-
1
-
-
0030960672
-
-
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
-
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
-
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
-
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
-
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
-
7
-
-
0033543765
-
Activities of constitutive promoters in Escherichia coli
-
Liang, S.-T., M. Bipitnath, Y.-C. Xu, S.-L. Chen, P. Dennis, M. Ehrenberg, and H. Bremer. 1999. Activities of constitutive promoters in Escherichia coli. J. Mol. Biol. 292:19-37.
-
(1999)
J. Mol. Biol
, vol.292
, pp. 19-37
-
-
Liang, S.-T.1
Bipitnath, M.2
Xu, Y.-C.3
Chen, S.-L.4
Dennis, P.5
Ehrenberg, M.6
Bremer, H.7
-
8
-
-
0018604734
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
-
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
-
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
-
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
-
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
-
22
-
-
34548507690
-
In vivo dynamics of RNA polymerase II transcription
-
Darzacq, X., Y. Shav-Tal, V. de Turris, Y. Brody, S. M. Shenoy, R. D. Phair, and R. H. Singer. 2007. In vivo dynamics of RNA polymerase II transcription. Nat. Struct. Mol. Biol. 14:796-806.
-
(2007)
Nat. Struct. Mol. Biol
, vol.14
, pp. 796-806
-
-
Darzacq, X.1
Shav-Tal, Y.2
de Turris, V.3
Brody, Y.4
Shenoy, S.M.5
Phair, R.D.6
Singer, R.H.7
-
23
-
-
0345077411
-
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
-
-
Reference deleted in proof
-
Reference deleted in proof.
-
-
-
-
25
-
-
85031367531
-
-
Reference deleted in proof
-
Reference deleted in proof.
-
-
-
-
27
-
-
33748994704
-
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
-
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
-
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
-
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
-
31
-
-
33845616177
-
Phenotypic consequences of promoter-mediated transcriptional noise
-
Blake, W. J., G. Balázsi, M. A. Kohanski, F. J. Isaacs, K. F. Murphy, Y. Kuang, C. R. Cantor, D. R. Walt, and J. J. Collins. 2006. Phenotypic consequences of promoter-mediated transcriptional noise. Mol. Cell. 24:853-865.
-
(2006)
Mol. Cell
, vol.24
, pp. 853-865
-
-
Blake, W.J.1
Balázsi, G.2
Kohanski, M.A.3
Isaacs, F.J.4
Murphy, K.F.5
Kuang, Y.6
Cantor, C.R.7
Walt, D.R.8
Collins, J.J.9
-
32
-
-
34547925618
-
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
-
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
-
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
-
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
-
36
-
-
1042278041
-
Cooperativity in long-range gene regulation by the λ CI repressor
-
Dodd, I. B., K. E. Shearwin, A. J. Perkins, T. Burr, A. Hochschild, and J. B. Egan. 2004. Cooperativity in long-range gene regulation by the λ CI repressor. Genes Dev. 18:344-354.
-
(2004)
Genes Dev
, vol.18
, pp. 344-354
-
-
Dodd, I.B.1
Shearwin, K.E.2
Perkins, A.J.3
Burr, T.4
Hochschild, A.5
Egan, J.B.6
-
37
-
-
85031355319
-
-
Reference deleted in proof
-
Reference deleted in proof.
-
-
-
-
38
-
-
0033517148
-
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
-
39
-
-
37649030145
-
Stability puzzles in phage λ
-
Aurell, E., S. Brown, J. Johansen, and K. Sneppen. 2002. Stability puzzles in phage λ. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 65:51914
-
(2002)
Phys. Rev. E Stat. Nonlin. Soft Matter Phys
, vol.65
, pp. 51914
-
-
Aurell, E.1
Brown, S.2
Johansen, J.3
Sneppen, K.4
-
40
-
-
0025309753
-
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
-
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
-
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
-
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
-
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
-
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
-
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
|