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Volumn 100, Issue 1, 2010, Pages 31-38

Toward a system-level understanding of microRNA pathway via mathematical modeling

Author keywords

Deterministic models; MicroRNA pathway; Noise; Sensitivity analysis; Stochastic models

Indexed keywords

MESSENGER RNA; MICRORNA; RNA INDUCED SILENCING COMPLEX;

EID: 77249176042     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2009.12.005     Document Type: Article
Times cited : (36)

References (58)
  • 1
    • 0036784630 scopus 로고    scopus 로고
    • In vivo kinetics of mRNA splicing and transport in mammalian cells
    • Audibert A., Weil D., and Dautry F. In vivo kinetics of mRNA splicing and transport in mammalian cells. Mol. Cell Biol. 22 (2002) 6706-6718
    • (2002) Mol. Cell Biol. , vol.22 , pp. 6706-6718
    • Audibert, A.1    Weil, D.2    Dautry, F.3
  • 2
    • 43049101535 scopus 로고    scopus 로고
    • miRNA modulation of the cellular stress response
    • Babar I.A., Slack F.J., and Weidhaas J.B. miRNA modulation of the cellular stress response. Future Oncol. 4 (2008) 289-298
    • (2008) Future Oncol. , vol.4 , pp. 289-298
    • Babar, I.A.1    Slack, F.J.2    Weidhaas, J.B.3
  • 3
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: genomics, biogenesis, mechanism, and function
    • Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116 (2004) 281-297
    • (2004) Cell , vol.116 , pp. 281-297
    • Bartel, D.P.1
  • 4
    • 31544456413 scopus 로고    scopus 로고
    • Insights into the kinetics of siRNA-mediated gene silencing from live-cell and live-animal bioluminescent imaging
    • Bartlett D.W., and Davis M.E. Insights into the kinetics of siRNA-mediated gene silencing from live-cell and live-animal bioluminescent imaging. Nucleic Acids Res. 34 (2006) 322-333
    • (2006) Nucleic Acids Res. , vol.34 , pp. 322-333
    • Bartlett, D.W.1    Davis, M.E.2
  • 5
    • 1942435249 scopus 로고    scopus 로고
    • Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs
    • Bartel D.P., and Chen C.Z. Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat. Rev. Genet. 5 (2004) 396-400
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 396-400
    • Bartel, D.P.1    Chen, C.Z.2
  • 6
    • 27144515901 scopus 로고    scopus 로고
    • Movement of eukaryotic mRNAs between polysomes and cytoplasmic processing bodies
    • Brengues M., Teixeira D., and Parker R. Movement of eukaryotic mRNAs between polysomes and cytoplasmic processing bodies. Science 310 (2005) 486-489
    • (2005) Science , vol.310 , pp. 486-489
    • Brengues, M.1    Teixeira, D.2    Parker, R.3
  • 7
    • 33645027986 scopus 로고    scopus 로고
    • Stochastic protein expression in individual cells at the single molecule level
    • Cai L., Friedman N., and Xie X.S. Stochastic protein expression in individual cells at the single molecule level. Nature 440 (2006) 358-362
    • (2006) Nature , vol.440 , pp. 358-362
    • Cai, L.1    Friedman, N.2    Xie, X.S.3
  • 8
    • 0034731365 scopus 로고    scopus 로고
    • Dynamic shuttling of nuclear factor kappa B between the nucleus and cytoplasm as a consequence of inhibitor dissociation
    • Carlotti F., Dower S.K., and Qwarnstrom E.E. Dynamic shuttling of nuclear factor kappa B between the nucleus and cytoplasm as a consequence of inhibitor dissociation. J. Biol. Chem. 275 (2000) 41028-41034
    • (2000) J. Biol. Chem. , vol.275 , pp. 41028-41034
    • Carlotti, F.1    Dower, S.K.2    Qwarnstrom, E.E.3
  • 11
    • 0001144902 scopus 로고    scopus 로고
    • Efficient exact stochastic simulation of chemical systems with many species and many channels
    • Gibson M.A., and Bruck J. Efficient exact stochastic simulation of chemical systems with many species and many channels. J. Phys. Chem. A 104 (2000) 1876-1889
    • (2000) J. Phys. Chem. A , vol.104 , pp. 1876-1889
    • Gibson, M.A.1    Bruck, J.2
  • 12
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie D.T. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81 (1977) 2340-2361
    • (1977) J. Phys. Chem. , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 13
    • 3042602447 scopus 로고    scopus 로고
    • Kinetic analysis of the RNAi enzyme complex
    • Haley B., and Zamore P.D. Kinetic analysis of the RNAi enzyme complex. Nat. Struct. Mol. Biol. 11 (2004) 599-606
    • (2004) Nat. Struct. Mol. Biol. , vol.11 , pp. 599-606
    • Haley, B.1    Zamore, P.D.2
  • 14
    • 0027172425 scopus 로고
    • Microcomputer-assisted kinetic modeling of mammalian gene expression
    • Hargrove J.L. Microcomputer-assisted kinetic modeling of mammalian gene expression. FASEB J. 7 (1993) 1163-1170
    • (1993) FASEB J. , vol.7 , pp. 1163-1170
    • Hargrove, J.L.1
  • 15
    • 0026287765 scopus 로고
    • The kinetics of mammalian gene expression
    • Hargrove J.L., Hulsey M.G., and Beale E.G. The kinetics of mammalian gene expression. Bioessays 13 (1991) 667-674
    • (1991) Bioessays , vol.13 , pp. 667-674
    • Hargrove, J.L.1    Hulsey, M.G.2    Beale, E.G.3
  • 16
    • 0032444348 scopus 로고    scopus 로고
    • Inducible and constitutive transcription factors in the mammalian nervous system: control of gene expression by Jun, Fos and Krox, and CREB/ATF proteins
    • Herdegen T., and Leah J.D. Inducible and constitutive transcription factors in the mammalian nervous system: control of gene expression by Jun, Fos and Krox, and CREB/ATF proteins. Brain. Res. Brain Res. Rev. 28 (1998) 370-490
    • (1998) Brain. Res. Brain Res. Rev. , vol.28 , pp. 370-490
    • Herdegen, T.1    Leah, J.D.2
  • 18
    • 33749528151 scopus 로고    scopus 로고
    • miRNAs and apoptosis: RNAs to die for
    • Jovanovic M., and Hengartner M.O. miRNAs and apoptosis: RNAs to die for. Oncogene 25 (2006) 6176-6187
    • (2006) Oncogene , vol.25 , pp. 6176-6187
    • Jovanovic, M.1    Hengartner, M.O.2
  • 19
    • 19544379881 scopus 로고    scopus 로고
    • Stochasticity in gene expression: from theories to phenotypes
    • Kaern M., Elston T.C., Blake W.J., and Collins J.J. Stochasticity in gene expression: from theories to phenotypes. Nat. Rev. Genet. 6 (2005) 451-464
    • (2005) Nat. Rev. Genet. , vol.6 , pp. 451-464
    • Kaern, M.1    Elston, T.C.2    Blake, W.J.3    Collins, J.J.4
  • 20
    • 52649087274 scopus 로고    scopus 로고
    • Modelling and analysis of gene regulatory networks
    • Karlebach G., and Shamir R. Modelling and analysis of gene regulatory networks. Nat. Rev. Mol. Cell Biol. 9 (2008) 770-780
    • (2008) Nat. Rev. Mol. Cell Biol. , vol.9 , pp. 770-780
    • Karlebach, G.1    Shamir, R.2
  • 21
    • 33748928159 scopus 로고    scopus 로고
    • The diverse functions of microRNAs in animal development and disease
    • Kloosterman W.P., and Plasterk R.H. The diverse functions of microRNAs in animal development and disease. Dev. Cell 11 (2006) 441-450
    • (2006) Dev. Cell , vol.11 , pp. 441-450
    • Kloosterman, W.P.1    Plasterk, R.H.2
  • 22
    • 0026862118 scopus 로고
    • Induction mechanism of a single gene molecule: stochastic or deterministic?
    • Ko M.S. Induction mechanism of a single gene molecule: stochastic or deterministic?. Bioessays 14 (1992) 341-346
    • (1992) Bioessays , vol.14 , pp. 341-346
    • Ko, M.S.1
  • 23
    • 0035830451 scopus 로고    scopus 로고
    • Kinetic studies of Fos.Jun.DNA complex formation: DNA binding prior to dimerization
    • Kohler J.J., and Schepartz A. Kinetic studies of Fos.Jun.DNA complex formation: DNA binding prior to dimerization. Biochemistry 40 (2001) 130-142
    • (2001) Biochemistry , vol.40 , pp. 130-142
    • Kohler, J.J.1    Schepartz, A.2
  • 24
    • 34447632218 scopus 로고    scopus 로고
    • Role of Dicer and Drosha for endothelial microRNA expression and angiogenesis
    • Kuehbacher A., Urbich C., Zeiher A.M., and Dimmeler S. Role of Dicer and Drosha for endothelial microRNA expression and angiogenesis. Circ. Res. 101 (2007) 59-68
    • (2007) Circ. Res. , vol.101 , pp. 59-68
    • Kuehbacher, A.1    Urbich, C.2    Zeiher, A.M.3    Dimmeler, S.4
  • 25
    • 38049046644 scopus 로고    scopus 로고
    • Systematic evaluation of microRNA processing patterns in tissues, cell lines, and tumors
    • Lee E.J., Baek M., Gusev Y., Brackett D.J., Nuovo G.J., and Schmittgen T.D. Systematic evaluation of microRNA processing patterns in tissues, cell lines, and tumors. RNA 14 (2008) 35-42
    • (2008) RNA , vol.14 , pp. 35-42
    • Lee, E.J.1    Baek, M.2    Gusev, Y.3    Brackett, D.J.4    Nuovo, G.J.5    Schmittgen, T.D.6
  • 27
    • 55949097145 scopus 로고    scopus 로고
    • Small RNAs establish delays and temporal thresholds in gene expression
    • Legewie S., Dienst D., Wilde A., Herzel H., and Axmann I.M. Small RNAs establish delays and temporal thresholds in gene expression. Biophys. J. 95 (2008) 3232-3238
    • (2008) Biophys. J. , vol.95 , pp. 3232-3238
    • Legewie, S.1    Dienst, D.2    Wilde, A.3    Herzel, H.4    Axmann, I.M.5
  • 28
    • 33845295461 scopus 로고    scopus 로고
    • Quantitative analysis of Argonaute protein reveals microRNA-dependent localization to stress granules
    • Leung A.K., Calabrese J.M., and Sharp P.A. Quantitative analysis of Argonaute protein reveals microRNA-dependent localization to stress granules. Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 18125-18130
    • (2006) Proc. Natl. Acad. Sci. U.S.A. , vol.103 , pp. 18125-18130
    • Leung, A.K.1    Calabrese, J.M.2    Sharp, P.A.3
  • 29
    • 36849064251 scopus 로고    scopus 로고
    • Target-specific and global effectors in gene regulation by MicroRNA
    • Levine E., Ben Jacob E., and Levine H. Target-specific and global effectors in gene regulation by MicroRNA. Biophys. J. 93 (2007) L52-L54
    • (2007) Biophys. J. , vol.93
    • Levine, E.1    Ben Jacob, E.2    Levine, H.3
  • 30
    • 36949029208 scopus 로고    scopus 로고
    • Small regulatory RNAs may sharpen spatial expression patterns
    • Levine E., McHale P., and Levine H. Small regulatory RNAs may sharpen spatial expression patterns. PLoS Comput. Biol. 3 (2007) 2356-2365
    • (2007) PLoS Comput. Biol. , vol.3 , pp. 2356-2365
    • Levine, E.1    McHale, P.2    Levine, H.3
  • 31
    • 85194540918 scopus 로고    scopus 로고
    • Levine, E., Huang, M., Huang, Y.M., Kuhlman, T., Shi, H.L., Zhang, Z.G., Hwa, T., submitted for publication. On noise and silence in small RNA regulation. Proc. Natl. Acad. Sci. http://matisse.ucsd.edu/%7Ehwa/pub/sRNA-noise.pdf.
    • Levine, E., Huang, M., Huang, Y.M., Kuhlman, T., Shi, H.L., Zhang, Z.G., Hwa, T., submitted for publication. On noise and silence in small RNA regulation. Proc. Natl. Acad. Sci. http://matisse.ucsd.edu/%7Ehwa/pub/sRNA-noise.pdf.
  • 32
    • 44649136660 scopus 로고    scopus 로고
    • A. Autoinhibition of human dicer by its internal helicase domain
    • Ma E., MacRae I.J., Kirsch J.F., and Doudna J. A. Autoinhibition of human dicer by its internal helicase domain. J. Mol. Biol. 380 (2008) 237-243
    • (2008) J. Mol. Biol. , vol.380 , pp. 237-243
    • Ma, E.1    MacRae, I.J.2    Kirsch, J.F.3    Doudna, J.4
  • 33
    • 46149102667 scopus 로고    scopus 로고
    • MicroRNA-directed regulation: to cleave or not to cleave
    • Mallory A.C., and Bouche N. MicroRNA-directed regulation: to cleave or not to cleave. Trends Plant Sci. 13 (2008) 359-367
    • (2008) Trends Plant Sci. , vol.13 , pp. 359-367
    • Mallory, A.C.1    Bouche, N.2
  • 34
    • 33749439869 scopus 로고    scopus 로고
    • Impact of RNA interference on gene networks
    • Malphettes L., and Fussenegger M. Impact of RNA interference on gene networks. Metab. Eng. 8 (2006) 672-683
    • (2006) Metab. Eng. , vol.8 , pp. 672-683
    • Malphettes, L.1    Fussenegger, M.2
  • 37
    • 54049118804 scopus 로고    scopus 로고
    • A quantitative comparison of sRNA-based and protein-based gene regulation
    • Mehta P., Goyal S., and Wingreen N.S. A quantitative comparison of sRNA-based and protein-based gene regulation. Mol. Syst. Biol. 4 (2008) 221-230
    • (2008) Mol. Syst. Biol. , vol.4 , pp. 221-230
    • Mehta, P.1    Goyal, S.2    Wingreen, N.S.3
  • 38
    • 0043180477 scopus 로고    scopus 로고
    • Oscillatory expression of Hes1, p53, and NF-kappaB driven by transcriptional time delays
    • Monk N.A. Oscillatory expression of Hes1, p53, and NF-kappaB driven by transcriptional time delays. Curr. Biol. 13 (2003) 1409-1413
    • (2003) Curr. Biol. , vol.13 , pp. 1409-1413
    • Monk, N.A.1
  • 39
    • 33947104955 scopus 로고    scopus 로고
    • Dynamic regulation of miRNA expression in ordered stages of cellular development
    • Neilson J.R., Zheng G.X., Burge C.B., and Sharp P.A. Dynamic regulation of miRNA expression in ordered stages of cellular development. Genes Dev. 21 (2007) 578-589
    • (2007) Genes Dev. , vol.21 , pp. 578-589
    • Neilson, J.R.1    Zheng, G.X.2    Burge, C.B.3    Sharp, P.A.4
  • 40
    • 3142729150 scopus 로고    scopus 로고
    • Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways
    • Okamura K., Ishizuka A., Siomi H., and Siomi M.C. Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways. Genes Dev. 18 (2004) 1655-1666
    • (2004) Genes Dev. , vol.18 , pp. 1655-1666
    • Okamura, K.1    Ishizuka, A.2    Siomi, H.3    Siomi, M.C.4
  • 41
    • 38349185928 scopus 로고    scopus 로고
    • Effects of molecular memory and bursting on fluctuations in gene expression
    • Pedraza J.M., and Paulsson J. Effects of molecular memory and bursting on fluctuations in gene expression. Science 319 (2008) 339-343
    • (2008) Science , vol.319 , pp. 339-343
    • Pedraza, J.M.1    Paulsson, J.2
  • 42
    • 34247238676 scopus 로고    scopus 로고
    • Genomics and gene transcription kinetics in yeast
    • Perez-Ortin J.E., Alepuz P.M., and Moreno J. Genomics and gene transcription kinetics in yeast. Trends Genet. 23 (2007) 250-257
    • (2007) Trends Genet. , vol.23 , pp. 250-257
    • Perez-Ortin, J.E.1    Alepuz, P.M.2    Moreno, J.3
  • 44
    • 27644538819 scopus 로고    scopus 로고
    • Tracing the sources of cellular variation
    • Ramanathan S., and Swain P.S. Tracing the sources of cellular variation. Dev. Cell 9 (2005) 576-578
    • (2005) Dev. Cell , vol.9 , pp. 576-578
    • Ramanathan, S.1    Swain, P.S.2
  • 47
    • 42749087154 scopus 로고    scopus 로고
    • Hybridization between mitochondrial heavy strand tDNA and expressed light strand tRNA modulates the function of heavy strand tDNA as light strand replication origin
    • Seligmann H. Hybridization between mitochondrial heavy strand tDNA and expressed light strand tRNA modulates the function of heavy strand tDNA as light strand replication origin. J. Mol. Biol. 379 (2008) 188-199
    • (2008) J. Mol. Biol. , vol.379 , pp. 188-199
    • Seligmann, H.1
  • 51
    • 33644768174 scopus 로고    scopus 로고
    • Control of translation and mRNA degradation by miRNAs and siRNAs
    • Valencia-Sanchez M.A., Liu J., Hannon G.J., and Parker R. Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev. 20 (2006) 515-524
    • (2006) Genes Dev. , vol.20 , pp. 515-524
    • Valencia-Sanchez, M.A.1    Liu, J.2    Hannon, G.J.3    Parker, R.4
  • 52
    • 33947262696 scopus 로고    scopus 로고
    • AU-rich-element-mediated upregulation of translation by FXR1 and Argonaute 2
    • Vasudevan S., and Steitz J.A. AU-rich-element-mediated upregulation of translation by FXR1 and Argonaute 2. Cell 128 (2007) 1105-1118
    • (2007) Cell , vol.128 , pp. 1105-1118
    • Vasudevan, S.1    Steitz, J.A.2
  • 53
    • 0034644270 scopus 로고    scopus 로고
    • The segment polarity network is a robust developmental module
    • von Dassow G., Meir E., Munro E.M., and Odell G.M. The segment polarity network is a robust developmental module. Nature 406 (2000) 188-192
    • (2000) Nature , vol.406 , pp. 188-192
    • von Dassow, G.1    Meir, E.2    Munro, E.M.3    Odell, G.M.4
  • 54
    • 34248347907 scopus 로고    scopus 로고
    • Stochastic simulations of the cytochrome P450 catalytic cycle
    • Wang Y., Li Y., and Wang B. Stochastic simulations of the cytochrome P450 catalytic cycle. J. Phys. Chem. B 111 (2007) 4251-4260
    • (2007) J. Phys. Chem. B , vol.111 , pp. 4251-4260
    • Wang, Y.1    Li, Y.2    Wang, B.3
  • 55
    • 61849137222 scopus 로고    scopus 로고
    • Many roads to maturity: microRNA biogenesis pathways and their regulation
    • Winter J., Jung S., Keller S., Gregory R.I., and Diederichs S. Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat. Cell Biol. 11 (2009) 228-234
    • (2009) Nat. Cell Biol. , vol.11 , pp. 228-234
    • Winter, J.1    Jung, S.2    Keller, S.3    Gregory, R.I.4    Diederichs, S.5
  • 56
  • 57
    • 34249006516 scopus 로고    scopus 로고
    • The role of microRNA in the delayed negative feedback regulation of gene expression
    • 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
    • (2007) Biochem. Biophys. Res. Commun. , vol.358 , pp. 722-726
    • Xie, Z.R.1    Yang, H.T.2    Liu, W.C.3    Hwang, M.J.4
  • 58
    • 0242490789 scopus 로고    scopus 로고
    • Importance of input perturbations and stochastic gene expression in the reverse engineering of genetic regulatory networks: insights from an identifiability analysis of an in silico network
    • Zak D.E., Gonye G.E., Schwaber J.S., and Doyle III F.J. Importance of input perturbations and stochastic gene expression in the reverse engineering of genetic regulatory networks: insights from an identifiability analysis of an in silico network. Genome Res. 13 (2003) 2396-2405
    • (2003) Genome Res. , vol.13 , pp. 2396-2405
    • Zak, D.E.1    Gonye, G.E.2    Schwaber, J.S.3    Doyle III, F.J.4


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