-
1
-
-
0343240577
-
Chromosomes in living Escherichia coli cells are segregated into domains of supercoiling
-
R.R. Sinden, and D.E. Pettijohn Chromosomes in living Escherichia coli cells are segregated into domains of supercoiling Proc Natl Acad Sci USA 78 1981 224 228
-
(1981)
Proc Natl Acad Sci USA
, vol.78
, pp. 224-228
-
-
Sinden, R.R.1
Pettijohn, D.E.2
-
2
-
-
3142774839
-
Topological domain structure of the Escherichia coli chromosome
-
L. Postow, C.D. Hardy, J. Arsuaga, and N.R. Cozzarelli Topological domain structure of the Escherichia coli chromosome Genes Dev 18 2004 1766 1779 The authors provide a rigorous examination of the higher-order structure of supercoiled domains in the E. coli chromosome.
-
(2004)
Genes Dev
, vol.18
, pp. 1766-1779
-
-
Postow, L.1
Hardy, C.D.2
Arsuaga, J.3
Cozzarelli, N.R.4
-
3
-
-
0029863159
-
Surveying a supercoil domain by using the γδ resolution system in Salmonella typhimurium
-
N.P. Higgins, X. Yang, Q. Fu, and J.R. Roth Surveying a supercoil domain by using the γδ resolution system in Salmonella typhimurium J Bacteriol 178 1996 2825 2835
-
(1996)
J Bacteriol
, vol.178
, pp. 2825-2835
-
-
Higgins, N.P.1
Yang, X.2
Fu, Q.3
Roth, J.R.4
-
4
-
-
18444412915
-
Measuring chromosome dynamics on different time scales using resolvases with varying half lives
-
R.A. Stein, S. Deng, and N.P. Higgins Measuring chromosome dynamics on different time scales using resolvases with varying half lives Mol Microbiol 56 2005 1049 1061 The authors undertake a controlled examination of the extent of domains that enable supercoil diffusion.
-
(2005)
Mol Microbiol
, vol.56
, pp. 1049-1061
-
-
Stein, R.A.1
Deng, S.2
Higgins, N.P.3
-
5
-
-
3242812952
-
Periodic transcriptional organization of the E. coli genome
-
F. Képès Periodic transcriptional organization of the E. coli genome J Mol Biol 340 2004 957 964
-
(2004)
J Mol Biol
, vol.340
, pp. 957-964
-
-
Képès, F.1
-
6
-
-
0031712188
-
Gyrase and topo IV modulate chromosome domain size in vivo
-
P. Staczek, and N.P. Higgins Gyrase and topo IV modulate chromosome domain size in vivo Mol Microbiol 29 1998 1435 1448
-
(1998)
Mol Microbiol
, vol.29
, pp. 1435-1448
-
-
Staczek, P.1
Higgins, N.P.2
-
7
-
-
1542618333
-
Transcription-induced barriers to supercoil diffusion in the Salmonella typhimurium genome
-
S. Deng, R.A. Stein, and M.P. Higgins Transcription-induced barriers to supercoil diffusion in the Salmonella typhimurium genome Proc Natl Acad Sci USA 101 2004 3398 3403 This study demonstrates directly that highly active transcriptons create barriers to supercoil diffusion.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 3398-3403
-
-
Deng, S.1
Stein, R.A.2
Higgins, M.P.3
-
8
-
-
0346887121
-
The distribution of polymerase in Escherichia coli is dynamic and sensitive to environmental cues
-
J.E. Cabrera, and D.J. Jin The distribution of polymerase in Escherichia coli is dynamic and sensitive to environmental cues Mol Microbiol 50 2003 1493 1505 A novel use of GFP (green fluorescent protein)-tagged polymerase to show that the occurrence of highly active transcription centres alters the overall structure of the nucleoid.
-
(2003)
Mol Microbiol
, vol.50
, pp. 1493-1505
-
-
Cabrera, J.E.1
Jin, D.J.2
-
9
-
-
13144257718
-
Topological insulators inhibit diffusion of transcription-induced positive supercoils in the chromosome of Escherichia coli
-
L. Moulin, A.R. Rahmouni, and F. Boccard Topological insulators inhibit diffusion of transcription-induced positive supercoils in the chromosome of Escherichia coli Mol Microbiol 55 2005 601 610 A novel approach to the identification of topological barriers, showing that functional gyrase binding site can delimit topological domains.
-
(2005)
Mol Microbiol
, vol.55
, pp. 601-610
-
-
Moulin, L.1
Rahmouni, A.R.2
Boccard, F.3
-
10
-
-
11344293422
-
Spatial parameters of transcriptional activity in the chromosome
-
K.S. Jeong, J. Ahn, and A.B. Khodursky Spatial parameters of transcriptional activity in the chromosome Genome Biol 5 2004 R86
-
(2004)
Genome Biol
, vol.5
, pp. 86
-
-
Jeong, K.S.1
Ahn, J.2
Khodursky, A.B.3
-
11
-
-
19944428078
-
Chromatin architecture and gene expression in Escherichia coli
-
H. Willenbrock, and D.W. Ussery Chromatin architecture and gene expression in Escherichia coli Genome Biol 5 2004 252 Mapping of genes sensitive to relaxation onto the E. coli genome reveals higher order clstering of function.
-
(2004)
Genome Biol
, vol.5
, pp. 252
-
-
Willenbrock, H.1
Ussery, D.W.2
-
12
-
-
0034650256
-
Dynamic organization of chromosomal DNA in Escherichia coli
-
H. Niki, Y. Yamamichi, and S. Hiraga Dynamic organization of chromosomal DNA in Escherichia coli Genes Dev 14 2000 212 223
-
(2000)
Genes Dev
, vol.14
, pp. 212-223
-
-
Niki, H.1
Yamamichi, Y.2
Hiraga, S.3
-
13
-
-
9144264275
-
Macrodomain organization of the Escherichia coli chromosome
-
M. Valens, S. Penaud, M. Rossignol, F. Cornet, and F. Boccard Macrodomain organization of the Escherichia coli chromosome EMBO J 23 2004 4330 4341 A reinvestigation of the long-range structure of the E. coli chromosome.
-
(2004)
EMBO J
, vol.23
, pp. 4330-4341
-
-
Valens, M.1
Penaud, S.2
Rossignol, M.3
Cornet, F.4
Boccard, F.5
-
14
-
-
1942436944
-
Unequal access of chromosomal regions to each other in Salmonella: Probing chromosome structure with phage λ integrase-mediated long-range rearrangements
-
N. Garcia-Russell, T.G. Harmon, T.Q. Le, N.H. Amaladas, R.D. Mathewson, and A.M. Segall Unequal access of chromosomal regions to each other in Salmonella: probing chromosome structure with phage λ integrase-mediated long-range rearrangements Mol Microbiol 52 2004 329 344
-
(2004)
Mol Microbiol
, vol.52
, pp. 329-344
-
-
Garcia-Russell, N.1
Harmon, T.G.2
Le, T.Q.3
Amaladas, N.H.4
Mathewson, R.D.5
Segall, A.M.6
-
17
-
-
3042599315
-
Linear ordering and dynamic segregation of the bacterial chromosome
-
A.M. Breier, and N.R. Cozzarelli Linear ordering and dynamic segregation of the bacterial chromosome Proc Natl Acad Sci USA 101 2004 9175 9176
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 9175-9176
-
-
Breier, A.M.1
Cozzarelli, N.R.2
-
18
-
-
22944489133
-
Bacillus subtilis actin-like protein MreB influences the positioning of the replication machinery and requires membrane proteins MreC/D and other actin-like proteins for proper localization
-
H.J. Defeu Soufo, and P.L. Graumann Bacillus subtilis actin-like protein MreB influences the positioning of the replication machinery and requires membrane proteins MreC/D and other actin-like proteins for proper localization BMC Cell Biol 6 2005 10
-
(2005)
BMC Cell Biol
, vol.6
, pp. 10
-
-
Defeu Soufo, H.J.1
Graumann, P.L.2
-
19
-
-
0942279510
-
Nucleoid restructuring in stationary-state bacteria
-
D. Frenkiel-Krispin, I. Ben-Avraham, J. Englander, E. Shimoni, S.G. Wolf, and A. Minsky Nucleoid restructuring in stationary-state bacteria Mol Microbiol 51 2004 395 405 A novel approach to the structure of the nucleoid in stationary phase, showing how the nucleoid-associated protein Dps organises the structure.
-
(2004)
Mol Microbiol
, vol.51
, pp. 395-405
-
-
Frenkiel-Krispin, D.1
Ben-Avraham, I.2
Englander, J.3
Shimoni, E.4
Wolf, S.G.5
Minsky, A.6
-
20
-
-
11344266685
-
Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli
-
B.J. Peter, J. Arsuaga, A. Breier, A.B. Khodursky, P.O. Brown, and N.R. Cozzarelli Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli Genome Biol 5 2004 R87 A rigorous identification of genes that are primarily regulated by changes in negative superhelicity in mid-exponential growth.
-
(2004)
Genome Biol
, vol.5
, pp. 87
-
-
Peter, B.J.1
Arsuaga, J.2
Breier, A.3
Khodursky, A.B.4
Brown, P.O.5
Cozzarelli, N.R.6
-
21
-
-
15544376421
-
Long-term experimental evolution in Escherichia coli. XII. DNA topology as a key target of selection
-
E. Crozat, N. Phillippe, R.E. Lenski, J. Geiselmann, and D. Schneider Long-term experimental evolution in Escherichia coli. XII. DNA topology as a key target of selection Genetics 169 2005 523 532 A direct confirmation of the importance of DNA topology in global transcription regulation in E. coli.
-
(2005)
Genetics
, vol.169
, pp. 523-532
-
-
Crozat, E.1
Phillippe, N.2
Lenski, R.E.3
Geiselmann, J.4
Schneider, D.5
-
22
-
-
0037417962
-
Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli
-
T.F. Cooper, D.E. Rozen, and R.E. Lenski Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli Proc Natl Acad Sci USA 100 2003 1072 1077
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 1072-1077
-
-
Cooper, T.F.1
Rozen, D.E.2
Lenski, R.E.3
-
23
-
-
0022017340
-
Supercoiling response of a bacterial tRNA gene
-
A.I. Lamond Supercoiling response of a bacterial tRNA gene EMBO J 4 1985 501 507
-
(1985)
EMBO J
, vol.4
, pp. 501-507
-
-
Lamond, A.I.1
-
24
-
-
0028148504
-
Escherichia coli tyrT gene transcription is sensitive to DNA supercoiling in its native chromosomal context: Effect of DNA topoisomerase IV overexpression on tyrT promoter function
-
A. Free, and C.J. Dorman Escherichia coli tyrT gene transcription is sensitive to DNA supercoiling in its native chromosomal context: effect of DNA topoisomerase IV overexpression on tyrT promoter function Mol Microbiol 14 1994 151 161
-
(1994)
Mol Microbiol
, vol.14
, pp. 151-161
-
-
Free, A.1
Dorman, C.J.2
-
25
-
-
0036251235
-
Promoter protection by a transcription factor acting as a local topological homeostat
-
M. Rochman, M. Aviv, G. Glaser, and G. Muskhelishvili Promoter protection by a transcription factor acting as a local topological homeostat EMBO Rep 3 2002 335 360
-
(2002)
EMBO Rep
, vol.3
, pp. 335-360
-
-
Rochman, M.1
Aviv, M.2
Glaser, G.3
Muskhelishvili, G.4
-
26
-
-
0041848580
-
Mechanism of transcriptional activation by FIS: Role of core promoter structure and DNA topology
-
H. Auner, M. Buckle, A. Deufel, T. Kutateladze, L. Lazarus, R. Mavathur, G. Muskhelishvili, I. Pemberton, R. Schneider, and A. Travers Mechanism of transcriptional activation by FIS: role of core promoter structure and DNA topology J Mol Biol 331 2003 331 344
-
(2003)
J Mol Biol
, vol.331
, pp. 331-344
-
-
Auner, H.1
Buckle, M.2
Deufel, A.3
Kutateladze, T.4
Lazarus, L.5
Mavathur, R.6
Muskhelishvili, G.7
Pemberton, I.8
Schneider, R.9
Travers, A.10
-
27
-
-
3142588939
-
Buffering of stable RNA promoter activity against promoter relaxation requires a far upstream sequence
-
M. Rochman, N. Blot, M. Dyachenko, G. Glaser, A. Travers, and G. Muskhelishvili Buffering of stable RNA promoter activity against promoter relaxation requires a far upstream sequence Mol Microbiol 53 2004 143 152 A demonstration that a transcriptional activator can directly compensate for changes in negative superhelicity in vivo.
-
(2004)
Mol Microbiol
, vol.53
, pp. 143-152
-
-
Rochman, M.1
Blot, N.2
Dyachenko, M.3
Glaser, G.4
Travers, A.5
Muskhelishvili, G.6
-
28
-
-
0030668269
-
FIS modulates growth phase-dependent topological transitions of DNA in Escherichia coli
-
R. Schneider, A. Travers, and G. Muskhelishvili FIS modulates growth phase-dependent topological transitions of DNA in Escherichia coli Mol Microbiol 26 1997 519 530
-
(1997)
Mol Microbiol
, vol.26
, pp. 519-530
-
-
Schneider, R.1
Travers, A.2
Muskhelishvili, G.3
-
29
-
-
0033814887
-
The expression of the Escherichia coli fis gene is strongly dependent on the superhelical density of DNA
-
R. Schneider, A. Travers, and G. Muskhelishvili The expression of the Escherichia coli fis gene is strongly dependent on the superhelical density of DNA Mol Microbiol 38 2000 167 175
-
(2000)
Mol Microbiol
, vol.38
, pp. 167-175
-
-
Schneider, R.1
Travers, A.2
Muskhelishvili, G.3
-
30
-
-
0033404486
-
A DNA architectural protein couples cellular physiology and DNA topology in Escherichia coli
-
R. Schneider, A. Travers, T. Kutateladze, and G. Muskhelishvili A DNA architectural protein couples cellular physiology and DNA topology in Escherichia coli Mol Microbiol 34 1999 953 964
-
(1999)
Mol Microbiol
, vol.34
, pp. 953-964
-
-
Schneider, R.1
Travers, A.2
Kutateladze, T.3
Muskhelishvili, G.4
-
31
-
-
0142075908
-
The gyr genes of Salmonella enterica serovar Typhimurium are repressed by the factor for inversion stimulation
-
O.M. Keane, and C.J. Dorman The gyr genes of Salmonella enterica serovar Typhimurium are repressed by the factor for inversion stimulation Fis. Mol Genet Genomics 270 2003 56 65
-
(2003)
Fis. Mol Genet Genomics
, vol.270
, pp. 56-65
-
-
Keane, O.M.1
Dorman, C.J.2
-
32
-
-
0035945265
-
An architectural role of the Escherichia coli chromatin protein FIS in organising DNA
-
R. Schneider, R. Lürz, G. Luder, C. Tolksdorf, A. Travers, and G. Muskhelishvili An architectural role of the Escherichia coli chromatin protein FIS in organising DNA Nucleic Acids Res 29 2001 5107 5114
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 5107-5114
-
-
Schneider, R.1
Lürz, R.2
Luder, G.3
Tolksdorf, C.4
Travers, A.5
Muskhelishvili, G.6
-
33
-
-
13444288385
-
DNA supercoiling: A global transcriptional regulator for enterobacterial growth
-
A. Travers, and G. Muskhelishvili DNA supercoiling: a global transcriptional regulator for enterobacterial growth Nat Rev Microbiol 3 2005 157 166 A model for global transcriptional regulation in E. coli, describing how DNA supercoiling, nucleoid-associated proteins and RNA polymerase and its effectors form a coherent regulatory network.
-
(2005)
Nat Rev Microbiol
, vol.3
, pp. 157-166
-
-
Travers, A.1
Muskhelishvili, G.2
-
34
-
-
0032716841
-
Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid
-
T. Ali Azam, A. Iwata, A. Nishimura, S. Ueda, and A. Ishihama Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid J Bacteriol 181 1999 6361 6370
-
(1999)
J Bacteriol
, vol.181
, pp. 6361-6370
-
-
Ali Azam, T.1
Iwata, A.2
Nishimura, A.3
Ueda, S.4
Ishihama, A.5
-
36
-
-
0028085068
-
The chromatin-associated protein H-NS alters DNA topology in vitro
-
A.E. Tupper, T.A. Owen-Hughes, D.W. Ussery, D.S. Santos, D.J. Ferguson, J.M. Sidebotham, J.C. Hinton, and C.F. Higgins The chromatin-associated protein H-NS alters DNA topology in vitro EMBO J 13 1994 258 268
-
(1994)
EMBO J
, vol.13
, pp. 258-268
-
-
Tupper, A.E.1
Owen-Hughes, T.A.2
Ussery, D.W.3
Santos, D.S.4
Ferguson, D.J.5
Sidebotham, J.M.6
Hinton, J.C.7
Higgins, C.F.8
-
37
-
-
0041312645
-
Flexible DNA bending in HU-DNA cocrystal structures
-
K. Swinger, K.M. Lemberg, Y. Zhang, and P.A. Rice Flexible DNA bending in HU-DNA cocrystal structures EMBO J 22 2003 3749 3760 A crystal structure demonstrating how HU but not IHF can constrain negative supercoils.
-
(2003)
EMBO J
, vol.22
, pp. 3749-3760
-
-
Swinger, K.1
Lemberg, K.M.2
Zhang, Y.3
Rice, P.A.4
-
38
-
-
0026754366
-
The chromatin-associated protein H-NS interacts with curved DNA to influence DNA topology and gene expression
-
T.A. Owen-Hughes, G.D. Pavitt, D.S. Santos, J.M. Sidebotham, C.S. Hulton, J.C. Hinton, and C.F. Higgins The chromatin-associated protein H-NS interacts with curved DNA to influence DNA topology and gene expression Cell 71 1992 255 265
-
(1992)
Cell
, vol.71
, pp. 255-265
-
-
Owen-Hughes, T.A.1
Pavitt, G.D.2
Santos, D.S.3
Sidebotham, J.M.4
Hulton, C.S.5
Hinton, J.C.6
Higgins, C.F.7
-
39
-
-
0028559940
-
Interaction of Fis protein with DNA: Bending and specificity of binding
-
M. Betermier, D.J. Galas, and M. Chandler Interaction of Fis protein with DNA: bending and specificity of binding Biochimie 76 1994 958 967
-
(1994)
Biochimie
, vol.76
, pp. 958-967
-
-
Betermier, M.1
Galas, D.J.2
Chandler, M.3
-
40
-
-
1842453825
-
Structure of the histone-like protein H-NS and its role in regulation and genome superstructure
-
S. Rimsky Structure of the histone-like protein H-NS and its role in regulation and genome superstructure Curr Opin Microbiol 7 2004 109 114
-
(2004)
Curr Opin Microbiol
, vol.7
, pp. 109-114
-
-
Rimsky, S.1
-
41
-
-
2442560235
-
H-NS: A universal regulator of for a dynamic genome
-
C.J. Dorman H-NS: a universal regulator of for a dynamic genome Nat Rev Microbiol 2 2004 391 400
-
(2004)
Nat Rev Microbiol
, vol.2
, pp. 391-400
-
-
Dorman, C.J.1
-
42
-
-
4344716137
-
A global role for Fis in the transcriptional control of metabolism and type III secretion in Salmonella enterica serovar Typhimurium
-
A. Kelly, M.D. Goldberg, R.K. Carroll, V. Danino, J.C. Hinton, and C.J. Dorman A global role for Fis in the transcriptional control of metabolism and type III secretion in Salmonella enterica serovar Typhimurium Microbiology 150 2004 2037 2053 Microarray analysis reveals the extent of pleiotropic regulation by the DNA-bending protein FIS.
-
(2004)
Microbiology
, vol.150
, pp. 2037-2053
-
-
Kelly, A.1
Goldberg, M.D.2
Carroll, R.K.3
Danino, V.4
Hinton, J.C.5
Dorman, C.J.6
-
43
-
-
13444310900
-
A truncated H-NS-like protein from enteropathogenic Escherichia coli acts as an H-NS antagonist
-
H.S. Williamson, and A. Free A truncated H-NS-like protein from enteropathogenic Escherichia coli acts as an H-NS antagonist Mol Microbiol 55 2005 808 827
-
(2005)
Mol Microbiol
, vol.55
, pp. 808-827
-
-
Williamson, H.S.1
Free, A.2
-
44
-
-
18444369954
-
The role of nucleoid associated proteins in the organization and compaction of bacterial chromatin
-
R.T. Dame The role of nucleoid associated proteins in the organization and compaction of bacterial chromatin Mol Microbiol 56 2005 858 870
-
(2005)
Mol Microbiol
, vol.56
, pp. 858-870
-
-
Dame, R.T.1
-
45
-
-
0037047088
-
Potent stimulation of transcription-coupled DNA supercoiling by sequence-specific DNA-binding proteins
-
F. Leng, and R. McMacken Potent stimulation of transcription-coupled DNA supercoiling by sequence-specific DNA-binding proteins Proc Natl Acad Sci USA 99 2002 9139 9144
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 9139-9144
-
-
Leng, F.1
McMacken, R.2
-
46
-
-
0035077729
-
Genome organisation and chromatin structure in Escherichia coli
-
D. Ussery, T.S. Larsen, K.T. Wilkes, C. Friis, P. Worning, A. Krogh, and S. Brunak Genome organisation and chromatin structure in Escherichia coli Biochimie 83 2001 201 212
-
(2001)
Biochimie
, vol.83
, pp. 201-212
-
-
Ussery, D.1
Larsen, T.S.2
Wilkes, K.T.3
Friis, C.4
Worning, P.5
Krogh, A.6
Brunak, S.7
|