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Volumn 17, Issue 2, 2007, Pages 107-112

Stochastic gene expression: from single molecules to the proteome

Author keywords

[No Author keywords available]

Indexed keywords

GREEN FLUORESCENT PROTEIN; PROTEOME;

EID: 34047262163     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gde.2007.02.007     Document Type: Review
Times cited : (143)

References (40)
  • 1
    • 0001674670 scopus 로고
    • Induced synthesis of enzymes in bacteria analyzed at the cellular level
    • Benzer S. Induced synthesis of enzymes in bacteria analyzed at the cellular level. Biochim Biophys Acta 11 (1953) 383-395
    • (1953) Biochim Biophys Acta , vol.11 , pp. 383-395
    • Benzer, S.1
  • 2
    • 0015547229 scopus 로고
    • Distribution of suboptimally induces -D-galactosidase in Escherichia coli. The enzyme content of individual cells
    • Maloney P.C., and Rotman B. Distribution of suboptimally induces -D-galactosidase in Escherichia coli. The enzyme content of individual cells. J Mol Biol 73 (1973) 77-91
    • (1973) J Mol Biol , vol.73 , pp. 77-91
    • Maloney, P.C.1    Rotman, B.2
  • 3
    • 0017833657 scopus 로고
    • A model for the statistical fluctuations of protein numbers in a microbial population
    • Berg O.G. A model for the statistical fluctuations of protein numbers in a microbial population. J Theor Biol 71 (1978) 587-603
    • (1978) J Theor Biol , vol.71 , pp. 587-603
    • Berg, O.G.1
  • 4
    • 0001389945 scopus 로고
    • Enzyme induction as an all-or-none phenomenon
    • Novick A., and Weiner M. Enzyme induction as an all-or-none phenomenon. Proc Natl Acad Sci USA 43 (1957) 553-566
    • (1957) Proc Natl Acad Sci USA , vol.43 , pp. 553-566
    • Novick, A.1    Weiner, M.2
  • 5
    • 0017185026 scopus 로고
    • Non-genetic individuality: chance in the single cell
    • Spudich J.L., and Koshland Jr. D.E. Non-genetic individuality: chance in the single cell. Nature 262 (1976) 467-471
    • (1976) Nature , vol.262 , pp. 467-471
    • Spudich, J.L.1    Koshland Jr., D.E.2
  • 6
    • 0025127307 scopus 로고
    • The dose dependence of glucocorticoid-inducible gene expression results from changes in the number of transcriptionally active templates
    • Ko M.S., Nakauchi H., and Takahashi N. The dose dependence of glucocorticoid-inducible gene expression results from changes in the number of transcriptionally active templates. EMBO J 9 (1990) 2835-2842
    • (1990) EMBO J , vol.9 , pp. 2835-2842
    • Ko, M.S.1    Nakauchi, H.2    Takahashi, N.3
  • 7
    • 0034212551 scopus 로고    scopus 로고
    • Engineering stability in gene networks by autoregulation
    • Becskei A., and Serrano L. Engineering stability in gene networks by autoregulation. Nature 405 (2000) 590-593
    • (2000) Nature , vol.405 , pp. 590-593
    • Becskei, A.1    Serrano, L.2
  • 8
    • 25144450143 scopus 로고    scopus 로고
    • Contributions of low molecule number and chromosomal positioning to stochastic gene expression
    • Becskei A., Kaufmann B.B., and van Oudenaarden A. Contributions of low molecule number and chromosomal positioning to stochastic gene expression. Nat Genet 37 (2005) 937-944
    • (2005) Nat Genet , vol.37 , pp. 937-944
    • Becskei, A.1    Kaufmann, B.B.2    van Oudenaarden, A.3
  • 9
    • 0242416539 scopus 로고    scopus 로고
    • Blake WJ, M KA, Cantor CR, Collins JJ: Noise in eukaryotic gene expression. Nature 2003. 422:633-637.
  • 11
    • 15544388848 scopus 로고    scopus 로고
    • Noise propagation in gene networks
    • Pedraza J.M., and van Oudenaarden A. Noise propagation in gene networks. Science 307 (2005) 1965-1969
    • (2005) Science , vol.307 , pp. 1965-1969
    • Pedraza, J.M.1    van Oudenaarden, A.2
  • 12
  • 13
    • 33745287724 scopus 로고    scopus 로고
    • Noise in protein expression scales with natural protein abundance
    • The authors measured expression from 43 genes in each of 11 conditions, resulting in a global trend wherein noise scales inversely with mean. This paper mathematically discusses many possible origins of the observed scaling, including global factors, pathway-specific factors, promoter activation kinetics, and randomness of mRNA production.
    • Bar-Even A., Paulsson J., Maheshri N., Carmi M., O'Shea E., Pilpel Y., and Barkai N. Noise in protein expression scales with natural protein abundance. Nat Genet 38 (2006) 636-643. The authors measured expression from 43 genes in each of 11 conditions, resulting in a global trend wherein noise scales inversely with mean. This paper mathematically discusses many possible origins of the observed scaling, including global factors, pathway-specific factors, promoter activation kinetics, and randomness of mRNA production.
    • (2006) Nat Genet , vol.38 , pp. 636-643
    • Bar-Even, A.1    Paulsson, J.2    Maheshri, N.3    Carmi, M.4    O'Shea, E.5    Pilpel, Y.6    Barkai, N.7
  • 14
    • 33745220278 scopus 로고    scopus 로고
    • Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
    • The largest survey to date of noise across the proteome. The authors argued that stochastic creation and destruction of mRNA describes the bulk of the observed variation. They showed that classes of genes regulated by the same proteins have similar noise levels and that essential genes are often less noisy than inessential ones.
    • Newman J.R., Ghaemmaghami S., Ihmels J., Breslow D.K., Noble M., DeRisi J.L., and Weissman J.S. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441 (2006) 840-846. The largest survey to date of noise across the proteome. The authors argued that stochastic creation and destruction of mRNA describes the bulk of the observed variation. They showed that classes of genes regulated by the same proteins have similar noise levels and that essential genes are often less noisy than inessential ones.
    • (2006) Nature , vol.441 , pp. 840-846
    • Newman, J.R.1    Ghaemmaghami, S.2    Ihmels, J.3    Breslow, D.K.4    Noble, M.5    DeRisi, J.L.6    Weissman, J.S.7
  • 15
    • 2942718723 scopus 로고    scopus 로고
    • Control of stochasticity in eukaryotic gene expression
    • Raser J.M., and O'Shea E.K. Control of stochasticity in eukaryotic gene expression. Science 304 (2004) 1811-1814
    • (2004) Science , vol.304 , pp. 1811-1814
    • Raser, J.M.1    O'Shea, E.K.2
  • 18
    • 33746868344 scopus 로고    scopus 로고
    • Monitoring dynamics of single-cell gene expression over multiple cell cycles
    • 2005 0024
    • Cookson S., Ostroff N., Pang W.L., Volfson D., and Hasty J. Monitoring dynamics of single-cell gene expression over multiple cell cycles. Mol Syst Biol 1 (2005) 2005 0024
    • (2005) Mol Syst Biol , vol.1
    • Cookson, S.1    Ostroff, N.2    Pang, W.L.3    Volfson, D.4    Hasty, J.5
  • 20
    • 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
  • 21
    • 3843126332 scopus 로고    scopus 로고
    • RNA dynamics in live Escherichia coli cells
    • Golding I., and Cox E.C. RNA dynamics in live Escherichia coli cells. Proc Natl Acad Sci USA 101 (2004) 11310-11315
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 11310-11315
    • Golding, I.1    Cox, E.C.2
  • 23
    • 33645293152 scopus 로고    scopus 로고
    • An excitable gene regulatory circuit induces transient cellular differentiation
    • Suel G.M., Garcia-Ojalvo J., Liberman L.M., and Elowitz M.B. An excitable gene regulatory circuit induces transient cellular differentiation. Nature 440 (2006) 545-550
    • (2006) Nature , vol.440 , pp. 545-550
    • Suel, G.M.1    Garcia-Ojalvo, J.2    Liberman, L.M.3    Elowitz, M.B.4
  • 26
    • 28944434119 scopus 로고    scopus 로고
    • Real-time kinetics of gene activity in individual bacteria
    • This study was the first to directly demonstrate transcriptional bursting by tracking the birth dynamics of individual mRNAs. While in the active state, genes were found to produce mRNAs at a constant rate. The authors also showed that mRNAs partition approximately binomially at cell division, leading to a cell cycle dependence in the correlation between mRNAs and proteins.
    • Golding I., Paulsson J., Zawilski S.M., and Cox E.C. Real-time kinetics of gene activity in individual bacteria. Cell 123 (2005) 1025-1036. This study was the first to directly demonstrate transcriptional bursting by tracking the birth dynamics of individual mRNAs. While in the active state, genes were found to produce mRNAs at a constant rate. The authors also showed that mRNAs partition approximately binomially at cell division, leading to a cell cycle dependence in the correlation between mRNAs and proteins.
    • (2005) Cell , vol.123 , pp. 1025-1036
    • Golding, I.1    Paulsson, J.2    Zawilski, S.M.3    Cox, E.C.4
  • 27
    • 33748994704 scopus 로고    scopus 로고
    • Stochastic mRNA Synthesis in mammalian cells
    • The authors used a FISH-based technique to demonstrate massive transcriptional bursting in mammalian cells. Gene activation events were found to simultaneously affect several genes at a single genomic locus, whereas chromosomally distinct loci switched between active and inactive states independently.
    • Raj A., Peskin C.S., Tranchina D., Vargas D.Y., and Tyagi S. Stochastic mRNA Synthesis in mammalian cells. PLoS Biol 4 (2006) e309. The authors used a FISH-based technique to demonstrate massive transcriptional bursting in mammalian cells. Gene activation events were found to simultaneously affect several genes at a single genomic locus, whereas chromosomally distinct loci switched between active and inactive states independently.
    • (2006) PLoS Biol , vol.4
    • Raj, A.1    Peskin, C.S.2    Tranchina, D.3    Vargas, D.Y.4    Tyagi, S.5
  • 28
  • 29
    • 0034608143 scopus 로고    scopus 로고
    • Random signal fluctuations can reduce random fluctuations in regulated components of chemical regulatory networks
    • Paulsson J., and Ehrenberg M. Random signal fluctuations can reduce random fluctuations in regulated components of chemical regulatory networks. Phys Rev Lett 84 (2000) 5447-5450
    • (2000) Phys Rev Lett , vol.84 , pp. 5447-5450
    • Paulsson, J.1    Ehrenberg, M.2
  • 30
    • 0034691214 scopus 로고    scopus 로고
    • Stochastic focusing: fluctuation-enhanced sensitivity of intracellular regulation
    • Paulsson J., Berg O.G., and Ehrenberg M. Stochastic focusing: fluctuation-enhanced sensitivity of intracellular regulation. Proc Natl Acad Sci USA 97 (2000) 7148-7153
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 7148-7153
    • Paulsson, J.1    Berg, O.G.2    Ehrenberg, M.3
  • 31
    • 0034981558 scopus 로고    scopus 로고
    • Noise in a minimal regulatory network: plasmid copy number control
    • Paulsson J., and Ehrenberg M. Noise in a minimal regulatory network: plasmid copy number control. Q Rev Biophys 34 (2001) 1-59
    • (2001) Q Rev Biophys , vol.34 , pp. 1-59
    • Paulsson, J.1    Ehrenberg, M.2
  • 32
    • 0017780941 scopus 로고
    • Stochastic model of linear, continuous protein synthesis in bacterial populations
    • Rigney D.R., and Schieve W.C. Stochastic model of linear, continuous protein synthesis in bacterial populations. J Theor Biol 69 (1977) 761-766
    • (1977) J Theor Biol , vol.69 , pp. 761-766
    • Rigney, D.R.1    Schieve, W.C.2
  • 34
    • 33645033645 scopus 로고    scopus 로고
    • Probing gene expression in live cells, one protein molecule at a time
    • The authors developed a novel assay allowing the detection of single YFP molecules in living cells. Leaky expression from the repressed lac promoter in Escherichia coli cells was then shown to result in geometrically distributed protein bursts that were probably the result of single, stochastically produced mRNAs.
    • Yu J., Xiao J., Ren X., Lao K., and Xie X.S. Probing gene expression in live cells, one protein molecule at a time. Science 311 (2006) 1600-1603. The authors developed a novel assay allowing the detection of single YFP molecules in living cells. Leaky expression from the repressed lac promoter in Escherichia coli cells was then shown to result in geometrically distributed protein bursts that were probably the result of single, stochastically produced mRNAs.
    • (2006) Science , vol.311 , pp. 1600-1603
    • Yu, J.1    Xiao, J.2    Ren, X.3    Lao, K.4    Xie, X.S.5
  • 35
    • 33745295645 scopus 로고    scopus 로고
    • Predictable trends in protein noise
    • Baetz K., and Kaern M. Predictable trends in protein noise. Nat Genet 38 (2006) 610-611
    • (2006) Nat Genet , vol.38 , pp. 610-611
    • Baetz, K.1    Kaern, M.2
  • 36
    • 33646568466 scopus 로고    scopus 로고
    • Eukaryotic transcription: what does it mean for a gene to be 'on'?
    • Golding I., and Cox E.C. Eukaryotic transcription: what does it mean for a gene to be 'on'?. Curr Biol 16 (2006) R371-R373
    • (2006) Curr Biol , vol.16
    • Golding, I.1    Cox, E.C.2
  • 37
    • 33646591544 scopus 로고    scopus 로고
    • Transcriptional pulsing of a developmental gene
    • Chubb J.R., Trcek T., Shenoy S.M., and Singer R.H. Transcriptional pulsing of a developmental gene. Curr Biol 16 (2006) 1018-1025
    • (2006) Curr Biol , vol.16 , pp. 1018-1025
    • Chubb, J.R.1    Trcek, T.2    Shenoy, S.M.3    Singer, R.H.4
  • 40
    • 0030861452 scopus 로고    scopus 로고
    • Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements
    • Lutz R., and Bujard H. Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucleic Acids Res 25 (1997) 1203-1210
    • (1997) Nucleic Acids Res , vol.25 , pp. 1203-1210
    • Lutz, R.1    Bujard, H.2


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