메뉴 건너뛰기




Volumn 95, Issue 9, 2008, Pages 4228-4240

Dynamical analysis on gene activity in the presence of repressors and an interfering promoter

Author keywords

[No Author keywords available]

Indexed keywords

DNA DIRECTED RNA POLYMERASE; REPRESSOR PROTEIN; TRANSCRIPTION FACTOR;

EID: 58149145142     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.108.132894     Document Type: Article
Times cited : (11)

References (46)
  • 1
    • 0030960672 scopus 로고    scopus 로고
    • Ptashne, M., and A. Gann. 1997. Transcriptional activation by recruitment. Nature. 386:569-577.
    • Ptashne, M., and A. Gann. 1997. Transcriptional activation by recruitment. Nature. 386:569-577.
  • 2
    • 0032486385 scopus 로고    scopus 로고
    • Activation and repression of transcription by differential contact: Two sides of a coin
    • Roy, S., S. Garges, and S. Adhya. 1998. Activation and repression of transcription by differential contact: two sides of a coin. J. Biol. Chem. 273:14059-14062.
    • (1998) J. Biol. Chem , vol.273 , pp. 14059-14062
    • Roy, S.1    Garges, S.2    Adhya, S.3
  • 3
    • 0022429106 scopus 로고
    • The OR control system of bacteriophage λ. A physical-chemical model for gene regulation
    • Shea, M. A., and G. K. Ackers. 1985. The OR control system of bacteriophage λ. A physical-chemical model for gene regulation. J. Mol. Biol. 181:211-230.
    • (1985) J. Mol. Biol , vol.181 , pp. 211-230
    • Shea, M.A.1    Ackers, G.K.2
  • 5
    • 0019867850 scopus 로고
    • Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli Lac repressor-operator interaction: Kinetic measurements and conclusions
    • Winter, R. B., O. G. Berg, and P. H. von Hippel. 1981. Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli Lac repressor-operator interaction: kinetic measurements and conclusions. Biochemistry. 20:6961-6977.
    • (1981) Biochemistry , vol.20 , pp. 6961-6977
    • Winter, R.B.1    Berg, O.G.2    von Hippel, P.H.3
  • 6
    • 34249932435 scopus 로고    scopus 로고
    • Probing transcription factor dynamics at the single molecule level in a living cell
    • Elf, J., G.-W. Li, and S. Xie. 2007. Probing transcription factor dynamics at the single molecule level in a living cell. Science. 316:1191-1194.
    • (2007) Science , vol.316 , pp. 1191-1194
    • Elf, J.1    Li, G.-W.2    Xie, S.3
  • 8
    • 0018604734 scopus 로고
    • Convergent transcription in bacteriophage λ: Interference with gene expression
    • Ward, D. F., and N. E. Murray. 1979. Convergent transcription in bacteriophage λ: interference with gene expression. J. Mol. Biol. 133:249-266.
    • (1979) J. Mol. Biol , vol.133 , pp. 249-266
    • Ward, D.F.1    Murray, N.E.2
  • 9
    • 0019994521 scopus 로고
    • Promoter occlusion: Transcription through a promoter may inhibit its activity
    • Adhya, S., and M. Gottesman. 1982. Promoter occlusion: transcription through a promoter may inhibit its activity. Cell. 29:939-944.
    • (1982) Cell , vol.29 , pp. 939-944
    • Adhya, S.1    Gottesman, M.2
  • 10
    • 0023661348 scopus 로고
    • A new target for CRP action at the malt promoter
    • Menendez, M., A. Kolb, and H. Buc. 1987. A new target for CRP action at the malt promoter. EMBO J. 6:4227-4234.
    • (1987) EMBO J , vol.6 , pp. 4227-4234
    • Menendez, M.1    Kolb, A.2    Buc, H.3
  • 11
    • 2942574509 scopus 로고    scopus 로고
    • Transcriptional interference between convergent promoters caused by elongation over the promoter
    • Callen, B. P., K. E. Shearwin, and J. B. Egan. 2004. Transcriptional interference between convergent promoters caused by elongation over the promoter. Mol. Cell. 14:647-656.
    • (2004) Mol. Cell , vol.14 , pp. 647-656
    • Callen, B.P.1    Shearwin, K.E.2    Egan, J.B.3
  • 12
    • 0034682534 scopus 로고    scopus 로고
    • Balancing transcriptional interference and initiation on the GAL7 promoter of Saccharomyces cerevisiae
    • Greger, I. H., A. Aranda, and N. Proudfoot. 2000. Balancing transcriptional interference and initiation on the GAL7 promoter of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA. 97:8415-8420.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 8415-8420
    • Greger, I.H.1    Aranda, A.2    Proudfoot, N.3
  • 13
    • 0037173089 scopus 로고    scopus 로고
    • Transcriptional collision between convergent genes in budding yeast
    • Prescott, E. M., and N. J. Proudfoot. 2002. Transcriptional collision between convergent genes in budding yeast. Proc. Natl. Acad. Sci. USA. 99:8796-8801.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 8796-8801
    • Prescott, E.M.1    Proudfoot, N.J.2
  • 14
    • 12544251077 scopus 로고    scopus 로고
    • A mathematical model for transcriptional interference by RNA polymerase traffic in Escherichia coli
    • Sneppen, K., I. B. Dodd, K. E. Shearwin, A. C. Palmer, R. A. Schubert, B. P. Callen, and J. B. Egan. 2005. A mathematical model for transcriptional interference by RNA polymerase traffic in Escherichia coli. J. Mol. Biol. 346:399-409.
    • (2005) J. Mol. Biol , vol.346 , pp. 399-409
    • Sneppen, K.1    Dodd, I.B.2    Shearwin, K.E.3    Palmer, A.C.4    Schubert, R.A.5    Callen, B.P.6    Egan, J.B.7
  • 15
    • 34248641123 scopus 로고    scopus 로고
    • Modeling transcriptional interference and DNA looping in gene regulation
    • Dodd, I. B., K. E. Shearwin, and K. Sneppen. 2007. Modeling transcriptional interference and DNA looping in gene regulation. J. Mol. Biol. 369:1200-1213.
    • (2007) J. Mol. Biol , vol.369 , pp. 1200-1213
    • Dodd, I.B.1    Shearwin, K.E.2    Sneppen, K.3
  • 16
    • 0020490669 scopus 로고
    • Mechanism of activation of transcription initiation from the λ PRM promoter
    • Hawley, D., and W. McClure. 1982. Mechanism of activation of transcription initiation from the λ PRM promoter. J. Mol. Biol. 57:493-525.
    • (1982) J. Mol. Biol , vol.57 , pp. 493-525
    • Hawley, D.1    McClure, W.2
  • 17
    • 0021857751 scopus 로고
    • Kinetics of open complex formation between Escherichia coli RNA polymerase and the Lac UV5 promoter. Evidence for a sequential mechanism involving three steps
    • Buc, H., and W. R. McClure. 1985. Kinetics of open complex formation between Escherichia coli RNA polymerase and the Lac UV5 promoter. Evidence for a sequential mechanism involving three steps. Biochemistry. 24:2712-2723.
    • (1985) Biochemistry , vol.24 , pp. 2712-2723
    • Buc, H.1    McClure, W.R.2
  • 18
    • 85031356694 scopus 로고    scopus 로고
    • Record, Jr., M. T., W. S. Reznikoff, M. L. Craig, K. L. McQuade, and P. J. Schlax. 1996. Escherichia coli RNA polymerase (Eσ70) promoters, and the kinetics of the steps of transcription initiation. In Escherichia coli and Salmonella typhimurium. F. C. Neidhardt, R. Curtiss III, J. L. Ingraham, E. C. C. Lin, K. R. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger, editors. American Society for Microbiology, Washington, DC.
    • Record, Jr., M. T., W. S. Reznikoff, M. L. Craig, K. L. McQuade, and P. J. Schlax. 1996. Escherichia coli RNA polymerase (Eσ70) promoters, and the kinetics of the steps of transcription initiation. In Escherichia coli and Salmonella typhimurium. F. C. Neidhardt, R. Curtiss III, J. L. Ingraham, E. C. C. Lin, K. R. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger, editors. American Society for Microbiology, Washington, DC.
  • 19
    • 0037073077 scopus 로고    scopus 로고
    • Promoter clearance and escape in prokaryotes
    • Hsu, L. M. 2002. Promoter clearance and escape in prokaryotes. Biochim. Biophys. Acta. 1577:191-207.
    • (2002) Biochim. Biophys. Acta , vol.1577 , pp. 191-207
    • Hsu, L.M.1
  • 20
    • 0024077617 scopus 로고
    • PL of coliphage λ: An alternate solution for an efficient promoter
    • Knaus, R., and H. Bujard. 1988. PL of coliphage λ: an alternate solution for an efficient promoter. EMBO J. 7:2919-2923.
    • (1988) EMBO J , vol.7 , pp. 2919-2923
    • Knaus, R.1    Bujard, H.2
  • 21
    • 0019967737 scopus 로고
    • 5′ nucleotide heterogeneity and altered initiation of transcription at mutant Lac promoters
    • Carpousis, A. J., J. E. Stefano, and J. D. Gralla. 1982. 5′ nucleotide heterogeneity and altered initiation of transcription at mutant Lac promoters. J. Mol. Biol. 157:619-633.
    • (1982) J. Mol. Biol , vol.157 , pp. 619-633
    • Carpousis, A.J.1    Stefano, J.E.2    Gralla, J.D.3
  • 23
    • 0345077411 scopus 로고
    • Promoters largely determine the efficiency of repressor action
    • Lanzer, M., and H. Bujard. 1988. Promoters largely determine the efficiency of repressor action. Proc. Natl. Acad. Sci. USA. 85:8973-8977.
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 8973-8977
    • Lanzer, M.1    Bujard, H.2
  • 24
    • 85031364444 scopus 로고    scopus 로고
    • Reference deleted in proof
    • Reference deleted in proof.
  • 25
    • 85031367531 scopus 로고    scopus 로고
    • Reference deleted in proof
    • Reference deleted in proof.
  • 26
  • 27
    • 33748994704 scopus 로고    scopus 로고
    • Stochastic mRNA synthesis in mammalian cell
    • DOI: 10.1371/journal.pbio.0040309
    • Raj, A., C. Peskin, D. Tranchina, D. Y. Vargas, and S. Tyagi. 2006. Stochastic mRNA synthesis in mammalian cell. PLoS Biol. DOI: 10.1371/journal.pbio.0040309.
    • (2006) PLoS Biol
    • Raj, A.1    Peskin, C.2    Tranchina, D.3    Vargas, D.Y.4    Tyagi, S.5
  • 28
    • 0033546210 scopus 로고    scopus 로고
    • The organization of replication and transcription
    • Cook, P. R. 1999. The organization of replication and transcription. Science. 284:1790-1795.
    • (1999) Science , vol.284 , pp. 1790-1795
    • Cook, P.R.1
  • 29
    • 28944434119 scopus 로고    scopus 로고
    • Real time kinetics of gene activity in individual bacteria
    • Golding, I., J. Paulsson, S. M. Zawilski, and E. Cox. 2005. Real time kinetics of gene activity in individual bacteria. Cell. 123:1025-1036.
    • (2005) Cell , vol.123 , pp. 1025-1036
    • Golding, I.1    Paulsson, J.2    Zawilski, S.M.3    Cox, E.4
  • 30
    • 48249138167 scopus 로고    scopus 로고
    • The generation of promoter-mediated transcriptional noise in bacteria
    • Accepted for publication
    • Mitarai, N., I. B. Dodd, M. T. Crooks, and K. Sneppen. 2008. The generation of promoter-mediated transcriptional noise in bacteria. PloS Comput. Biol. Accepted for publication.
    • (2008) PloS Comput. Biol
    • Mitarai, N.1    Dodd, I.B.2    Crooks, M.T.3    Sneppen, K.4
  • 32
    • 34547925618 scopus 로고    scopus 로고
    • Combinatorial promoter design for engineering noisy gene expression
    • Murphy, K. F., G. Balázsi, and J. J. Collins. 2007. Combinatorial promoter design for engineering noisy gene expression. Proc. Natl. Acad. Sci. USA. 104:12726-12731.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 12726-12731
    • Murphy, K.F.1    Balázsi, G.2    Collins, J.J.3
  • 33
    • 0020432792 scopus 로고
    • Mutants in the Y-region of bacteriophage λ constitutive for repressor synthesis: Their isolation and the characterization of the Hyp phenotype
    • Eisen, H., P. Barrand, W. Spiegelman, L. F. Reichardt, S. Heineman, and C. Georgopoulos. 1982. Mutants in the Y-region of bacteriophage λ constitutive for repressor synthesis: their isolation and the characterization of the Hyp phenotype. Gene. 20:71-81.
    • (1982) Gene , vol.20 , pp. 71-81
    • Eisen, H.1    Barrand, P.2    Spiegelman, W.3    Reichardt, L.F.4    Heineman, S.5    Georgopoulos, C.6
  • 34
    • 0020451895 scopus 로고
    • An IS4 transposition causes a 13-bp duplication of phage-λ DNA and results in the constitutive expression of the CI and Cro Gene-products
    • Georgopoulos, C., N. McKittrick, G. Herrick, and H. Eisen. 1982. An IS4 transposition causes a 13-bp duplication of phage-λ DNA and results in the constitutive expression of the CI and Cro Gene-products. Gene. 20:83-90.
    • (1982) Gene , vol.20 , pp. 83-90
    • Georgopoulos, C.1    McKittrick, N.2    Herrick, G.3    Eisen, H.4
  • 35
    • 0033545416 scopus 로고    scopus 로고
    • Four dimers of λ-repressor bound to two suitably spaced pairs of λ-operators form octamers and DNA loops over large distances
    • Revet, B., B. von Wilcken-Bergmann, H. Bessert, A. Barker, and B. Muller-Hill. 1999. Four dimers of λ-repressor bound to two suitably spaced pairs of λ-operators form octamers and DNA loops over large distances. Curr. Biol. 9:151-154.
    • (1999) Curr. Biol , vol.9 , pp. 151-154
    • Revet, B.1    von Wilcken-Bergmann, B.2    Bessert, H.3    Barker, A.4    Muller-Hill, B.5
  • 37
    • 85031355319 scopus 로고    scopus 로고
    • Reference deleted in proof
    • Reference deleted in proof.
  • 38
    • 0033517148 scopus 로고    scopus 로고
    • Robustness of a gene regulatory circuit
    • Little, J. W., D. P. Shepley, and D. W. Wert. 1999. Robustness of a gene regulatory circuit. EMBO J. 18:4299-4307.
    • (1999) EMBO J , vol.18 , pp. 4299-4307
    • Little, J.W.1    Shepley, D.P.2    Wert, D.W.3
  • 40
    • 0025309753 scopus 로고
    • Elongation by Escherichia coli RNA polymerase is blocked in vitro by a site-specific DNA binding protein
    • Pavco, P., and D. Steege. 1990. Elongation by Escherichia coli RNA polymerase is blocked in vitro by a site-specific DNA binding protein. J. Biol. Chem. 265:9960-9969.
    • (1990) J. Biol. Chem , vol.265 , pp. 9960-9969
    • Pavco, P.1    Steege, D.2
  • 41
    • 0025877255 scopus 로고
    • Transcription on nucleosomal templates by RNA polymerase II in vitro: Inhibition of elongation with enhancement of sequence-specific pausing
    • Iban, M. G., and D. S. Luse. 1991. Transcription on nucleosomal templates by RNA polymerase II in vitro: inhibition of elongation with enhancement of sequence-specific pausing. Genes Dev. 5:683-696.
    • (1991) Genes Dev , vol.5 , pp. 683-696
    • Iban, M.G.1    Luse, D.S.2
  • 42
    • 0027447687 scopus 로고
    • Elongation factor SII-dependent transcription by RNA polymerase II through a sequence-specific DNA-binding protein
    • Reines, D., and J. Mote. 1993. Elongation factor SII-dependent transcription by RNA polymerase II through a sequence-specific DNA-binding protein. Proc. Natl. Acad. Sci. USA. 90:1917-1921.
    • (1993) Proc. Natl. Acad. Sci. USA , vol.90 , pp. 1917-1921
    • Reines, D.1    Mote, J.2
  • 43
    • 0034671841 scopus 로고    scopus 로고
    • GreA and GreB proteins revive backtracked RNA polymerase in vivo by promoting transcript trimming
    • Toulmé, F., C. Mosrin-Huaman, J. Sparkowski, A. Das, M. Leng, and A. Rahmouni. 2000. GreA and GreB proteins revive backtracked RNA polymerase in vivo by promoting transcript trimming. EMBO J. 19: 6853-6859.
    • (2000) EMBO J , vol.19 , pp. 6853-6859
    • Toulmé, F.1    Mosrin-Huaman, C.2    Sparkowski, J.3    Das, A.4    Leng, M.5    Rahmouni, A.6
  • 44
    • 0141625269 scopus 로고    scopus 로고
    • Transcription through the roadblocks: The role of RNA polymerase cooperation
    • Epstein, V., F. Toulmé, A. Rahmouni, S. Borukhov, and E. Nudler. 2003. Transcription through the roadblocks: the role of RNA polymerase cooperation. EMBO J. 22:4719-4727.
    • (2003) EMBO J , vol.22 , pp. 4719-4727
    • Epstein, V.1    Toulmé, F.2    Rahmouni, A.3    Borukhov, S.4    Nudler, E.5
  • 45
    • 0036203807 scopus 로고    scopus 로고
    • Nucleosome remodeling induced by RNA polymerase II: Loss of the H2A/H2B dimer during transcription
    • Kireeva, M. L., W. Walter, V. Tchernajenko, V. Bondarenko, M. Kashlev, and V. M. Studitsky. 2002. Nucleosome remodeling induced by RNA polymerase II: loss of the H2A/H2B dimer during transcription. Mol. Cell. 9:541-552.
    • (2002) Mol. Cell , vol.9 , pp. 541-552
    • Kireeva, M.L.1    Walter, W.2    Tchernajenko, V.3    Bondarenko, V.4    Kashlev, M.5    Studitsky, V.M.6
  • 46
    • 0141704307 scopus 로고    scopus 로고
    • Bacterial polymerase and yeast polymerase II use similar mechanisms for transcription through nucleosomes
    • Walter, W., M. L. Kireeva, V. M. Studitsky, and M. Kashlev. 2003. Bacterial polymerase and yeast polymerase II use similar mechanisms for transcription through nucleosomes. J. Biol. Chem. 278:36148-36156.
    • (2003) J. Biol. Chem , vol.278 , pp. 36148-36156
    • Walter, W.1    Kireeva, M.L.2    Studitsky, V.M.3    Kashlev, M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.