Oscillatory dynamics in a simple gene regulatory network mediated by small RNAs

Physica A: Statistical Mechanics and its Applications

Volumn 388, Issue 14, 2009, Pages 2995-3000

  Shen, Jianwei ^a,b   Liu, Zengrong ^b   Zheng, Weixing ^c   Xu, Fengdan ^b   Chen, Luonan ^b,d  

^a XUCHANG UNIVERSITY   (China)

^b SHANGHAI UNIVERSITY   (China)

^c UNIVERSITY OF WESTERN SYDNEY   (Australia)

^d OSAKA SANGYO UNIVERSITY   (Japan)

Author keywords

Gene regulatory network; Hopf bifurcation; Mathematical model; Oscillation; Small RNA

Indexed keywords

ASYMPTOTIC STABILITY; GENE EXPRESSION; MATHEMATICAL MODELS;

DYNAMICAL BEHAVIORS; GENE REGULATORY NETWORKS; GLOBALLY ASYMPTOTIC STABILITY; MESSENGER RNA; OSCILLATION; OSCILLATORY DYNAMICS; SMALL RNA;

HOPF BIFURCATION;

EID: 67349142577     PISSN: 03784371     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.physa.2009.03.032     Document Type: Article

References (27)

1. Chen L., and Aihara K. Stability of genetic regulatory networks with time delay. IEEE Trans. Circuits Syst. I: Fundamental Theory Appl. 49 5 (2002) 602-608
2. Monk N.A. Oscillatory expression of Hes1, p53, and NF-kappaB driven by transcriptional time delays. Curr. Biol. 13 (2003) 1409-1413
3. Dunlap J.C. Molecular bases for circadian. Cell 96 (1999) 271-290
4. Lewis J. Autoinhibition with transcriptional delay: A simple mechanism for the zebrafish somitogenesis oscillator. Curr. Biol. 19 (2003) 1398-1408
5. Hirata H., Bessho Y., Kokubu H., Masamizu Y., Yamada S., Lewis J., and Kageyama R. Instability of Hes7 protein is critical for the somite segmentation clock. Nat. Genet. 36 (2004) 750-754
6. Zeiser S., Liebscher H.V., Tiedemann H., Rubio-Aliaga I., Przemeck G.K., Hrabeä de Angelis M., and Winkler G. Number of active transcription factor binding sites is essential for the Hes7 oscillator. Theor. Biol. Med. Model 23 (2006) 11
7. Chen L., and Aihara K. Stability of genetic regulatory networks with time delay. IEEE Trans. Circuits Syst. I: Fundamental Theory Appl. 49 (2002) 602-608
8. Wang R., Zhou T., Jing Z., and Chen L. Modelling periodic oscillation of biological systems with multiple time scale networks. IET Syst. Biol. 1 (2004) 71-84
9. Chen L., Wang R., Kobayashi T., and Aihara K. Dynamics of gene regulatory networks with cell division cycle. Phys. Rev. E 70 (2004) 011909
10. Wang R., Li C., Chen L., and Aihara K. Modeling and analyzing biological oscillations in molecular networks. Proc. IEEE 96 (2008) 1361-1385
11. Bartel D.P. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116 (2004) 281-297
12. Gottesman S. Micros for microes: Non-coding regulatory RNA in bacteria. Trands Genet. 21 (2005) 399-404
13. Storz G., Altuvia S., and Wassarman K.M. An abundance of RNA regulators. Annu. Rev. Biochem. 74 (2005) 199-217
14. Zamore P.D., and Haley B. Ribo-gnome: The big world of small RNAs. Science 309 (2005) 1519-1524
15. Ambros V. The functions of animal microRNAs. Nature 431 (2004) 350-355
16. Chen L., Wang R.-S., and Zhang X.-S. Biomolecular Networks: Methods and Applications in Systems Biology (2009), John Wiley & Sons
17. Altuvia S., and Wagner E.G. Switching on and off with RNA. Proc. Natl. Acad. Sci. 97 (2000) 9824-9826
18. Gregory R.I., Yan K.P., Amuthan G., Chendrimada T., Doratotaj B., Cooch N., and Shiekhattar R. The microprocessor complex mediates the genesis of microRNAs. Nature 432 (2004) 235-240
19. Doench J.G., and Sharp P.A. Specificity of microRNA target selection in translational repression. Genes Dev. 18 (2004) 504-511
20. Hermeking H. p53 Enters the MicroRNA World, Cancer. Cell 12 (2007) 414-418
21. Lin H., He X., et al. A microRNA component of the p53 tumour suppressor network. Nature 447 (2007) 1130-1134
22. Levine E., and Ben Jacob E. Herbert Levine. Target-specific and global effectors in gene regulation by microRNA. Biophys. J. 93 11 (2007) L52-4
23. Lewis J. Autoinhibition with transcriptional delay: A simple mechanism for the zebrafish somitogenesis oscillator. Curr. Biol. 19 (2003) 1398-1408
24. Levine E., Zhang Z., Kuhlman T., and Hwa T. Quantitative characteristic of gene regulation by small RNA. PLoS Biology 5 9 (2007) 1998-2010
25. Shimoni Y., Friedlander G., Hetzroni G., Niv G., Altuvia S., Biham O., and Marglit H. Regulation of gene expression by small non-coding RNAs: A quantitative view. Molecular Syst. Biol. 3 138 (2007) 1-9
26. Xie Z.-R., Yang H.-T., Liu W.-C., and Hwang M.-J. The role of microRNA in the delayed negative feedback regulation of gene expression. Biochem. Biophys. Res. Commun. 358 (2007) 722-726
27. Ruan S., and Wei J. On the zeros of a third degree exponential polynomial with application to a delayed model for the control of testosterone secretion. IMA J. Math. Appl. Medicine Biol. 18 (2001) 41-52