Skip to content
BY-NC-ND 3.0 license Open Access Published by De Gruyter Open Access April 30, 2011

Non-coding RNAs and complex distributed genetic networks

  • Vladimir Zhdanov EMAIL logo
From the journal Open Physics

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.

[1] S. Bornholdt, Science 310, 449 (2005) http://dx.doi.org/10.1126/science.111995910.1126/science.1119959Search in Google Scholar PubMed

[2] G. Karlebach, R. Shamir, Nat. Rev. Mol. Cell Bio. 9, 771 (2008) http://dx.doi.org/10.1038/nrm250310.1038/nrm2503Search in Google Scholar PubMed

[3] Y. Bar-Yam, D. Harmon, B. de Bivort, Science 323, 1016 (2009) http://dx.doi.org/10.1126/science.116322510.1126/science.1163225Search in Google Scholar PubMed

[4] M.C. Lagomarsino, B. Bassetti, G. Castellani, D. Remondini, Mol. Biosyst. 5, 335 (2009) http://dx.doi.org/10.1039/b816841p10.1039/b816841pSearch in Google Scholar PubMed

[5] D.F.T. Veiga, B. Dutta, G. Balazsi, Mol. Biosyst. 6, 469 (2010) http://dx.doi.org/10.1039/b916989j10.1039/B916989JSearch in Google Scholar PubMed PubMed Central

[6] T.R. Mercer, M.E. Dinger, J.S. Mattick, Nat. Rev. Genet. 10, 155 (2009) http://dx.doi.org/10.1038/nrg252110.1038/nrg2521Search in Google Scholar PubMed

[7] J. Whitehead, G.K. Pandey, C. Kanduri, Biochim. Biophys. Acta 1790, 936 (2009) http://dx.doi.org/10.1016/j.bbagen.2008.10.00710.1016/j.bbagen.2008.10.007Search in Google Scholar PubMed

[8] J.E. Wilusz, H. Sunwoo, D.L. Spector, Gene. Dev. 23, 1494 (2009) http://dx.doi.org/10.1101/gad.180090910.1101/gad.1800909Search in Google Scholar PubMed PubMed Central

[9] D.P. Bartel, Cell 136, 215 (2009) http://dx.doi.org/10.1016/j.cell.2009.01.00210.1016/j.cell.2009.01.002Search in Google Scholar PubMed PubMed Central

[10] M. Ghildiyal, P.D. Zamore, Nat. Rev. Genet. 10, 94 (2009) http://dx.doi.org/10.1038/nrg250410.1038/nrg2504Search in Google Scholar PubMed PubMed Central

[11] V. N. Kim, J. Han, M.C. Siomi, Nat. Rev. Mol. Cell Bio. 10, 126 (2009) http://dx.doi.org/10.1038/nrm263210.1038/nrm2632Search in Google Scholar PubMed

[12] K.K.H. Farh et al., Science 310, 1817 (2005) http://dx.doi.org/10.1126/science.112115810.1126/science.1121158Search in Google Scholar PubMed

[13] J. Gao et al., Nature 466, 1105 (2010) http://dx.doi.org/10.1038/nature0927110.1038/nature09271Search in Google Scholar PubMed PubMed Central

[14] E. Barbarotto, T.G. Schmittgen, G.A. Calin, Int. J. Cancer 122, 969 (2008) http://dx.doi.org/10.1002/ijc.2334310.1002/ijc.23343Search in Google Scholar PubMed

[15] F.C. Lynn, Trends Endocrin. Met. 20, 452 (2009) http://dx.doi.org/10.1016/j.tem.2009.05.00710.1016/j.tem.2009.05.007Search in Google Scholar PubMed

[16] D.H. Lenz et al., Cell 118, 69 (2004) http://dx.doi.org/10.1016/j.cell.2004.06.00910.1016/j.cell.2004.06.009Search in Google Scholar PubMed

[17] S. Semsey et al., Nucleic Acids Res. 34, 4960 (2006) http://dx.doi.org/10.1093/nar/gkl62710.1093/nar/gkl627Search in Google Scholar PubMed PubMed Central

[18] E. Levine, E.B. Jacob, H. Levine, Biophys. J. 93, L52 (2007) http://dx.doi.org/10.1529/biophysj.107.11844810.1529/biophysj.107.118448Search in Google Scholar PubMed PubMed Central

[19] E. Levine, P. McHale, H. Levine, PLOS Comput. Biol. 3, e233 (2007) http://dx.doi.org/10.1371/journal.pcbi.003023310.1371/journal.pcbi.0030233Search in Google Scholar PubMed PubMed Central

[20] E. Levine, Z. Zhang, T. Kuhlman, T. Hwa, PLOS Biol. 5, e229 (2007) http://dx.doi.org/10.1371/journal.pbio.005022910.1371/journal.pbio.0050229Search in Google Scholar PubMed PubMed Central

[21] N. Mitarai, A.M.C. Andersson, S. Krishna, S. Semsey, K. Sneppen, Phys. Biol. 4, 164 (2007) http://dx.doi.org/10.1088/1478-3975/4/3/00310.1088/1478-3975/4/3/003Search in Google Scholar PubMed

[22] Y. Shimoni et al., Mol. Syst. Biol. 3, 138 (2007) http://dx.doi.org/10.1038/msb410018110.1038/msb4100181Search in Google Scholar PubMed PubMed Central

[23] S. Legewie, D. Dienst, A. Wilde, H. Herzel, I.M. Axmann, Biophys. J. 95, 3232 (2008) http://dx.doi.org/10.1529/biophysj.108.13381910.1529/biophysj.108.133819Search in Google Scholar PubMed PubMed Central

[24] E. Levine, T. Hwa, Curr. Opin. Microbiol. 11, 574 (2008) http://dx.doi.org/10.1016/j.mib.2008.09.01610.1016/j.mib.2008.09.016Search in Google Scholar PubMed PubMed Central

[25] P. Mehta, S. Goyal, N.S. Wingreen, Mol. Syst. Biol. 4, 221 (2008) http://dx.doi.org/10.1038/msb.2008.5810.1038/msb.2008.58Search in Google Scholar PubMed PubMed Central

[26] N. Mitarai et al., P. Natl Acad. Sci. USA 106, 10655 (2009) http://dx.doi.org/10.1073/pnas.090146610610.1073/pnas.0901466106Search in Google Scholar PubMed PubMed Central

[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.2009.04.00110.1016/j.bpc.2009.04.001Search in Google Scholar PubMed

[28] V.P. Zhdanov, Mol. Biosyst. 5, 638 (2009) http://dx.doi.org/10.1039/b808095j10.1039/b808095jSearch in Google Scholar PubMed

[29] V.P. Zhdanov, Biophys. Rev. Lett. 4, 267 (2009) http://dx.doi.org/10.1142/S179304800900103410.1142/S1793048009001034Search in Google Scholar

[30] V. Elgart, T. Jia, R. Kulkarni, Biophys. J. 98, 2780 (2010) http://dx.doi.org/10.1016/j.bpj.2010.03.02210.1016/j.bpj.2010.03.022Search in Google Scholar PubMed PubMed Central

[31] V. Elgart, T. Jia, R.V. Kulkarni, Phys. Rev. E 82, 021901 (2010) http://dx.doi.org/10.1103/PhysRevE.82.02190110.1103/PhysRevE.82.021901Search in Google Scholar PubMed

[32] V.P. Zhdanov, JETP Lett. 92, 410 (2010) http://dx.doi.org/10.1134/S002136401018010410.1134/S0021364010180104Search in Google 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.2007.04.20710.1016/j.bbrc.2007.04.207Search in Google Scholar PubMed

[34] V.P. Zhdanov, Chem. Phys. Lett. 458, 359 (2008) http://dx.doi.org/10.1016/j.cplett.2008.04.11110.1016/j.cplett.2008.04.111Search in Google Scholar

[35] V.P. Zhdanov, J. Phys. A-Math. Theor. 41, 285101 (2008) http://dx.doi.org/10.1088/1751-8113/41/28/28510110.1088/1751-8113/41/28/285101Search in Google Scholar

[36] V.P. Zhdanov, JETP Lett. 88, 466 (2008) http://dx.doi.org/10.1134/S002136400819012010.1134/S0021364008190120Search in Google 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.2009.03.03210.1016/j.physa.2009.03.032Search in Google Scholar

[38] A. Nandi, C. Vaz, A. Bhattacharya, R. Ramaswamy, BMC Syst. Biol. 3, 45 (2009) http://dx.doi.org/10.1186/1752-0509-3-4510.1186/1752-0509-3-45Search in Google Scholar PubMed PubMed Central

[39] V.P. Zhdanov, Biosystems 95, 75 (2009) http://dx.doi.org/10.1016/j.biosystems.2008.07.00210.1016/j.biosystems.2008.07.002Search in Google Scholar PubMed

[40] L.P. Xiong, Y.-Q. Ma, L.H. Tang, Chinese Phys. Lett. 27, 098701 (2010) http://dx.doi.org/10.1088/0256-307X/27/9/09870110.1088/0256-307X/27/9/098701Search in Google Scholar

[41] V.P. Zhdanov, Biophys. Rev. Lett. 5, 89 (2010) http://dx.doi.org/10.1142/S179304801000115910.1142/S1793048010001159Search in Google Scholar

[42] V.P. Zhdanov, Physica A 389, 887 (2010) http://dx.doi.org/10.1016/j.physa.2009.11.02810.1016/j.physa.2009.11.028Search in Google 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.081116610610.1073/pnas.0811166106Search in Google Scholar PubMed PubMed Central

[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-S610.1186/1471-2105-10-S4-S6Search in Google Scholar PubMed PubMed Central

[45] V.P. Zhdanov, Cent. Eur. J. Phys. 8, 864 (2010) http://dx.doi.org/10.2478/s11534-010-0025-910.2478/s11534-010-0025-9Search in Google Scholar

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

[47] J.C. Nacher, N. Araki, Biosystems 101, 10 (2010) http://dx.doi.org/10.1016/j.biosystems.2010.02.00510.1016/j.biosystems.2010.02.005Search in Google Scholar PubMed

[48] H.H. Chang, M. Hemberg, M. Barahona, D.E. Ingber, S. Huang, Nature 453, 544 (2008) http://dx.doi.org/10.1038/nature0696510.1038/nature06965Search in Google Scholar PubMed PubMed Central

[49] N. Bhardwaj, K.K. Yan, M.B. Gerstein, P. Natl Acad. Sci. USA 107, 6841 (2010) http://dx.doi.org/10.1073/pnas.091086710710.1073/pnas.0910867107Search in Google Scholar PubMed PubMed Central

[50] B.D. MacArthur, A. Ma’ayan, I.R. Lemischka, Nat. Rev. Mol. Cell Bio. 10, 672 (2009) 10.1038/nrm2766Search in Google Scholar PubMed PubMed Central

[51] T. Gedeon, K. Mischaikow, K. Patterson, E. Traldid, B. Math. Biol. 70, 1660 (2008) http://dx.doi.org/10.1007/s11538-008-9313-610.1007/s11538-008-9313-6Search in Google Scholar PubMed

[52] D. Müller, J. Stelling, PLOS Comput. Biol. 5, e1000279 (2009) http://dx.doi.org/10.1371/journal.pcbi.100027910.1371/journal.pcbi.1000279Search in Google Scholar PubMed PubMed Central

[53] A. Coulon, O. Gandrillon, G. Beslon, BMC Syst. Biol. 4, 2 (2010) http://dx.doi.org/10.1186/1752-0509-4-210.1186/1752-0509-4-2Search in Google Scholar PubMed PubMed Central

[54] D. Michel, Prog. Biophys. Mol. Bio. 102, 16 (2010) http://dx.doi.org/10.1016/j.pbiomolbio.2009.12.00710.1016/j.pbiomolbio.2009.12.007Search in Google Scholar PubMed

[55] E. Yang et al., Genome Res. 13, 1863 (2003) http://dx.doi.org/10.1101/gr.99770310.1101/gr.997703Search in Google Scholar PubMed PubMed Central

[56] A. Beyer, J. Hollunder, H.-P. Nasheuer, T. Wilhelm, Mol. Cell. Proteomics 3, 1083 (2004) http://dx.doi.org/10.1074/mcp.M400099-MCP20010.1074/mcp.M400099-MCP200Search in Google Scholar PubMed

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

[58] B. Derrida, Y. Pomeau, Europhys. Lett. 1, 45 (1986) http://dx.doi.org/10.1209/0295-5075/1/2/00110.1209/0295-5075/1/2/001Search in Google Scholar

[59] M. Andrecut, S.A. Kauffman, Phys. Lett. A 372, 4757 (2008) http://dx.doi.org/10.1016/j.physleta.2008.05.04110.1016/j.physleta.2008.05.041Search in Google Scholar

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

Published Online: 2011-4-30
Published in Print: 2011-8-1

© 2011 Versita Warsaw

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Downloaded on 6.2.2023 from https://www.degruyter.com/document/doi/10.2478/s11534-010-0104-y/html
Scroll Up Arrow