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Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli
Brian J Peter, Javier Arsuaga, Adam M Breier, Arkady B Khodursky, Patrick O Brown, Nicholas R Cozzarelli
Genome Biol. 2004; 5(11): R87. Published online 2004 November 1. doi: 10.1186/gb-2004-5-11-r87
PMCID:
PMC545778
Abstract Full Text PDF–983K Supplementary Material

Is Cited by the Following 49 Articles in this Archive:

Torque measurements reveal sequence-specific cooperative transitions in supercoiled DNA
Florian C. Oberstrass, Louis E. Fernandes, Zev Bryant
Proc Natl Acad Sci U S A. 2012 April 17; 109(16): 6106-6111. Published online 2012 April 2. doi: 10.1073/pnas.1113532109
PMCID:
PMC3341030
Abstract Full Text PDF–1.0M Supplementary Material
A Fundamental Regulatory Mechanism Operating through OmpR and DNA Topology Controls Expression of Salmonella Pathogenicity Islands SPI-1 and SPI-2
Andrew D. S. Cameron, Charles J. Dorman
PLoS Genet. 2012 March; 8(3): e1002615. Published online 2012 March 22. doi: 10.1371/journal.pgen.1002615
PMCID:
PMC3310775
Abstract Full Text PDF–409K Supplementary Material
Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle
Patrick Sobetzko, Andrew Travers, Georgi Muskhelishvili
Proc Natl Acad Sci U S A. 2012 January 10; 109(2): E42–E50. Published online 2011 December 19. doi: 10.1073/pnas.1108229109
Includes additional comments & authors
PMCID:
PMC3258614
Abstract Full Text PDF–1.7M Supplementary Material
Cruciform structures are a common DNA feature important for regulating biological processes
Václav Brázda, Rob C Laister, Eva B Jagelská, Cheryl Arrowsmith
BMC Mol Biol. 2011; 12: 33. Published online 2011 August 5. doi: 10.1186/1471-2199-12-33
PMCID:
PMC3176155
Abstract Full Text PDF–1.1M
Structural Coupling between RNA Polymerase Composition and DNA Supercoiling in Coordinating Transcription: a Global Role for the Omega Subunit?
Marcel Geertz, Andrew Travers, Sanja Mehandziska, Patrick Sobetzko, Sarath Chandra Janga, Nobuo Shimamoto, Georgi Muskhelishvili
mBio. 2011 Jul-Aug; 2(4): e00034-11. Published online 2011 August 2. doi: 10.1128/mBio.00034-11
PMCID:
PMC3147163
Abstract Full Text PDF–1.0M Supplementary Material
Analog regulation of metabolic demand
Nikolaus Sonnenschein, Marcel Geertz, Georgi Muskhelishvili, Marc-Thorsten Hütt
BMC Syst Biol. 2011; 5: 40. Published online 2011 March 15. doi: 10.1186/1752-0509-5-40
PMCID:
PMC3068955
Abstract Full Text PDF–4.3M Supplementary Material
Nonoptimal DNA Topoisomerases Allow Maintenance of Supercoiling Levels and Improve Fitness of Streptococcus pneumoniae
Luz Balsalobre, María José Ferrándiz, Gabriela de Alba, Adela G. de la Campa
Antimicrob Agents Chemother. 2011 March; 55(3): 1097–1105. Published online 2010 December 20. doi: 10.1128/AAC.00783-10
PMCID:
PMC3067103
Abstract Full Text PDF–877K
Structure and dynamics of the operon map of Buchnera aphidicola sp. strain APS
Lilia Brinza, Federica Calevro, Gabrielle Duport, Karen Gaget, Christian Gautier, Hubert Charles
BMC Genomics. 2010; 11: 666. Published online 2010 November 25. doi: 10.1186/1471-2164-11-666
PMCID:
PMC3091783
Abstract Full Text PDF–1.0M Supplementary Material
Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli
Christina Kahramanoglou, Aswin S. N. Seshasayee, Ana I. Prieto, David Ibberson, Sabine Schmidt, Jurgen Zimmermann, Vladimir Benes, Gillian M. Fraser, Nicholas M. Luscombe
Nucleic Acids Res. 2011 March; 39(6): 2073–2091. Published online 2010 November 20. doi: 10.1093/nar/gkq934
PMCID:
PMC3064808
Abstract Full Text PDF–2.3M Supplementary Material
Coupling of transcription and replication machineries in λ DNA replication initiation: evidence for direct interaction of Escherichia coli RNA polymerase and the λO protein
Anna Szambowska, Marcin Pierechod, Grzegorz Węgrzyn, Monika Glinkowska
Nucleic Acids Res. 2011 January; 39(1): 168–177. Published online 2010 September 9. doi: 10.1093/nar/gkq752
PMCID:
PMC3017604
Abstract Full Text PDF–2.3M Supplementary Material
Cellular strategies for regulating DNA supercoiling: A single-molecule perspective
Daniel A. Koster, Aurélien Crut, Stewart Shuman, Mary-Ann Bjornsti, Nynke H. Dekker
Cell. Author manuscript; available in PMC 2011 August 20.
Published in final edited form as: Cell. 2010 August 20; 142(4): 519–530. doi: 10.1016/j.cell.2010.08.001
PMCID:
PMC2997354
Abstract Full Text PDF–1.4M Supplementary Material
Comparative Analysis of Sequence Periodicity among Prokaryotic Genomes Points to Differences in Nucleoid Structure and a Relationship to Gene Expression
Jan Mrázek
J Bacteriol. 2010 July; 192(14): 3763–3772. Published online 2010 May 21. doi: 10.1128/JB.00149-10
PMCID:
PMC2897355
Abstract Full Text PDF–2.9M Supplementary Material
Chromosomal periodicity and positional networks of genes in Escherichia coli
Anthony Mathelier, Alessandra Carbone
Mol Syst Biol. 2010; 6: 366. Published online 2010 May 11. doi: 10.1038/msb.2010.21
PMCID:
PMC2890325
Abstract Full Text PDF–944K Supplementary Material
The genome of Streptococcus pneumoniae is organized in topology-reacting gene clusters
María-José Ferrándiz, Antonio J. Martín-Galiano, Jorge B. Schvartzman, Adela G. de la Campa
Nucleic Acids Res. 2010 June; 38(11): 3570–3581. Published online 2010 February 20. doi: 10.1093/nar/gkq106
PMCID:
PMC2887967
Abstract Full Text PDF–1.9M Supplementary Material
Hfq affects mRNA levels independently of degradation
Jacques Le Derout, Irina V Boni, Philippe Régnier, Eliane Hajnsdorf
BMC Mol Biol. 2010; 11: 17. Published online 2010 February 18. doi: 10.1186/1471-2199-11-17
PMCID:
PMC2834685
Abstract Full Text PDF–1.7M
DNA supercoiling helps to unlink sister duplexes after replication
Alexander Vologodskii
Bioessays. Author manuscript; available in PMC 2011 January 1.
Published in final edited form as: Bioessays. 2010 January; 32(1): 9–12. doi: 10.1002/bies.200900143
PMCID:
PMC2845520
Abstract Full Text PDF–234K
Ranges of control in the transcriptional regulation of Escherichia coli
Nikolaus Sonnenschein, Marc-Thorsten Hütt, Helga Stoyan, Dietrich Stoyan
BMC Syst Biol. 2009; 3: 119. Published online 2009 December 24. doi: 10.1186/1752-0509-3-119
PMCID:
PMC2804738
Abstract Full Text PDF–599K Supplementary Material
Oscillations in supercoiling drive circadian gene expression in cyanobacteria
Vikram Vijayan, Rick Zuzow, Erin K. O'Shea
Proc Natl Acad Sci U S A. 2009 December 29; 106(52): 22564–22568. Published online 2009 December 14. doi: 10.1073/pnas.0912673106
PMCID:
PMC2799730
Abstract Full Text PDF–1.0M Supplementary Material
Genome-wide colonization of gene regulatory elements by G4 DNA motifs
Zhuo Du, Yiqiang Zhao, Ning Li
Nucleic Acids Res. 2009 November; 37(20): 6784–6798. Published online 2009 November. doi: 10.1093/nar/gkp710
PMCID:
PMC2777415
Abstract Full Text PDF–11M Supplementary Material
Regulation of Gene Expression by PrrA in Rhodobacter sphaeroides 2.4.1: Role of Polyamines and DNA Topology
Jesus M. Eraso, Samuel Kaplan
J Bacteriol. 2009 July; 191(13): 4341–4352. Published online 2009 May 1. doi: 10.1128/JB.00243-09
PMCID:
PMC2698473
Abstract Full Text PDF–772K
In Vivo and In Vitro Patterns of the Activity of Simocyclinone D8, an Angucyclinone Antibiotic from Streptomyces antibioticus
Lisa M. Oppegard, Bree L. Hamann, Kathryn R. Streck, Keith C. Ellis, Hans-Peter Fiedler, Arkady B. Khodursky, Hiroshi Hiasa
Antimicrob Agents Chemother. 2009 May; 53(5): 2110–2119. Published online 2009 March 9. doi: 10.1128/AAC.01440-08
PMCID:
PMC2681514
Abstract Full Text PDF–1.0M Supplementary Material
The HU Regulon Is Composed of Genes Responding to Anaerobiosis, Acid Stress, High Osmolarity and SOS Induction
Jacques Oberto, Sabrina Nabti, Valérie Jooste, Hervé Mignot, Josette Rouviere-Yaniv
PLoS ONE. 2009; 4(2): e4367. Published online 2009 February 4. doi: 10.1371/journal.pone.0004367
PMCID:
PMC2634741
Abstract Full Text PDF–2.4M Supplementary Material
Bacterial topoisomerase I as a target for discovery of antibacterial compounds
Yuk-Ching Tse-Dinh
Nucleic Acids Res. 2009 February; 37(3): 731–737. Published online 2009 February. doi: 10.1093/nar/gkn936
PMCID:
PMC2647297
Abstract Full Text PDF–1.0M
Bacteria as computers making computers
Antoine Danchin
FEMS Microbiol Rev. 2009 January; 33(1): 3–26. Published online 2008 November 11. doi: 10.1111/j.1574-6976.2008.00137.x
PMCID:
PMC2704931
Abstract Full Text PDF–553K
General stress response signaling: unwrapping transcription complexes by DNA relaxation via the sigma38 CTD
Yi-Xin Huo, Adam Z. Rosenthal, Jay D. Gralla
Mol Microbiol. Author manuscript; available in PMC 2009 November 10.
Published in final edited form as: Mol Microbiol. 2008 October; 70(2): 369–378. Published online 2008 August 22. doi: 10.1111/j.1365-2958.2008.06412.x
PMCID:
PMC2775543
Abstract Full Text PDF–976K Supplementary Material
DNA Supercoiling-Dependent Gene Regulation in Chlamydia
Eike Niehus, Eric Cheng, Ming Tan
J Bacteriol. 2008 October; 190(19): 6419–6427. Published online 2008 July 25. doi: 10.1128/JB.00431-08
Correction in:
J Bacteriol. 2008 December; 190(24): 8249.
PMCID:
PMC2566011
Abstract Full Text PDF–890K Correction
The Generation of Promoter-Mediated Transcriptional Noise in Bacteria
Namiko Mitarai, Ian B. Dodd, Michael T. Crooks, Kim Sneppen
PLoS Comput Biol. 2008 July; 4(7): e1000109. Published online 2008 July 11. doi: 10.1371/journal.pcbi.1000109
PMCID:
PMC2442219
Abstract Full Text PDF–811K Supplementary Material
Role of the Global Transcriptional Regulator PrrA in Rhodobacter sphaeroides 2.4.1: Combined Transcriptome and Proteome Analysis
Jesus M. Eraso, Jung Hyeob Roh, Xiaohua Zeng, Stephen J. Callister, Mary S. Lipton, Samuel Kaplan
J Bacteriol. 2008 July; 190(14): 4831–4848. Published online 2008 May 16. doi: 10.1128/JB.00301-08
PMCID:
PMC2447010
Abstract Full Text PDF–1015K Supplementary Material
Dissecting the logical types of network control in gene expression profiles
Carsten Marr, Marcel Geertz, Marc-Thorsten Hütt, Georgi Muskhelishvili
BMC Syst Biol. 2008; 2: 18. Published online 2008 February 19. doi: 10.1186/1752-0509-2-18
PMCID:
PMC2263018
Abstract Full Text PDF–780K Supplementary Material
Superhelical Destabilization in Regulatory Regions of Stress Response Genes
Huiquan Wang, Craig J Benham
PLoS Comput Biol. 2008 January; 4(1): e17. Published online 2008 January 18. doi: 10.1371/journal.pcbi.0040017
PMCID:
PMC2211533
Abstract Full Text PDF–608K Supplementary Material
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