M.G. Piper-Hunter, A. Friedman, C.B. Marsh, P. Natl Acad. Sci. USA 105, 19678 (2008) http://dx.doi.org/10.1073/pnas.0811166106CrossrefGoogle Scholar

  • [44] R.S. Wang, G. Jin, X.S. Zhang, L.N. Chen, BMC Bioinformatics 10, S6 (2009) http://dx.doi.org/10.1186/1471-2105-10-S4-S6CrossrefGoogle Scholar

  • [45] V.P. Zhdanov, Cent. Eur. J. Phys. 8, 864 (2010) http://dx.doi.org/10.2478/s11534-010-0025-9CrossrefGoogle Scholar

  • [46] V.P. Zhdanov, Chaos (in press) Google Scholar

  • [47] J.C. Nacher, N. Araki, Biosystems 101, 10 (2010) http://dx.doi.org/10.1016/j.biosystems.2010.02.005CrossrefGoogle Scholar

  • [48] H.H. Chang, M. Hemberg, M. Barahona, D.E. Ingber, S. Huang, Nature 453, 544 (2008) http://dx.doi.org/10.1038/nature06965CrossrefGoogle Scholar

  • [49] N. Bhardwaj, K.K. Yan, M.B. Gerstein, P. Natl Acad. Sci. USA 107, 6841 (2010) http://dx.doi.org/10.1073/pnas.0910867107CrossrefGoogle Scholar

  • [50] B.D. MacArthur, A. Ma’ayan, I.R. Lemischka, Nat. Rev. Mol. Cell Bio. 10, 672 (2009) Google Scholar

  • [51] T. Gedeon, K. Mischaikow, K. Patterson, E. Traldid, B. Math. Biol. 70, 1660 (2008) http://dx.doi.org/10.1007/s11538-008-9313-6CrossrefGoogle Scholar

  • [52] D. Müller, J. Stelling, PLOS Comput. Biol. 5, e1000279 (2009) http://dx.doi.org/10.1371/journal.pcbi.1000279CrossrefGoogle Scholar

  • [53] A. Coulon, O. Gandrillon, G. Beslon, BMC Syst. Biol. 4, 2 (2010) http://dx.doi.org/10.1186/1752-0509-4-2CrossrefGoogle Scholar

  • [54] D. Michel, Prog. Biophys. Mol. Bio. 102, 16 (2010) http://dx.doi.org/10.1016/j.pbiomolbio.2009.12.007CrossrefGoogle Scholar

  • [55] E. Yang et al., Genome Res. 13, 1863 (2003) http://dx.doi.org/10.1101/gr.997703CrossrefGoogle Scholar

  • [56] A. Beyer, J. Hollunder, H.-P. Nasheuer, T. Wilhelm, Mol. Cell. Proteomics 3, 1083 (2004) http://dx.doi.org/10.1074/mcp.M400099-MCP200CrossrefGoogle Scholar

  • [57] R. de Sousa Abreu, L.O. Penalva, E.M. Marcotte, C. Vogel, Mol. Biosyst. 5, 1512 (2009) Google Scholar

  • [58] B. Derrida, Y. Pomeau, Europhys. Lett. 1, 45 (1986) http://dx.doi.org/10.1209/0295-5075/1/2/001CrossrefGoogle Scholar

  • [59] M. Andrecut, S.A. Kauffman, Phys. Lett. A 372, 4757 (2008) http://dx.doi.org/10.1016/j.physleta.2008.05.041CrossrefGoogle Scholar

  • [60] V.P. Zhdanov, JETP Lett. (in press) Google Scholar

About the article

Published Online: 2011-04-30

Published in Print: 2011-08-01


Citation Information: Open Physics, Volume 9, Issue 4, Pages 909–918, ISSN (Online) 2391-5471, DOI: https://doi.org/10.2478/s11534-010-0104-y.

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