Transcriptional regulation by the numbers: applications
Tài liệu tham khảo
Ptashne, 2004
Guet, 2002, Combinatorial synthesis of genetic networks, Science, 296, 1466, 10.1126/science.1067407
Hasty, 2002, Computational studies of gene regulation networks: in numero molecular biology, Nat Rev Genet, 2, 268, 10.1038/35066056
McAdams, 2004, The evolution of genetic regulatory systems in bacteria, Nat Rev Genet, 5, 169, 10.1038/nrg1292
Davidson, 2002, A genomic regulatory network for development, Science, 295, 1669, 10.1126/science.1069883
Thomas, 1990
Wolf, 1998, On the relationship between genomic regulatory element organization and gene regulatory dynamics, J Theor Biol, 195, 167, 10.1006/jtbi.1998.0790
Browning, 2004, The regulation of bacterial transcription initiation, Nat Rev Microbiol, 2, 1, 10.1038/nrmicro787
Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Phillips R: Transcriptional regulation by the numbers: models. Curr Opin Genetics Dev 2005, 15:116-124.
Setty, 2003, Detailed map of a cis-regulatory input function, Proc Natl Acad Sci USA, 100, 7702, 10.1073/pnas.1230759100
Kalir, 2004, Using a quantitative blueprint to reprogram the dynamics of the flagella gene network, Cell, 117, 713, 10.1016/j.cell.2004.05.010
Wei, 2001, High-density microarray-mediated gene expression profiling of Escherichia coli, J Bacteriol, 183, 545, 10.1128/JB.183.2.545-556.2001
Ebright, 1992, Transcription activation at class I CAP-dependent promoters, Mol Microbiol, 8, 797, 10.1111/j.1365-2958.1993.tb01626.x
Müller-Hill, 1996
Wall, 2004, Design of gene circuits: lessons from bacteria, Nat Rev Genet, 5, 34, 10.1038/nrg1244
Wade, 2001, A simple mechanism for co-dependence on two activators at an Escherichia coli promoter, EMBO J, 20, 7160, 10.1093/emboj/20.24.7160
Buchler, 2003, On schemes of combinatorial transcription control, Proc Natl Acad Sci USA, 100, 5136, 10.1073/pnas.0930314100
Ptashne, 1998, Imposing specificity by localization: mechanism and evolvability, Curr Biol, 8, R897, 10.1016/S0960-9822(07)00508-8
Joung, 1993, Synergistic activation of transcription by E. coli cAMP receptor protein, Proc Natl Acad Sci USA, 90, 3083, 10.1073/pnas.90.7.3083
Busby, 1994, Transcription activation by the Escherichia coli cyclic AMP receptor protein. Receptors bound in tandem at promoters can interact synergistically, J Mol Biol, 241, 341, 10.1006/jmbi.1994.1511
Joung, 1994, Synergistic activation of transcription by bacteriophage lambda cI protein and E. coli cAMP receptor protein, Science, 265, 1863, 10.1126/science.8091212
Scott, 1995, Transcriptional co-activation at the ansB promoters: involvement of the activating regions of CRP and FNR when bound in tandem, Mol Microbiol, 18, 521, 10.1111/j.1365-2958.1995.mmi_18030521.x
Belyaeva, 1998, Transcription activation at promoters carrying tandem DNA sites for the Escherichia coli cyclic AMP receptor protein: organisation of the RNA polymerase alpha subunits, J Mol Biol, 277, 789, 10.1006/jmbi.1998.1666
Tebbutt, 2002, Architectural requirements for optimal activation by tandem CRP molecules at a Class I CRP-dependent promoter, FEMS Microbiol Lett, 210, 55, 10.1111/j.1574-6968.2002.tb11159.x
Beatty, 2003, CRP-dependent activation of the E. coli acsP2 promoter by a synergistic Class III mechanism, J Bacteriol, 185, 5148, 10.1128/JB.185.17.5148-5157.2003
Busby, 1999, Transcription activation by catabolite activator protein (CAP), J Mol Biol, 293, 199, 10.1006/jmbi.1999.3161
Oehler, 1994, Quality and position of the three lac operators of E. coli define efficiency of repression, EMBO J, 13, 3348, 10.1002/j.1460-2075.1994.tb06637.x
Vilar, 2003, DNA looping and physical constraints on transcription regulation, J Mol Biol, 331, 981, 10.1016/S0022-2836(03)00764-2
Lin, 1975, The general affinity of lac repressor for E. coli DNA: implications for gene regulation in procaryotes and eucaryotes, Cell, 4, 107, 10.1016/0092-8674(75)90116-6
Pfahl, 1979, “Second” and “third operator” of the lac operon: an investigation of their role in the regulatory mechanism, J Mol Biol, 127, 339, 10.1016/0022-2836(79)90333-4
Winter, 1981, Diffusion-driven mechanisms of protein translocation on nucleic acids. 2. The Escherichia coli repressor–operator interaction: equilibrium measurements, Biochemistry, 20, 6948, 10.1021/bi00527a029
Gerland, 2002, Physical constraints and functional characteristics of transcription factor-DNA interaction, Proc Natl Acad Sci USA, 99, 12015, 10.1073/pnas.192693599
Bellomy, 1990, Stable DNA loops in vivo and in vitro: roles in gene regulation at a distance and in biophysical characterization of DNA, Prog Nucleic Acid Res Mol Biol, 39, 81, 10.1016/S0079-6603(08)60624-8
Müller, 1996, Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator, J Mol Biol, 257, 21, 10.1006/jmbi.1996.0143
Dmitrova, 1998, A new LexA-based genetic system for monitoring and analyzing protein heterodimerization in Escherichia coli, Mol Gen Genet, 257, 205, 10.1007/s004380050640
Hu, 2000, E. coli one- and two-hybrid systems for the analysis and identification of protein–protein interactions, Methods, 20, 80, 10.1006/meth.1999.0908
Hays, 2000, Two-hybrid system for characterization of protein–protein interactions in E. coli, BioTechniques, 29, 288, 10.2144/00292st04
Lutz, 1997, 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, 1203, 10.1093/nar/25.6.1203
Miller, 2003, Collaborative competition mechanism for gene activation in vivo, Mol Cell Biol, 23, 1623, 10.1128/MCB.23.5.1623-1632.2003
Ptashne, 2002
Beckwith, 1972, Evidence for two sites in the lac promoter region, J Mol Biol, 69, 155, 10.1016/0022-2836(72)90031-9
Garner, 1982, Stoichiometry of catabolite activator protein/adenosine cyclic 3′ 5′-monophosphate interactions at the lac promoter of Escherichia coli, Biochemistry, 21, 6032, 10.1021/bi00267a001
Fried, 1984, Equilibrium studies of the cyclic AMP receptor protein–DNA interaction, J Mol Biol, 172, 241, 10.1016/S0022-2836(84)80025-X
Takahashi, 1989, Ligand-modulated binding of a gene regulatory protein to DNA: quantitative analysis of cyclic-AMP induced binding of CRP from Escherichia coli to non-specific and specific DNA targets, J Mol Biol, 207, 783, 10.1016/0022-2836(89)90244-1
Dodd, 2004, Cooperativity in long-range gene regulation by the lambda cI repressor, Genes Dev, 18, 344, 10.1101/gad.1167904
Hawley, 1982, Mechanism of activation of transcription initiation from the lambda PRM promoter, J Mol Biol, 157, 493, 10.1016/0022-2836(82)90473-9
Koblan, 1992, Site-specific enthalpic regulation of DNA transcription at bacteriophage lambda OR, Biochemistry, 31, 57, 10.1021/bi00116a010
Yamakawa H: In Helical Wormlike Chains in Polymer Solutions, Springer, New York, 1997.
Savageau, 1976
Burns, 1985, Control analysis of metabolic systems, Trends Biochem Sci, 10, 16, 10.1016/0968-0004(85)90008-8