메뉴 건너뛰기




Volumn 8, Issue 2, 2013, Pages

Cooperative RNA Polymerase Molecules Behavior on a Stochastic Sequence-Dependent Model for Transcription Elongation

Author keywords

[No Author keywords available]

Indexed keywords

RNA POLYMERASE;

EID: 84874302926     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0057328     Document Type: Article
Times cited : (11)

References (26)
  • 1
    • 50149109300 scopus 로고    scopus 로고
    • Single-molecule studies of RNA polymerase: Motoring along
    • Herbert KM, Greenleaf WJ, Block SM, (2008) Single-molecule studies of RNA polymerase: Motoring along. Annu Rev Biochem 77: 149-176.
    • (2008) Annu Rev Biochem , vol.77 , pp. 149-176
    • Herbert, K.M.1    Greenleaf, W.J.2    Block, S.M.3
  • 2
    • 33744981369 scopus 로고    scopus 로고
    • Sequence-resolved detecton of pausing by single RNA polymerase molecules
    • Herbert KM, La Porta A, Wong BJ, Mooney RA, Neuman KC, et al. (2006) Sequence-resolved detecton of pausing by single RNA polymerase molecules. Cell 125: 1083-1094.
    • (2006) Cell , vol.125 , pp. 1083-1094
    • Herbert, K.M.1    La Porta, A.2    Wong, B.J.3    Mooney, R.A.4    Neuman, K.C.5
  • 3
    • 0026084789 scopus 로고
    • A thermodynamic analysis of RNA transcript elongation and termination in Escherichia coli
    • Yager TD, vonHippel PH, (1991) A thermodynamic analysis of RNA transcript elongation and termination in Escherichia coli. Biochemistry 30: 1097-1118.
    • (1991) Biochemistry , vol.30 , pp. 1097-1118
    • Yager, T.D.1    vonHippel, P.H.2
  • 4
    • 7444253928 scopus 로고    scopus 로고
    • Sequence-dependent kinetic model for transcription elongation by RNA polymerase
    • Bai L, Shundrovsky A, Wang MD, (2004) Sequence-dependent kinetic model for transcription elongation by RNA polymerase. J Mol Biol 344: 335-349.
    • (2004) J Mol Biol , vol.344 , pp. 335-349
    • Bai, L.1    Shundrovsky, A.2    Wang, M.D.3
  • 6
    • 0017675903 scopus 로고
    • Modulation of ribosomal RNA synthesis in Oncopeltus fasciatus: An electron microscopic study of the relationship between changes in chromatin structure and transcriptional activity
    • Foe VE, (1977) Modulation of ribosomal RNA synthesis in Oncopeltus fasciatus: An electron microscopic study of the relationship between changes in chromatin structure and transcriptional activity. Cold Spring Harbor Symp Quant Biol 42: 723-740.
    • (1977) Cold Spring Harbor Symp Quant Biol , vol.42 , pp. 723-740
    • Foe, V.E.1
  • 7
    • 0019515818 scopus 로고
    • Electron microscopic analysis of transcription of a ribosomal RNA operon of E. coli
    • Hamming J, Arberg A, Ab G, Gruber M, (1981) Electron microscopic analysis of transcription of a ribosomal RNA operon of E. coli. Nucleic Acids Res 9: 1339-1350.
    • (1981) Nucleic Acids Res , vol.9 , pp. 1339-1350
    • Hamming, J.1    Arberg, A.2    Ab, G.3    Gruber, M.4
  • 8
    • 57449110975 scopus 로고    scopus 로고
    • Stochasticity and traffic jams in the transcription of ribosomal rna: Intriguing role of termination and antitermination
    • Klumpp S, Hwa T, (2008) Stochasticity and traffic jams in the transcription of ribosomal rna: Intriguing role of termination and antitermination. Proc Natl Acad Sci U S A 105: 18159-18164.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 18159-18164
    • Klumpp, S.1    Hwa, T.2
  • 9
    • 72049099609 scopus 로고    scopus 로고
    • Maximum rrn promoter activity in escherichia coli at saturating concentrations of free rna polymerase
    • Ehrenberg M, Dennis PP, Bremer H, (2010) Maximum rrn promoter activity in escherichia coli at saturating concentrations of free rna polymerase. Biochimie 92: 12-20.
    • (2010) Biochimie , vol.92 , pp. 12-20
    • Ehrenberg, M.1    Dennis, P.P.2    Bremer, H.3
  • 10
    • 0038756088 scopus 로고    scopus 로고
    • Cooperation between RNA polymerase molecules in transcription elongation
    • Epshtein V, Nudler E, (2003) Cooperation between RNA polymerase molecules in transcription elongation. Science 300: 801-805.
    • (2003) Science , vol.300 , pp. 801-805
    • Epshtein, V.1    Nudler, E.2
  • 11
    • 0141625269 scopus 로고    scopus 로고
    • Transcription through the roadblocks: the role of RNA polymerase cooperation
    • Epshtein V, Toulme F, Rahmouni AR, Borukhov S, Nudler E, (2003) Transcription through the roadblocks: the role of RNA polymerase cooperation. EMBO JOURNAL 22: 4719-4727.
    • (2003) EMBO JOURNAL , vol.22 , pp. 4719-4727
    • Epshtein, V.1    Toulme, F.2    Rahmouni, A.R.3    Borukhov, S.4    Nudler, E.5
  • 12
    • 79954632657 scopus 로고    scopus 로고
    • Pausing and backtracking in transcription under dense traffic conditions
    • Klumpp S, (2011) Pausing and backtracking in transcription under dense traffic conditions. J Stat Phys 142: 1252-1267.
    • (2011) J Stat Phys , vol.142 , pp. 1252-1267
    • Klumpp, S.1
  • 14
    • 38749103885 scopus 로고    scopus 로고
    • Interacting rna polymerase motors on a dna track: Effects of traffic congestion and intrinsic noise on rna synthesis
    • Tripathi T, Chowdhury D, (2008) Interacting rna polymerase motors on a dna track: Effects of traffic congestion and intrinsic noise on rna synthesis. Phys Rev E 77: 011921.
    • (2008) Phys Rev E , vol.77 , pp. 011921
    • Tripathi, T.1    Chowdhury, D.2
  • 15
    • 33846958387 scopus 로고    scopus 로고
    • Mechanochemical kinetics of transcription elongation
    • Bai L, Fulbright RM, Wang MD, (2007) Mechanochemical kinetics of transcription elongation. Phys Rev Lett 98.
    • (2007) Phys Rev Lett , vol.98
    • Bai, L.1    Fulbright, R.M.2    Wang, M.D.3
  • 16
    • 0031561795 scopus 로고    scopus 로고
    • A model for the mechanism of polymerase translocation
    • Guajardo R, Sousa R, (1997) A model for the mechanism of polymerase translocation. J Mol Biol 265: 8-19.
    • (1997) J Mol Biol , vol.265 , pp. 8-19
    • Guajardo, R.1    Sousa, R.2
  • 18
    • 0029968822 scopus 로고    scopus 로고
    • Improved nearest-neighbor parameters for predicting DNA duplex stability
    • SantaLucia J, Allawi HT, Seneviratne A, (1996) Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35: 3555-3562.
    • (1996) Biochemistry , vol.35 , pp. 3555-3562
    • SantaLucia, J.1    Allawi, H.T.2    Seneviratne, A.3
  • 19
    • 0029134549 scopus 로고
    • Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes
    • Sugimoto N, Nakano S, Katoh M, Matsumra A, Nakamuta H, et al. (1995) Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. Biochemistry 34: 11211-11216.
    • (1995) Biochemistry , vol.34 , pp. 11211-11216
    • Sugimoto, N.1    Nakano, S.2    Katoh, M.3    Matsumra, A.4    Nakamuta, H.5
  • 20
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie DT, (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81: 2340-2361.
    • (1977) J Phys Chem , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 21
    • 0037461036 scopus 로고    scopus 로고
    • Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations
    • Shapiro BE, Levchenko A, Meyerowitz EM, Wold BJ, Mjolsness ED, (2003) Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations. Bioinformatics 19: 677-678.
    • (2003) Bioinformatics , vol.19 , pp. 677-678
    • Shapiro, B.E.1    Levchenko, A.2    Meyerowitz, E.M.3    Wold, B.J.4    Mjolsness, E.D.5
  • 22
    • 0023645154 scopus 로고
    • Mapping and characterization of transcriptional pause sites in the early genetic region of bacteriophage T7
    • Levin JR, Chamberlin MJ, (1987) Mapping and characterization of transcriptional pause sites in the early genetic region of bacteriophage T7. J Mol Biol 196: 61-84.
    • (1987) J Mol Biol , vol.196 , pp. 61-84
    • Levin, J.R.1    Chamberlin, M.J.2
  • 23
    • 78650408616 scopus 로고    scopus 로고
    • Comparison of pause predictions of two sequence-dependent transcription models
    • Bai L, Wang MD, (2010) Comparison of pause predictions of two sequence-dependent transcription models. J Stat Mech-Theory Exp.
    • (2010) J Stat Mech-Theory Exp
    • Bai, L.1    Wang, M.D.2
  • 24
    • 0032582494 scopus 로고    scopus 로고
    • Force and velocity measured for single molecules of RNA polymerase
    • Wang MD, Schnitzer MJ, Yin H, Landick R, Gelles J, et al. (1998) Force and velocity measured for single molecules of RNA polymerase. Science 282: 902-907.
    • (1998) Science , vol.282 , pp. 902-907
    • Wang, M.D.1    Schnitzer, M.J.2    Yin, H.3    Landick, R.4    Gelles, J.5
  • 25
    • 83755167911 scopus 로고    scopus 로고
    • Transcriptional proofreading in dense rna polymerase traffic
    • Sahoo M, Klumpp S, (2011) Transcriptional proofreading in dense rna polymerase traffic. EPL (Europhysics Letters) 96: 60004.
    • (2011) EPL (Europhysics Letters) , vol.96 , pp. 60004
    • Sahoo, M.1    Klumpp, S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.