Two novel aspects of the kinetics of gene expression including miRNAs

• Authors: Vladimir Zhdanov
• Languages of publication: EN

Abstracts

EN

In eukaryotic cells, many genes are transcribed into non-coding RNAs. Small RNAs or, more specifically, microRNAs (miRNAs) form an abundant sub-class of such RNAs. miRNAs are transcribed as long noncoding RNA and then generated via a processing pathway down to the 20–24-nucleotide length. The key ability of miRNAs is to associate with target mRNAs and to suppress their translation and/or facilitate degradation. Using the mean-field kinetic equations and Monte Carlo simulations, we analyze two aspects of this interplay. First, we describe the situation when the formation of mRNA or miRNA is periodically modulated by a transcription factor which itself is not perturbed by these species. Depending on the ratio between the mRNA and miRNA formation rates, the corresponding induced periodic kinetics are shown to be either nearly harmonic or shaped as anti-phase pulses. The second part of the work is related to recent experimental studies indicating that differentiation of stem cells often involves changes in gene transcription into miRNAs and/or the interference between miRNAs, mRNAs and proteins. In particular, the regulatory protein obtained via mRNA translation may suppress the miRNA formation, and the latter may suppress in turn the miRNA-mRNA association and degradation. The corresponding bistable kinetics are described in detail.

Keywords

EN

subcellular processes; gene transcription; mRNA and miRNA association and degradation; mRNA translation; stem cells

• Publisher: De Gruyter Open
• Journal: Open Physics
• Year: 2013
• Volume: 11
• Issue: 4
• Pages: 448-456

Dates

published

1 - 4 - 2013

online

22 - 5 - 2013

Contributors

author

Vladimir Zhdanov

References

• [1] B. Alberts et al., Molecular Biology of the Cell (Garland, New York, 2002)
• [2] D.P. Bartel, Cell 136, 215 (2009) http://dx.doi.org/10.1016/j.cell.2009.01.002[Crossref]
• [3] V.N. Kim, J. Han, M.C. Siomi, Nat. Rev. Mol. Cell Bio. 10, 126 (2009) http://dx.doi.org/10.1038/nrm2632[Crossref]
• [4] J. Krol, I. Loedige, W. Filipowicz, Nat. Rev. Genet. 11, 597 (2009)
• [5] The ENCODE Project Consortium, Nature 489, 57 (2012) http://dx.doi.org/10.1038/nature11247[Crossref]
• [6] M.B. Gerstein et al., Nature 489, 91 (2012) http://dx.doi.org/10.1038/nature11245[Crossref]
• [7] Y.R. Yamada, C.S. Peskin, Biophys. J. 96, 3015 (2009) http://dx.doi.org/10.1016/j.bpj.2008.12.3955[Crossref]
• [8] V.P. Zhdanov, Phys. Rev. E 80, 051925 (2009) http://dx.doi.org/10.1103/PhysRevE.80.051925[Crossref]
• [9] D. Michel, Prog. Biophys. Mol. Bio. 102, 16 (2010) http://dx.doi.org/10.1016/j.pbiomolbio.2009.12.007[Crossref]
• [10] M. Kandhavelu, A. Häkkinen, O. Yli-Harja, A.S. Ribeiro, Phys. Biol. 9, 026004 (2012) http://dx.doi.org/10.1088/1478-3975/9/2/026004[Crossref]
• [11] L. Ciandrini, I. Stansfield, M.C. Romano, Phys. Rev. E 81, 051904 (2010) http://dx.doi.org/10.1103/PhysRevE.81.051904[Crossref]
• [12] A.K. Sharma, D. Chowdhury, J. Theor. Biol. 289, 36 (2011) http://dx.doi.org/10.1016/j.jtbi.2011.08.023[Crossref]
• [13] A. Valleriani, G. Zhang, A. Nagar, Z. Ignatova, R. Lipowsky, Phys. Rev. E 83, 042903 (2011) http://dx.doi.org/10.1103/PhysRevE.83.042903[Crossref]
• [14] M. Kaern, T.C. Elston, W.J. Blake, J.J. Collins, Nat. Rev. Genet. 6, 451 (2005) http://dx.doi.org/10.1038/nrg1615[Crossref]
• [15] J. Rausenberger, C. Fleck, J. Timmer, M. Kollmann, Prog. Biophys. Mol. Bio. 100, 57 (2009) http://dx.doi.org/10.1016/j.pbiomolbio.2009.06.003[Crossref]
• [16] A.S. Ribeiro, Math. Biosci. 223, 1 (2010) http://dx.doi.org/10.1016/j.mbs.2009.10.007[Crossref]
• [17] G. Tiana, S. Krishna, S. Pigolotti, M.H. Jensen, K. Sneppen, Phys. Biol. 4, R1 (2007) http://dx.doi.org/10.1088/1478-3975/4/2/R01[Crossref]
• [18] O. Purcell, N.J. Savery, C.S. Grierson, M. di Bernardo, J. R. Soc. Interface 7, 1503 (2010) http://dx.doi.org/10.1098/rsif.2010.0183[Crossref]
• [19] X. Zhu, M. Gerstein, M. Snyder, Gene. Dev. 21, 1010 (2007) http://dx.doi.org/10.1101/gad.1528707[Crossref]
• [20] G. Karlebach, R. Shamir, Nat. Rev. Mol. Cell Bio. 9, 771 (2008) http://dx.doi.org/10.1038/nrm2503[Crossref]
• [21] M.C. Lagomarsino, B. Bassetti, G. Castellani, D. Remondini, Mol. Biosyst. 5, 335 (2009) http://dx.doi.org/10.1039/b816841p[Crossref]
• [22] D.F.T. Veiga, B. Dutta, G. Balazsi, Mol. Biosyst. 6, 469 (2010) http://dx.doi.org/10.1039/b916989j[Crossref]
• [23] V.P. Zhdanov, Phys. Rep. 500, 1 (2011) http://dx.doi.org/10.1016/j.physrep.2010.12.002[Crossref]
• [24] B. Novak, J.J. Tyson, J. Theor. Biol. 230, 563 (2004) http://dx.doi.org/10.1016/j.jtbi.2004.04.039[Crossref]
• [25] C. Gerard, A. Goldbeter, Chaos 20, 045109 (2010) http://dx.doi.org/10.1063/1.3527998[Crossref]
• [26] R. Cheong, A. Levchenko, Curr. Opin. Genet. Dev. 20, 665 (2010) http://dx.doi.org/10.1016/j.gde.2010.08.007[Crossref]
• [27] D. Gonze, Biosystems 99, 60 (2010) http://dx.doi.org/10.1016/j.biosystems.2009.08.009[Crossref]
• [28] V.P. Zhdanov. Physica A 390, 57 (2011) http://dx.doi.org/10.1016/j.physa.2010.03.036[Crossref]
• [29] K. Tsumoto, G. Kurosawa, T. Yoshinaga, K. Aihara, PLoS One 6, e20880 (2011) http://dx.doi.org/10.1371/journal.pone.0020880[Crossref]
• [30] G. Bordyugov, A.E. Granada, H. Herzel, Eur. Phys. J. B 82, 227 (2011) http://dx.doi.org/10.1140/epjb/e2011-20337-1[Crossref]
• [31] V.P. Zhdanov, Chaos Soliton. Fract. 45, 577 (2012) http://dx.doi.org/10.1016/j.chaos.2011.12.008[Crossref]
• [32] S. Huang, Philos. T. R. Soc. B 366, 2247 (2011) http://dx.doi.org/10.1098/rstb.2011.0008[Crossref]
• [33] C. Furusawa, K. Kaneko, Science 338, 215 (2012) http://dx.doi.org/10.1126/science.1224311[Crossref]
• [34] K. Lai, M.J. Robertson, D.V. Schaffer, Biophys. J. 86, 2748 (2004) http://dx.doi.org/10.1016/S0006-3495(04)74328-3[Crossref]
• [35] L. Mariani, M. Löhning, A. Radbruch, T. Höfer, Prog. Biophys. Mol. Bio. 86, 45 (2004) http://dx.doi.org/10.1016/j.pbiomolbio.2004.02.007[Crossref]
• [36] V. Chickarmane et al., PLoS Comput. Biol. 2, 1080 (2006) http://dx.doi.org/10.1371/journal.pcbi.0020123[Crossref]
• [37] R.E. Callard, Immunol. Cell Biol. 85, 300 (2007) http://dx.doi.org/10.1038/sj.icb.7100060[Crossref]
• [38] S. Huang, Y.P. Guo, G. May, T. Enver, Dev. Biol. 305, 695 (2007) http://dx.doi.org/10.1016/j.ydbio.2007.02.036[Crossref]
• [39] R. Guantes, J.F. Poyatos, PLoS Comput. Biol. 4, e1000235 (2008) http://dx.doi.org/10.1371/journal.pcbi.1000235[Crossref]
• [40] B.D. MacArthur, C.P. Please, R.O.C. Oreffo, PLoS One 3, e3086 (2008) http://dx.doi.org/10.1371/journal.pone.0003086[Crossref]
• [41] H.-J. van den Ham, R.J. de Boer, Int. Immunol. 20, 1269 (2008) http://dx.doi.org/10.1093/intimm/dxn093[Crossref]
• [42] V. Chickarmane, T. Enver, C. Peterson, PLoS Comput. Biol. 5, e1000268 (2009) http://dx.doi.org/10.1371/journal.pcbi.1000268[Crossref]
• [43] T. Kalmar et al., PLoS Biol. 7, e1000149 (2009) http://dx.doi.org/10.1371/journal.pbio.1000149[Crossref]
• [44] L. Wang et al., P. Natl Acad. Sci. USA 106, 6638 (2009) http://dx.doi.org/10.1073/pnas.0806137106[Crossref]
• [45] V.P. Zhdanov, J. Phys. A-Math. Theor. 42, 065102 (2009) http://dx.doi.org/10.1088/1751-8113/42/6/065102[Crossref]
• [46] S. Bhattacharya et al., Toxicol. Sci. 115, 51 (2010) http://dx.doi.org/10.1093/toxsci/kfq035[Crossref]
• [47] J. Wang, L. Xu, E. Wang, S. Huang, Biophys. J. 99, 29 (2010) http://dx.doi.org/10.1016/j.bpj.2010.03.058[Crossref]
• [48] Q. Zhang et al., BMC Syst. Biol. 4, 40 (2010) http://dx.doi.org/10.1186/1752-0509-4-40[Crossref]
• [49] C. Duff, K. Smith-Miles, L. Lopes, T. Tian, J. Math. Biol. 64, 449 (2012) http://dx.doi.org/10.1007/s00285-011-0419-3[Crossref]
• [50] B. Juliandi, M. Abematsu, K. Nakashima, Dev. Growth Differ. 52, 493 (2010) http://dx.doi.org/10.1111/j.1440-169X.2010.01175.x[Crossref]
• [51] E. Vreugdenhil, E. Berezikov, Front. Neuroendocrin. 31, 128 (2010) http://dx.doi.org/10.1016/j.yfrne.2009.08.001[Crossref]
• [52] D. Subramanyam, R. Blelloch, Curr. Opin. Genet. Dev. 21, 498 (2011) http://dx.doi.org/10.1016/j.gde.2011.04.011[Crossref]
• [53] R. Yi, E. Fuchs, J. Cell Sci. 124, 1775 (2011) http://dx.doi.org/10.1242/jcs.069104[Crossref]
• [54] C. Conaco, S. Otto, J.J. Han, G. Mandel, P. Natl Acad. Sci. USA 103, 2422 (2006) http://dx.doi.org/10.1073/pnas.0511041103[Crossref]
• [55] V.P. Zhdanov, Biosystems 95, 75 (2009) http://dx.doi.org/10.1016/j.biosystems.2008.07.002[Crossref]
• [56] P. Zhou, S. Cai, Z. Liu, R. Wang, PLoS One 6, e17029 (2011) http://dx.doi.org/10.1371/journal.pone.0017029[Crossref]
• [57] V.P. Zhdanov, JETP Lett. 88, 466 (2008) http://dx.doi.org/10.1134/S0021364008190120[Crossref]
• [58] Y. Zeng, Mol. Pharm. 75, 259 (2009) http://dx.doi.org/10.1124/mol.108.052118[Crossref]
• [59] V.P. Zhdanov, Neural Networks 25, 200 (2012) http://dx.doi.org/10.1016/j.neunet.2011.08.006[Crossref]

Identifiers

DOI

10.2478/s11534-013-0190-8