Microrna-mediated positive feedback loop and optimized bistable switch in a cancer network involving miR-17-92

PLoS ONE

Volumn 6, Issue 10, 2011, Pages

  Li, Yichen ^a,b   Li, Yumin ^a,b   Zhang, Hui ^a   Chen, Yong ^a,b  

^a LANZHOU UNIVERSITY   (China)

^b Key Laboratory of Digestive System Tumors   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; MICRORNA 17-92; MYC PROTEIN; TRANSCRIPTION FACTOR E2F; UNCLASSIFIED DRUG; MIRN17 92 MICRORNA, HUMAN; MIRN17-92 MICRORNA, HUMAN;

ARTICLE; CELL DEATH; GENE REGULATORY NETWORK; GENE SWITCHING; MATHEMATICAL MODEL; NEGATIVE FEEDBACK; NOISE; ONCOGENE; ONCOGENE E2F; ONCOGENE MYC; PHENOTYPE; POSITIVE FEEDBACK; PROCESS OPTIMIZATION; REGULATORY MECHANISM; SIGNAL DETECTION; BIOLOGICAL MODEL; FEEDBACK SYSTEM; GENETICS; HUMAN; METABOLISM; NEOPLASM; TIME;

E2F TRANSCRIPTION FACTORS; FEEDBACK, PHYSIOLOGICAL; GENE REGULATORY NETWORKS; HUMANS; MICRORNAS; MODELS, BIOLOGICAL; NEOPLASMS; PROTO-ONCOGENE PROTEINS C-MYC; TIME FACTORS;

EID: 80054711591     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0026302     Document Type: Article

References (54)

1. Lee RC, Feinbaum RL, Ambros V, (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854.
2. Wightman B, Ha I, Ruvkun G, (1993) Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75: 855-862.
3. Bartel DP, (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
4. Carthew RW, (2006) Gene regulation by microRNAs. Curr Opin Genet Dev 16: 203-208.
5. Cui Q, Yu Z, Purisima EO, Wang E, (2007) MicroRNA regulation and interspecific variation of gene expression. Trends Genet 23: 372-375.
6. Kim VN, (2005) MicroRNA biogenesis: coordinated cropping and dicing. Nat Rev Mol Cell Biol 6: 376-385.
7. Calin GA, Sevignani C, Dumitru CD, Hyslop T, Noche E, et al. (2004) Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc Natl Acad Sci USA 101: 2999-3004.
8. Garzon R, Calin GA, Croce CM, (2009) MicroRNAs in Cancer. Annu Rev Med 60: 167-179.
9. Li M, Li J, Ding X, He M, Cheng SY, (2010) microRNA and Cancer. The AAPS Journal 12: 309-317.
10. Tsang J, Zhu J, van Oudenaarden A, (2007) MicroRNAmediated feedback and feedforward loops are recurrent network motifs in mammals. Mol Cell 26: 753-767.
11. Inui M, Martello G, Piccolo S, (2010) MicroRNA control of signal transduction. Nat Rev Mol Cell Biol 11: 252-263.
12. Aguda BD, Kim Y, (2008) MicroRNA regulation of a cancer network: Consequences of the feedback loops involving miR-17-92, E2F, and Myc. Proc Natl Acad Sci USA 105: 19678-19683.
13. Brandman O, Ferrell JE Jr, Li R, Meyer T, (2005) Interlinked fast and slow positive feedback loops drive reliable cell decisions. Science 310: 496-498.
14. Yao G, Lee TJ, Mori S, Nevins JR, You L, (2008) A bistable Rb-E2F switch underlies the restriction point. Nat Cell Biol 10: 476-482.
15. Khanin R, Vinciotti V, (2008) Computational modeling of post-transcriptional gene regulation by microRNAs. J Comput Biol 15: 305-316.
16. Xiong W, Ferrell JE Jr, (2003) A positive-feedback-based bistable 'memory module' that governs a cell fate decision. Nature 426: 460-465.
17. Tian XJ, Zhang XP, Liu F, Wang W, (2009) Interlinking positive and negative feedback loops creates a tunable motif in gene regulatory networks. Physical Review E 80: 011926.
18. Nevozhay D, Adams RM, Murphy KF, Josić L, Balázsi G, (2009) Negative autoregulation linearizes the doseresponse and suppresses the heterogeneity of gene expression. Proc Natl Acad Sci U S A 106: 5123-5128.
19. Becskei A, Serrano L, (2000) Engineering stability in gene networks by autoregulation. Nature 405: 590-593.
20. Wolf DM, Arkin AP, (2003) Motifs, modules and games in bacteria. Curr Opin Microbiol 6: 125-134.
21. van der Pol B, (1926) On relaxation-oscillations. Phil Mag 7: 978-992.
22. Novak B, Tyson JJ, (2008) Design principles of biochemical oscillators. Nat Rev Mol Cell Biol 9: 981-991.
23. Tyson JJ, Chen KC, Novak B, (2003) Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol 15: 221-231.
24. Lindner B, García-Ojalvo J, Neiman A, Schimansky-Geiere L, (2004) Effects of noise in excitable systems. Phys Rep 392: 321-424.
25. Schlicht R, Winkler G, (2008) A delay stochastic process with applications in molecular biology. J Math Biol 57: 613-648.
26. Barrio M, Burrage K, Leier A, Tian T, (2006) Oscillatory regulation of Hes1: Discrete stochastic delay modelling and simulation. PLoS Comput Biol 2: e117.
27. Bratsun D, Volfson D, Tsimring LS, Hasty J, (2005) Delay-induced stochastic oscillations in gene regulation. Proc Natl Acad Sci U S A 102: 14593-14598.
28. Zhang XP, Liu F, Cheng Z, Wang W, (2009) Cell fate decision mediated by p53 pulses. Proc Natl Acad Sci U S A 106: 12245-12250.
29. Wee KB, Surana U, Aguda BD, (2009) Oscillations of the p53-Akt Network: Implications on Cell Survival and Death. PLoS ONE 4: e4407.
30. Zhang XP, Zhang C, Liu F, Wang W, (2007) Linking fast and slow positive feedback loops creates an optimal bistable switch in cell signaling. Physical Review E 76: 031924.
31. Smolen P, Baxter DA, Byrne JH, (92009) Interlinked dual-time feedback loops can enhance robustness to stochasticity and persistence of memory. Physical Review E 79: 031902.
32. Paulsson J, (2004) Summing up the noise in gene networks. Nature 427: 415-418.
33. Becskei A, Seraphin B, Serrano L, (2001) Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion. Embo J 20: 2528-2535.
34. Blake WJ, Karn M, Cantor CR, Collins JJ, (2003) Noise in eukaryotic gene expression. Nature 422: 633-637.
35. Hornung G, Barkai N, (2008) Noise propagation and signaling sensitivity in biological networks: A role for positive feedback. PLoS Comput Biol 4: e8.
36. Mendell JT, (2008) my Riad roles for the miR-17-92 cluster in development and disease. Cell 133: 217-222.
37. Coller HA, Forman JJ, Legesse-Miller A, (2007) Myced Messages: Myc induces transcription of E2F1 while inhibiting its translation via a microRNA polycistron. PLoS Genet 3: e146.
38. Acar M, Becskei A, van Oudenaarden A, (2005) Enhancement of cellular memory by reducing stochastic transitions. Nature 435: 228-232.
39. Ramsey SA, Smith JJ, Orrell D, Marelli M, Petersen TW, et al. (2006) Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast. Nat Genet 38: 1082-1087.
40. Bhalla US, Iyengar R, (2001) Robustness of the bistable behavior of a biological signaling feedback loop. Chaos 11: 221-226.
41. Bhalla US, Ram PT, Iyengar R, (2002) MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network. Science 297: 1018-1023.
42. Lee K, Loros JJ, Dunlap JC, (2000) Interconnected feedback loops in the neurospora circadian system. Science 289: 107-110.
43. Shearman LP, Sriram S, Weaver DR, Maywood ES, Chaves I, et al. (2000) Interacting molecular loops in the mammalian circadian clock. Science 288: 1013-1019.
44. Pomerening JR, Kim SY, Ferrell JE Jr, (2005) Systems-level dissection of the cell-cycle oscillator: Bypassing positive feedback produces damped oscillations. Cell 122: 565-578.
45. Pomerening JR, Sontag ED, Ferrell JE Jr, (2003) Building a cell cycle oscillator: hysteresis and bistability in the activation of Cdc2. Nat Cell Biol 5: 346-351.
46. Tsai TY, Choi YS, Ma W, Pomerening JR, Tang C, et al. (2008) Robust, tunable biological oscillations from interlinked positive and negative feedback loops. Science 321: 126-129.
47. O'Donnell KA, Wentzel EA, Zeller KI, Dang CV, Mendell JT, (2005) c-Myc-regulated microRNAs modulate E2F1 expression. Nature 435: 839-843.
48. Ventura AG, Young MM, Winslow L, Lintault L, Meissner A, et al. (2008) Targeted deletion reveals essential and overlapping functions of the miR-17-92 family of miRNA clusters. Cell 132: 875-886.
49. Xiao C, Srinivasan L, Calao DP, Patterson HC, Zhang B, et al. (2008) Lymphoproliferative disease and autoimmunity in mice with elevated miR-17-92 expression in lymphocytes. Nat Immunol 9: 405-414.
50. Petrocca R, Visone MR, Onelli MH, Shah MH, Nicoloso MS, et al. (2008) E2F1-regulated microRNAs impair TGFβ-dependent cell cycle arrest and apoptosis in gastric cancer. Cancer Cell 13: 272-286.
51. Dews M, Homayouni A, Yu D, Murphy D, Sevignani C, et al. (2006) Augmentation of tumor angiogenesis by a Myc-activated microRNA cluster. Nat Genet 38: 1060-1065.
52. See http://oscill8.sourceforge.net/.
53. Kasdin J, (1995) Runge-Kutta algorithm for the numerical integration of stochastic differential equations. J Guid Control Dynam 18: 114-120.
54. Kasdin J, (1995) Discrete simulation of colored noise and stochastic processes and 1/fa power law noise generation. Proceedings of the IEEE 83: 802-827.