-
1
-
-
0022799080
-
Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction releases additional upstream activating DNA elements
-
Almer A, Rudolph H, Hinnen A, Horz W (1986) Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction releases additional upstream activating DNA elements. EMBO J 5: 2689-2696
-
(1986)
EMBO J
, vol.5
, pp. 2689-2696
-
-
Almer, A.1
Rudolph, H.2
Hinnen, A.3
Horz, W.4
-
2
-
-
0032716841
-
Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid
-
Azam TA, Iwata A, Nishimura A, Ueda S, Ishihama I (1999) Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J Bacteriol 181: 6361-6370
-
(1999)
J Bacteriol
, vol.181
, pp. 6361-6370
-
-
Azam, T.A.1
Iwata, A.2
Nishimura, A.3
Ueda, S.4
Ishihama, I.5
-
3
-
-
0037440734
-
Evolution of transcription factors and the gene regulatory network in Escherichia coli
-
Babu MM, Teichmann SA (2003) Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Res 31: 1234-1244
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 1234-1244
-
-
Babu, M.M.1
Teichmann, S.A.2
-
4
-
-
0014413509
-
The interaction of closed circular DNA with intercalative dyes. I. The superhelix density of SV40 DNA in the presence and absence of dye
-
Bauer W, Vinograd J (1968) The interaction of closed circular DNA with intercalative dyes. I. The superhelix density of SV40 DNA in the presence and absence of dye. J Mol Biol 33: 141-171
-
(1968)
J Mol Biol
, vol.33
, pp. 141-171
-
-
Bauer, W.1
Vinograd, J.2
-
5
-
-
19444387811
-
Bacterial repression loops require enhanced DNA flexibility
-
Becker NA, Kahn JD, Maher LJ III (2005) Bacterial repression loops require enhanced DNA flexibility. J Mol Biol 349: 716-730
-
(2005)
J Mol Biol
, vol.349
, pp. 716-730
-
-
Becker, N.A.1
Kahn, J.D.2
Maher III, L.J.3
-
6
-
-
33745612978
-
Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome
-
Blot N, Mavathur R, Geertz M, Travers A, Muskhelishvili G (2006) Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome. EMBO Rep 7: 710-715
-
(2006)
EMBO Rep
, vol.7
, pp. 710-715
-
-
Blot, N.1
Mavathur, R.2
Geertz, M.3
Travers, A.4
Muskhelishvili, G.5
-
7
-
-
2942574467
-
Removal of promoter nucleosomes by disassembly rather than sliding in vivo
-
Boeger H, Griesenbeck J, Strattan JS, Kornberg RD (2004) Removal of promoter nucleosomes by disassembly rather than sliding in vivo. Mol Cell 14: 667-673
-
(2004)
Mol Cell
, vol.14
, pp. 667-673
-
-
Boeger, H.1
Griesenbeck, J.2
Strattan, J.S.3
Kornberg, R.D.4
-
9
-
-
0026734674
-
DNA deformation in nucleoprotein complexes between RNA polymerase, cAMP receptor protein and the lac UV5 promoter probed by singlet oxygen
-
Buckle M, Buc H, Travers AA (1992) DNA deformation in nucleoprotein complexes between RNA polymerase, cAMP receptor protein and the lac UV5 promoter probed by singlet oxygen. EMBO J 11: 2619-2625
-
(1992)
EMBO J
, vol.11
, pp. 2619-2625
-
-
Buckle, M.1
Buc, H.2
Travers, A.A.3
-
10
-
-
0024264685
-
Differences in the binding of H1 variants to DNA. Cooperativity and linker-length related distribution
-
Clark DJ, Thomas JO (1988) Differences in the binding of H1 variants to DNA. Cooperativity and linker-length related distribution. Eur J Biochem 178: 225-233
-
(1988)
Eur J Biochem
, vol.178
, pp. 225-233
-
-
Clark, D.J.1
Thomas, J.O.2
-
11
-
-
0032983154
-
The topological mechanism of phage λ integrase
-
Crisona NJ, Weinberg RL, Peter BJ, Sumners DW, Cozzarelli NR (1999) The topological mechanism of phage λ integrase. J Mol Biol 289: 747-775
-
(1999)
J Mol Biol
, vol.289
, pp. 747-775
-
-
Crisona, N.J.1
Weinberg, R.L.2
Peter, B.J.3
Sumners, D.W.4
Cozzarelli, N.R.5
-
12
-
-
0034666271
-
H-NS mediated compaction of DNA visualised by atomic force microscopy
-
Dame RT, Wyman C, Goosen N (2000) H-NS mediated compaction of DNA visualised by atomic force microscopy. Nucleic Acids Res 28: 3504-3510
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 3504-3510
-
-
Dame, R.T.1
Wyman, C.2
Goosen, N.3
-
13
-
-
0037127209
-
Structural basis for H-NS-mediated trapping of RNA polymerase in the open initiation complex at the rrnB P1
-
Dame RT, Wyman C, Wurm R, Wagner R, Goosen N (2002) Structural basis for H-NS-mediated trapping of RNA polymerase in the open initiation complex at the rrnB P1. J Biol Chem 277: 2146-2150
-
(2002)
J Biol Chem
, vol.277
, pp. 2146-2150
-
-
Dame, R.T.1
Wyman, C.2
Wurm, R.3
Wagner, R.4
Goosen, N.5
-
14
-
-
0030871683
-
Structural kinetics of transcription activation at the malT promoter of Escherichia coli by UV laser footprinting
-
Eichenberger P, Dethiollaz S, Buc H, Geiselmann J (1997) Structural kinetics of transcription activation at the malT promoter of Escherichia coli by UV laser footprinting. Proc Natl Acad Sci USA 94: 9022-9027
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 9022-9027
-
-
Eichenberger, P.1
Dethiollaz, S.2
Buc, H.3
Geiselmann, J.4
-
15
-
-
0028303884
-
The high mobility group protein HMG1 can reversibly inhibit class II gene transcription by interaction with the TATA-binding protein
-
Ge H, Roeder RG (1994) The high mobility group protein HMG1 can reversibly inhibit class II gene transcription by interaction with the TATA-binding protein. J Biol Chem 269: 17136-17140
-
(1994)
J Biol Chem
, vol.269
, pp. 17136-17140
-
-
Ge, H.1
Roeder, R.G.2
-
16
-
-
0027229357
-
DNA looping and the helical repeat in vitro and in vivo: Effect of HU protein and enhancer location on Hin invertasome assembly
-
Haykinson MJ, Johnson RC (1993) DNA looping and the helical repeat in vitro and in vivo: Effect of HU protein and enhancer location on Hin invertasome assembly. EMBO J 12: 2503-2512
-
(1993)
EMBO J
, vol.12
, pp. 2503-2512
-
-
Haykinson, M.J.1
Johnson, R.C.2
-
17
-
-
28044436995
-
Nucleoid remodeling by an altered HU protein: Reorganization of the transcription program
-
Kar S, Edgar R, Adhya S (2005) Nucleoid remodeling by an altered HU protein: Reorganization of the transcription program. Proc Natl Acad Sci USA 102: 16397-16402
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 16397-16402
-
-
Kar, S.1
Edgar, R.2
Adhya, S.3
-
18
-
-
0024297575
-
Curved helix segments can uniquely orient the topology of supertwisted DNA
-
Laundon CH, Griffith JD (1988) Curved helix segments can uniquely orient the topology of supertwisted DNA. Cell 52: 545-549
-
(1988)
Cell
, vol.52
, pp. 545-549
-
-
Laundon, C.H.1
Griffith, J.D.2
-
19
-
-
0027510369
-
In vivo thermodynamic analysis of repression with and without looping in lac constructs. Estimates of free and local lac repressor concentrations and of physical properties of a region of supercoiled plasmid DNA in vivo
-
Law SM, Bellomy GR, Schlax PJ, Record MT Jr (1993) In vivo thermodynamic analysis of repression with and without looping in lac constructs. Estimates of free and local lac repressor concentrations and of physical properties of a region of supercoiled plasmid DNA in vivo. J Mol Biol 230: 161-173
-
(1993)
J Mol Biol
, vol.230
, pp. 161-173
-
-
Law, S.M.1
Bellomy, G.R.2
Schlax, P.J.3
Record Jr., M.T.4
-
20
-
-
0009699824
-
In vivo DNA loops in araCBAD: Size limits and helical repeat
-
Lee DH, Schleif RF (1989) In vivo DNA loops in araCBAD: Size limits and helical repeat. Proc Natl Acad Sci USA 86: 476-480
-
(1989)
Proc Natl Acad Sci USA
, vol.86
, pp. 476-480
-
-
Lee, D.H.1
Schleif, R.F.2
-
21
-
-
33748047157
-
RNA polymerase and an activator form discrete subcomplexes in a transcription initiation complex
-
Maurer S, Fritz J, Muskhelishvili G, Travers A (2006) RNA polymerase and an activator form discrete subcomplexes in a transcription initiation complex. EMBO J 25: 3784-3790
-
(2006)
EMBO J
, vol.25
, pp. 3784-3790
-
-
Maurer, S.1
Fritz, J.2
Muskhelishvili, G.3
Travers, A.4
-
22
-
-
0026012032
-
Negative supercoiling of DNA facilitates an interaction between transcription factor IID and the fibroin gene promoter
-
Mizutani M, Ohta T, Watanabe H, Handa H, Hirose S (1991) Negative supercoiling of DNA facilitates an interaction between transcription factor IID and the fibroin gene promoter. Proc Natl Acad Sci USA 88: 718-722
-
(1991)
Proc Natl Acad Sci USA
, vol.88
, pp. 718-722
-
-
Mizutani, M.1
Ohta, T.2
Watanabe, H.3
Handa, H.4
Hirose, S.5
-
23
-
-
0033485515
-
The structure of a chromosomal high mobility group protein-DNA complex reveals sequence-neural mechanisms important for non-sequence-specific DNA recognition
-
Murphy FV IV, Sweet RM, Churchill ME (1999) The structure of a chromosomal high mobility group protein-DNA complex reveals sequence-neural mechanisms important for non-sequence-specific DNA recognition. EMBO J 18: 6610-6618
-
(1999)
EMBO J
, vol.18
, pp. 6610-6618
-
-
Murphy IV, F.V.1
Sweet, R.M.2
Churchill, M.E.3
-
24
-
-
0034674176
-
A DNA structural atlas for Escherichia coli
-
Pedersen AG, Jensen LI, Brunak S, Staerfeldt HH, Ussery DW (2000) A DNA structural atlas for Escherichia coli. J Mol Biol 299: 907-930
-
(2000)
J Mol Biol
, vol.299
, pp. 907-930
-
-
Pedersen, A.G.1
Jensen, L.I.2
Brunak, S.3
Staerfeldt, H.H.4
Ussery, D.W.5
-
25
-
-
33846637687
-
The role of LRP and HNS in transcription regulation: Involvement of synergism, allostery and macromolecular crowding
-
[doi:10.1016/j.jmb.2006.11.067]
-
Pul Ü, Wurm R, Wagner R (2006) The role of LRP and HNS in transcription regulation: Involvement of synergism, allostery and macromolecular crowding. J Mol Biol [doi:10.1016/j.jmb.2006.11.067]
-
(2006)
J Mol Biol
-
-
Pul, Ü.1
Wurm, R.2
Wagner, R.3
-
26
-
-
0038094502
-
Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter
-
Reinke H, Hörz W (2003) Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter. Mol Cell 11: 1599-1607
-
(2003)
Mol Cell
, vol.11
, pp. 1599-1607
-
-
Reinke, H.1
Hörz, W.2
-
27
-
-
1842453825
-
Structure of the histone-like protein H-NS and its role in regulation and genome superstructure
-
Rimsky S (2004) Structure of the histone-like protein H-NS and its role in regulation and genome superstructure. Curr Opin Microbiol 7: 109-114
-
(2004)
Curr Opin Microbiol
, vol.7
, pp. 109-114
-
-
Rimsky, S.1
-
28
-
-
0028361219
-
The TATA-binding protein: A general transcription factor in eukaryotes and archaebacteria
-
Rowlands T, Baumann P, Jackson SP (1994) The TATA-binding protein: A general transcription factor in eukaryotes and archaebacteria. Science 264: 1326-1329
-
(1994)
Science
, vol.264
, pp. 1326-1329
-
-
Rowlands, T.1
Baumann, P.2
Jackson, S.P.3
-
29
-
-
0023001414
-
Sequence periodicities in chicken nucleosome core DNA
-
Satchwell SC, Drew HP, Travers AA (1986) Sequence periodicities in chicken nucleosome core DNA. J Mol Biol 191: 659-675
-
(1986)
J Mol Biol
, vol.191
, pp. 659-675
-
-
Satchwell, S.C.1
Drew, H.P.2
Travers, A.A.3
-
30
-
-
0035945265
-
An architectural role of the Escherichia coli chromatin protein FIS in organising DNA
-
Schneider R, Lurz R, Lüder G, Tolksdorf C, Travers A, Muskhelishvili G (2001) An architectural role of the Escherichia coli chromatin protein FIS in organising DNA. Nucleic Acids Res 29: 5107-5114
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 5107-5114
-
-
Schneider, R.1
Lurz, R.2
Lüder, G.3
Tolksdorf, C.4
Travers, A.5
Muskhelishvili, G.6
-
31
-
-
0018962604
-
Torsional tension in the DNA double helix measured with trimethylpsoralen in living E. coli cells: Analogous measurements in insect and human cells
-
Sinden RR, Carlson JO, Pettijohn DE (1980) Torsional tension in the DNA double helix measured with trimethylpsoralen in living E. coli cells: analogous measurements in insect and human cells. Cell 21: 773-783
-
(1980)
Cell
, vol.21
, pp. 773-783
-
-
Sinden, R.R.1
Carlson, J.O.2
Pettijohn, D.E.3
-
32
-
-
0028365309
-
Repression of basal transcription by HMG2 is counteracted by TFIIH-associated factors in an ATP-dependent process
-
Stelzer G, Goppelt A, Lottspeich F, Meisterernst M (1994) Repression of basal transcription by HMG2 is counteracted by TFIIH-associated factors in an ATP-dependent process. Mol Cell Biol 14: 4712-4721
-
(1994)
Mol Cell Biol
, vol.14
, pp. 4712-4721
-
-
Stelzer, G.1
Goppelt, A.2
Lottspeich, F.3
Meisterernst, M.4
-
33
-
-
0028359704
-
DNA looping by the HMG-box domains of HMG1 and modulation of DNA binding by the acidic C-terminal domain
-
Stros M, Stokrova J, Thomas JO (1994) DNA looping by the HMG-box domains of HMG1 and modulation of DNA binding by the acidic C-terminal domain. Nucleic Acids Res 22: 104410-104451
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 104410-104451
-
-
Stros, M.1
Stokrova, J.2
Thomas, J.O.3
-
34
-
-
0033538531
-
Fundamentally different logic of gene regulation in eukaryotes and prokaryotes
-
Struhl K (1999) Fundamentally different logic of gene regulation in eukaryotes and prokaryotes. Cell 98: 1-4
-
(1999)
Cell
, vol.98
, pp. 1-4
-
-
Struhl, K.1
-
35
-
-
0041312645
-
Flexible DNA bending in HU-DNA cocrystal structures
-
Swinger KK, Lemberg KM, Zhang Y, Rice PA (2003) Flexible DNA bending in HU-DNA cocrystal structures. EMBO J 22: 3749-3760
-
(2003)
EMBO J
, vol.22
, pp. 3749-3760
-
-
Swinger, K.K.1
Lemberg, K.M.2
Zhang, Y.3
Rice, P.A.4
-
36
-
-
0027182336
-
Underwinding of DNA on binding of yeast TFIID to the TATA element
-
Tabuchi H, Handa H, Hirose S (1993) Underwinding of DNA on binding of yeast TFIID to the TATA element. Biochem Biophys Res Comm 192: 1432-1438
-
(1993)
Biochem Biophys Res Comm
, vol.192
, pp. 1432-1438
-
-
Tabuchi, H.1
Handa, H.2
Hirose, S.3
-
37
-
-
0022124413
-
Visualization of RNA polymerase II ternary transcription complexes formed in vitro on a Xenopus laevis vitellogenin gene
-
ten Heggeler B, Wahli W (1985) Visualization of RNA polymerase II ternary transcription complexes formed in vitro on a Xenopus laevis vitellogenin gene. EMBO J 4: 2269-2273
-
(1985)
EMBO J
, vol.4
, pp. 2269-2273
-
-
ten Heggeler, B.1
Wahli, W.2
-
38
-
-
0035281548
-
HMG1 and 2, and related 'architectural' DNA-binding proteins
-
Thomas JO, Travers AA (2001) HMG1 and 2, and related 'architectural' DNA-binding proteins. Trends Biochem Sci 26: 167-174
-
(2001)
Trends Biochem Sci
, vol.26
, pp. 167-174
-
-
Thomas, J.O.1
Travers, A.A.2
-
39
-
-
13444288385
-
DNA supercoiling: A global transcriptional regulator for enterobacterial growth?
-
Travers A, Muskhelishvili G (2005) DNA supercoiling: A global transcriptional regulator for enterobacterial growth? Nat Rev Microbiol 3: 157-169
-
(2005)
Nat Rev Microbiol
, vol.3
, pp. 157-169
-
-
Travers, A.1
Muskhelishvili, G.2
-
40
-
-
2342454974
-
Dual architectural roles of HU: Formation of flexible hinges and rigid filaments
-
van Noort J, Verbrugge S, Goosen N, Dekker C, Dame RT (2004) Dual architectural roles of HU: Formation of flexible hinges and rigid filaments. Proc Natl Acad Sci USA 101: 6969-6974
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 6969-6974
-
-
van Noort, J.1
Verbrugge, S.2
Goosen, N.3
Dekker, C.4
Dame, R.T.5
-
41
-
-
0029862602
-
Chromatin remodeling during Saccharomyces cerevisiae ADH2 gene activation
-
Verdone L, Camilloni G, Di Mauro E, Caserta M (1996) Chromatin remodeling during Saccharomyces cerevisiae ADH2 gene activation. Mol Cell Biol 16: 1978-1988
-
(1996)
Mol Cell Biol
, vol.16
, pp. 1978-1988
-
-
Verdone, L.1
Camilloni, G.2
Di Mauro, E.3
Caserta, M.4
-
42
-
-
0023811057
-
Helical repeat and linking number of surface-wrapped DNA
-
White JH, Cozzarelli NR, Bauer WR (1988) Helical repeat and linking number of surface-wrapped DNA. Science 241: 323-327
-
(1988)
Science
, vol.241
, pp. 323-327
-
-
White, J.H.1
Cozzarelli, N.R.2
Bauer, W.R.3
-
43
-
-
0030596486
-
Short-range order in two eukaryotic genomes: Relation to chromosome structure
-
Widom J (1996) Short-range order in two eukaryotic genomes: Relation to chromosome structure. J Mol Biol 259: 579-588
-
(1996)
J Mol Biol
, vol.259
, pp. 579-588
-
-
Widom, J.1
-
44
-
-
0034141421
-
Structural analysis of DNA sequence: Evidence for lateral gene transfer in Thermotoga maritima
-
Worning P, Jensen LJ, Nelson KE, Brunak S, Ussery DW (2000) Structural analysis of DNA sequence: Evidence for lateral gene transfer in Thermotoga maritima. Nucleic Acids Res 28: 706-709
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 706-709
-
-
Worning, P.1
Jensen, L.J.2
Nelson, K.E.3
Brunak, S.4
Ussery, D.W.5
-
45
-
-
0024292379
-
Chromatin reconstitution on small DNA rings. II. DNA supercoiling on the nucleosome
-
Zivanovic Y, Goulet I, Revet B, Le Bret M, Prunell A (1988) Chromatin reconstitution on small DNA rings. II. DNA supercoiling on the nucleosome. J Mol Biol 200: 267-290
-
(1988)
J Mol Biol
, vol.200
, pp. 267-290
-
-
Zivanovic, Y.1
Goulet, I.2
Revet, B.3
Le Bret, M.4
Prunell, A.5
|