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Volumn 41, Issue 14, 2013, Pages 6808-6815

Modelling of crowded polymers elucidate effects of double-strand breaks in topological domains of bacterial chromosomes

Author keywords

[No Author keywords available]

Indexed keywords

POLYMER;

EID: 84881511009     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt480     Document Type: Article
Times cited : (26)

References (60)
  • 3
    • 3142774839 scopus 로고    scopus 로고
    • Topological domain structure of the Escherichia coli chromosome
    • Postow L., Hardy C.D., Arsuaga J. and Cozzarelli N.R. (2004) Topological domain structure of the Escherichia coli chromosome. Genes Dev., 18, 1766-1779
    • (2004) Genes Dev , vol.18 , pp. 1766-1779
    • Postow, L.1    Hardy, C.D.2    Arsuaga, J.3    Cozzarelli, N.R.4
  • 4
    • 0015506478 scopus 로고
    • On the structure of the folded chromosome of Escherichia coli
    • Worcel A. and Burgi E. (1972) On the structure of the folded chromosome of Escherichia coli. J. Mol. Biol., 71, 127-147
    • (1972) J. Mol. Biol , vol.71 , pp. 127-147
    • Worcel, A.1    Burgi, E.2
  • 5
    • 0029863159 scopus 로고    scopus 로고
    • Surveying a supercoil domain by using the gamma delta resolution system in Salmonella typhimurium
    • Higgins N.P., Yang X., Fu Q. and Roth J.R. (1996) Surveying a supercoil domain by using the gamma delta resolution system in Salmonella typhimurium. J. Bacteriol., 178, 2825-2835
    • (1996) J. Bacteriol , vol.178 , pp. 2825-2835
    • Higgins, N.P.1    Yang, X.2    Fu, Q.3    Roth, J.R.4
  • 6
    • 84863117103 scopus 로고    scopus 로고
    • A model for Escherichia coli chromosome packaging supports transcription factor-induced DNA domain formation
    • Fritsche M., Li S., Heermann D.W. and Wiggins P.A. (2012) A model for Escherichia coli chromosome packaging supports transcription factor-induced DNA domain formation. Nucleic Acids Res., 40, 972-980
    • (2012) Nucleic Acids Res , vol.40 , pp. 972-980
    • Fritsche, M.1    Li, S.2    Heermann, D.W.3    Wiggins, P.A.4
  • 7
    • 77950455981 scopus 로고    scopus 로고
    • Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament
    • Wiggins P.A., Cheveralls K.C., Martin J.S., Lintner R. and Kondev J. (2010) Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament. Proc. Natl Acad. Sci. USA, 107, 4991-4995
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 4991-4995
    • Wiggins, P.A.1    Cheveralls, K.C.2    Martin, J.S.3    Lintner, R.4    Kondev, J.5
  • 8
    • 84862996843 scopus 로고    scopus 로고
    • Spontaneous helicity of a polymer with side loops confined to a cylinder
    • Chaudhuri D. and Mulder B.M. (2012) Spontaneous helicity of a polymer with side loops confined to a cylinder. Phys. Rev. Lett., 108, 268305
    • (2012) Phys. Rev. Lett , vol.108 , pp. 268305
    • Chaudhuri, D.1    Mulder, B.M.2
  • 9
    • 0030758268 scopus 로고    scopus 로고
    • Simplification of DNA topology below equilibrium values by type II topoisomerases
    • Rybenkov V.V., Ullsperger C., Vologodskii A.V. and Cozzarelli N.R. (1997) Simplification of DNA topology below equilibrium values by type II topoisomerases. Science, 277, 690-693
    • (1997) Science , vol.277 , pp. 690-693
    • Rybenkov, V.V.1    Ullsperger, C.2    Vologodskii, A.V.3    Cozzarelli, N.R.4
  • 10
    • 20444390654 scopus 로고    scopus 로고
    • Chromosome and replisome dynamics in E. coli: Loss of sister cohesion triggers global chromosome movement and mediates chromosome segregation
    • Bates D. and Kleckner N. (2005) Chromosome and replisome dynamics in E. coli: Loss of sister cohesion triggers global chromosome movement and mediates chromosome segregation. Cell, 121, 899-911
    • (2005) Cell , vol.121 , pp. 899-911
    • Bates, D.1    Kleckner, N.2
  • 11
    • 78649369567 scopus 로고    scopus 로고
    • Independent segregation of the two arms of the Escherichia coli ori region requires neither RNA synthesis nor MreB dynamics
    • Wang X. and Sherratt D.J. (2010) Independent segregation of the two arms of the Escherichia coli ori region requires neither RNA synthesis nor MreB dynamics. J. Bacteriol., 192, 6143-6153
    • (2010) J. Bacteriol , vol.192 , pp. 6143-6153
    • Wang, X.1    Sherratt, D.J.2
  • 12
    • 79952591477 scopus 로고    scopus 로고
    • Escherichia coli sister chromosome separation includes an abrupt global transition with concomitant release of late-splitting intersister snaps
    • Joshi M.C., Bourniquel A., Fisher J., Ho B.T., Magnan D., Kleckner N. and Bates D. (2011) Escherichia coli sister chromosome separation includes an abrupt global transition with concomitant release of late-splitting intersister snaps. Proc. Natl Acad. Sci. USA, 108, 2765-2770
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. 2765-2770
    • Joshi, M.C.1    Bourniquel, A.2    Fisher, J.3    Ho, B.T.4    Magnan, D.5    Kleckner, N.6    Bates, D.7
  • 14
    • 33747615506 scopus 로고    scopus 로고
    • Entropy-driven spatial organization of highly confined polymers: Lessons for the bacterial chromosome
    • Jun S. and Mulder B. (2006) Entropy-driven spatial organization of highly confined polymers: Lessons for the bacterial chromosome. Proc. Natl Acad. Sci. USA, 103, 12388-12393
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 12388-12393
    • Jun, S.1    Mulder, B.2
  • 15
    • 0037169328 scopus 로고    scopus 로고
    • FtsK Is a DNA motor protein that activates chromosome dimer resolution by switching the catalytic state of the XerC and XerD recombinases
    • Aussel L., Barre F.X., Aroyo M., Stasiak A., Stasiak A.Z. and Sherratt D. (2002) FtsK Is a DNA motor protein that activates chromosome dimer resolution by switching the catalytic state of the XerC and XerD recombinases. Cell, 108, 195-205
    • (2002) Cell , vol.108 , pp. 195-205
    • Aussel, L.1    Barre, F.X.2    Aroyo, M.3    Stasiak, A.4    Stasiak, A.Z.5    Sherratt, D.6
  • 18
    • 0032715175 scopus 로고    scopus 로고
    • Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda
    • table of contents
    • Kuzminov A. (1999) Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda. Microbiol. Mol. Biol. Rev., 63, 751-813, table of contents
    • (1999) Microbiol. Mol. Biol. Rev , vol.63 , pp. 751-7813
    • Kuzminov, A.1
  • 20
    • 44249089250 scopus 로고    scopus 로고
    • Physical analyses of E. coli heteroduplex recombination products in vivo: On the prevalence of 50 and 3' patches
    • Gumbiner-Russo L.M. and Rosenberg S.M. (2007) Physical analyses of E. coli heteroduplex recombination products in vivo: On the prevalence of 50 and 3' patches. PLoS One, 2, e1242
    • (2007) PLoS One , vol.2
    • Gumbiner-Russo, L.M.1    Rosenberg, S.M.2
  • 21
    • 0028345621 scopus 로고
    • Structure and function of RecA-DNA complexes
    • Stasiak A. and Egelman E.H. (1994) Structure and function of RecA-DNA complexes. Experientia, 50, 192-203
    • (1994) Experientia , vol.50 , pp. 192-203
    • Stasiak, A.1    Egelman, E.H.2
  • 22
    • 0022181480 scopus 로고
    • The pairing activity of stable nucleoprotein filaments made from recA protein single-stranded DNA, and adenosine 5'-(gammathio) triphosphate
    • Honigberg S.M., Gonda D.K., Flory J. and Radding C.M. (1985) The pairing activity of stable nucleoprotein filaments made from recA protein, single-stranded DNA, and adenosine 5'-(gammathio) triphosphate. J. Biol. Chem., 260, 11845-11851
    • (1985) J. Biol. Chem , vol.260 , pp. 11845-11851
    • Honigberg, S.M.1    Gonda, D.K.2    Flory, J.3    Radding, C.M.4
  • 23
    • 0025166577 scopus 로고
    • Stable dna heteroduplex formation catalyzed by the escherichia coli reca protein in the absence of atp hydrolysis
    • Menetski J.P., Bear D.G. and Kowalczykowski S.C. (1990) Stable DNA heteroduplex formation catalyzed by the Escherichia coli RecA protein in the absence of ATP hydrolysis. Proc. Natl Acad. Sci. USA, 87, 21-25
    • (1990) Proc. Natl Acad. Sci. USA , vol.87 , pp. 21-25
    • Menetski, J.P.1    Bear, D.G.2    Kowalczykowski, S.C.3
  • 24
    • 0025634466 scopus 로고
    • Energetics of RecA-mediated recombination reactions Without ATP hydrolysis RecA can mediate polar strand exchange but is unable to recycle
    • Rosselli W. and Stasiak A. (1990) Energetics of RecA-mediated recombination reactions. Without ATP hydrolysis RecA can mediate polar strand exchange but is unable to recycle. J. Mol. Biol., 216, 335-352
    • (1990) J. Mol. Biol , vol.216 , pp. 335-352
    • Rosselli, W.1    Stasiak, A.2
  • 25
    • 84857118715 scopus 로고    scopus 로고
    • Single-molecule imaging of DNA pairing by RecA reveals a three-dimensional homology search
    • Forget A.L. and Kowalczykowski S.C. (2012) Single-molecule imaging of DNA pairing by RecA reveals a three-dimensional homology search. Nature, 482, 423-427
    • (2012) Nature , vol.482 , pp. 423-427
    • Forget, A.L.1    Kowalczykowski, S.C.2
  • 26
    • 0022909525 scopus 로고
    • Conjectures on the statistics of ring polymers
    • Cates M.E. and Deutsch J.M. (1986) Conjectures on the statistics of ring polymers. J. Physique, 47, 2121-2128
    • (1986) J. Physique , vol.47 , pp. 2121-2128
    • Cates, M.E.1    Deutsch, J.M.2
  • 28
    • 47849117193 scopus 로고    scopus 로고
    • Topological effect in ring polymers investigated with monte carlo simulation
    • Suzuki J., Takano A. and Matsushita Y. (2008) Topological effect in ring polymers investigated with Monte Carlo simulation. J. Chem. Phys., 129, 034903
    • (2008) J. Chem. Phys , vol.129 , pp. 034903
    • Suzuki, J.1    Takano, A.2    Matsushita, Y.3
  • 29
    • 70350433136 scopus 로고    scopus 로고
    • Dimension of ring polymers in bulk studied by Monte-Carlo simulation and self-consistent theory
    • Suzuki J., Takano A., Deguchi T. and Matsushita Y. (2009) Dimension of ring polymers in bulk studied by Monte-Carlo simulation and self-consistent theory. J. Chem. Phys., 131, 144902
    • (2009) J. Chem. Phys , vol.131 , pp. 144902
    • Suzuki, J.1    Takano, A.2    Deguchi, T.3    Matsushita, Y.4
  • 30
    • 2342612001 scopus 로고    scopus 로고
    • Computer simulation studies on overlapping polymer chains confined in narrow channels
    • Teraoka I. and Wang Y.M. (2004) Computer simulation studies on overlapping polymer chains confined in narrow channels. Polymer, 45, 3835-3843
    • (2004) Polymer , vol.45 , pp. 3835-3843
    • Teraoka, I.1    Wang, Y.M.2
  • 31
    • 84859579676 scopus 로고    scopus 로고
    • Intrachain ordering and segregation of polymers under confinement
    • Jung Y., Kim J., Jun S. and Ha B.Y. (2012) Intrachain Ordering and Segregation of Polymers under Confinement. Macromolecules, 45, 3256-3262
    • (2012) Macromolecules , vol.45 , pp. 3256-3262
    • Jung, Y.1    Kim, J.2    Jun, S.3    Ha, B.Y.4
  • 33
    • 78649902376 scopus 로고    scopus 로고
    • The role of transcription factories-mediated interchromosomal contacts in the organization of nuclear architecture
    • Dorier J. and Stasiak A. (2010) The role of transcription factories-mediated interchromosomal contacts in the organization of nuclear architecture. Nucleic Acids Res., 38, 7410-7421
    • (2010) Nucleic Acids Res , vol.38 , pp. 7410-7421
    • Dorier, J.1    Stasiak, A.2
  • 34
    • 36549102647 scopus 로고
    • Error estimates on averages of correlated data
    • Flyvbjerg H. and Petersen H.G. (1989) Error estimates on averages of correlated data. J. Chem. Phys., 91, 461-466
    • (1989) J. Chem. Phys , vol.91 , pp. 461-466
    • Flyvbjerg, H.1    Petersen, H.G.2
  • 35
    • 0016424156 scopus 로고
    • Enzymatic production of deoxyribonucleic acid double-strand breaks after ultraviolet irradiation of Escherichia coli K-12
    • Bonura T. and Smith K.C. (1975) Enzymatic production of deoxyribonucleic acid double-strand breaks after ultraviolet irradiation of Escherichia coli K-12. J. Bacteriol., 121, 511-517
    • (1975) J. Bacteriol , vol.121 , pp. 511-517
    • Bonura, T.1    Smith, K.C.2
  • 36
    • 0032514107 scopus 로고    scopus 로고
    • Osmotic compaction of supercoiled DNA into a bacterial nucleoid
    • Odijk T. (1998) Osmotic compaction of supercoiled DNA into a bacterial nucleoid. Biophys. Chem., 73, 23-29
    • (1998) Biophys. Chem , vol.73 , pp. 23-29
    • Odijk, T.1
  • 37
    • 33750504444 scopus 로고    scopus 로고
    • Structural and physical aspects of bacterial chromosome segregation
    • Woldringh C.L. and Nanninga N. (2006) Structural and physical aspects of bacterial chromosome segregation. J. Struct. Biol., 156, 273-283
    • (2006) J. Struct. Biol , vol.156 , pp. 273-283
    • Woldringh, C.L.1    Nanninga, N.2
  • 38
    • 84877694848 scopus 로고    scopus 로고
    • Four-dimensional imaging of E coli nucleoid organization and dynamics in living cells
    • Fisher J.K., Bourniquel A., Witz G., Weiner B., Prentiss M. and Kleckner N. (2013) Four-dimensional imaging of E. coli nucleoid organization and dynamics in living cells. Cell, 153, 882-895
    • (2013) Cell , vol.153 , pp. 882-895
    • Fisher, J.K.1    Bourniquel, A.2    Witz, G.3    Weiner, B.4    Prentiss, M.5    Kleckner, N.6
  • 39
    • 77954719357 scopus 로고    scopus 로고
    • Entropy as the driver of chromosome segregation
    • Jun S. and Wright A. (2010) Entropy as the driver of chromosome segregation. Nat. Rev. Microbiol., 8, 600-607
    • (2010) Nat. Rev. Microbiol , vol.8 , pp. 600-607
    • Jun, S.1    Wright, A.2
  • 40
    • 78651347562 scopus 로고    scopus 로고
    • Overlapping two self-Avoiding polymers in a closed cylindrical pore: Implications for chromosome segregation in a bacterial cell
    • Jung Y. and Ha B.Y. (2010) Overlapping two self-Avoiding polymers in a closed cylindrical pore: Implications for chromosome segregation in a bacterial cell. Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip Topics, 82, 051926
    • (2010) Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip Topics , vol.82 , pp. 051926
    • Jung, Y.1    Ha, B.Y.2
  • 42
    • 0025020967 scopus 로고
    • Cell volume increase in Escherichia coli after shifts to richer media
    • Kubitschek H.E. (1990) Cell volume increase in Escherichia coli after shifts to richer media. J. Bacteriol., 172, 94-101
    • (1990) J. Bacteriol , vol.172 , pp. 94-101
    • Kubitschek, H.E.1
  • 44
    • 80053391759 scopus 로고    scopus 로고
    • Capturing the essence of folding and functions of biomolecules using coarse-grained models
    • Hyeon C. and Thirumalai D. (2011) Capturing the essence of folding and functions of biomolecules using coarse-grained models. Nat. Commun., 2, 487
    • (2011) Nat. Commun , vol.2 , pp. 487
    • Hyeon, C.1    Thirumalai, D.2
  • 45
    • 77954625173 scopus 로고    scopus 로고
    • Action at hooked or twisted-hooked DNA juxtapositions rationalizes unlinking preference of type-2 topoisomerases
    • Liu Z., Zechiedrich L. and Chan H.S. (2010) Action at hooked or twisted-hooked DNA juxtapositions rationalizes unlinking preference of type-2 topoisomerases. J. Mol. Biol., 400, 963-982
    • (2010) J. Mol. Biol , vol.400 , pp. 963-982
    • Liu, Z.1    Zechiedrich, L.2    Chan, H.S.3
  • 46
    • 68349150613 scopus 로고    scopus 로고
    • Statistics of polymer rings in the melt: A numerical simulation study
    • Vettorel T., Grosberg A.Y. and Kremer K. (2009) Statistics of polymer rings in the melt: A numerical simulation study. Phys. Biol., 6, 025013
    • (2009) Phys. Biol , vol.6 , pp. 025013
    • Vettorel, T.1    Grosberg, A.Y.2    Kremer, K.3
  • 47
    • 70349280357 scopus 로고    scopus 로고
    • Recombinational DNA repair in a cellular context: A search for the homology search
    • Weiner A., Zauberman N. and Minsky A. (2009) Recombinational DNA repair in a cellular context: A search for the homology search. Nat. Rev. Microbiol., 7, 748-755
    • (2009) Nat. Rev. Microbiol , vol.7 , pp. 748-755
    • Weiner, A.1    Zauberman, N.2    Minsky, A.3
  • 48
    • 84865273051 scopus 로고    scopus 로고
    • Sister chromatid interactions in bacteria revealed by a site-specific recombination assay
    • Lesterlin C., Gigant E., Boccard F. and Espeli O. (2012) Sister chromatid interactions in bacteria revealed by a site-specific recombination assay. EMBO J., 31, 3468-3479
    • (2012) EMBO J. , vol.31 , pp. 3468-3479
    • Lesterlin, C.1    Gigant, E.2    Boccard, F.3    Espeli, O.4
  • 49
    • 0028858007 scopus 로고
    • Roles of topoisomerase IV and DNA gyrase in DNA unlinking during replication in Escherichia coli
    • Zechiedrich E.L. and Cozzarelli N.R. (1995) Roles of topoisomerase IV and DNA gyrase in DNA unlinking during replication in Escherichia coli. Genes Dev., 9, 2859-2869
    • (1995) Genes Dev , vol.9 , pp. 2859-2869
    • Zechiedrich, E.L.1    Cozzarelli, N.R.2
  • 50
    • 77952301118 scopus 로고    scopus 로고
    • DNA supercoiling and its role in DNA decatenation and unknotting
    • Witz G. and Stasiak A. (2010) DNA supercoiling and its role in DNA decatenation and unknotting. Nucleic Acids Res., 39, 2119-2133
    • (2010) Nucleic Acids Res , vol.39 , pp. 2119-2133
    • Witz, G.1    Stasiak, A.2
  • 51
    • 0021337860 scopus 로고
    • Role of RecA protein spiral filaments in genetic recombination
    • Howard-Flanders P., West S.C. and Stasiak A. (1984) Role of RecA protein spiral filaments in genetic recombination. Nature, 309, 215-219
    • (1984) Nature , vol.309 , pp. 215-219
    • Howard-Flanders, P.1    West, S.C.2    Stasiak, A.3
  • 52
    • 0026468267 scopus 로고
    • Three-stranded DNA structure; is this the secret of DNA homologous recognition
    • Stasiak A. (1992) Three-stranded DNA structure; is this the secret of DNA homologous recognitioñMol. Microbiol., 6, 3267-3276
    • (1992) Mol. Microbiol , vol.6 , pp. 3267-3276
    • Stasiak, A.1
  • 53
    • 67749116521 scopus 로고    scopus 로고
    • The search for a human Holliday junction resolvase
    • West S.C. (2009) The search for a human Holliday junction resolvase. Biochem. Soc. Trans., 37, 519-526
    • (2009) Biochem. Soc. Trans , vol.37 , pp. 519-526
    • West, S.C.1
  • 54
    • 84861095603 scopus 로고    scopus 로고
    • Topological domains in mammalian genomes identified by analysis of chromatin interactions
    • Dixon J.R., Selvaraj S., Yue F., Kim A., Li Y., Shen Y., Hu M., Liu J.S. and Ren B. (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485, 376-380
    • (2012) Nature , vol.485 , pp. 376-380
    • Dixon, J.R.1    Selvaraj, S.2    Yue, F.3    Kim, A.4    Li, Y.5    Shen, Y.6    Hu, M.7    Liu, J.S.8    Ren, B.9
  • 56
    • 70349944662 scopus 로고    scopus 로고
    • Entropic organization of interphase chromosomes
    • Cook P.R. and Marenduzzo D. (2009) Entropic organization of interphase chromosomes. J. Cell Biol., 186, 825-834
    • (2009) J. Cell Biol , vol.186 , pp. 825-834
    • Cook, P.R.1    Marenduzzo, D.2
  • 57
    • 67649873461 scopus 로고    scopus 로고
    • Non-specific interactions are sufficient to explain the position of heterochromatic chromocenters and nucleoli in interphase nuclei
    • de Nooijer S., Wellink J., Mulder B. and Bisseling T. (2009) Non-specific interactions are sufficient to explain the position of heterochromatic chromocenters and nucleoli in interphase nuclei. Nucleic Acids Res., 37, 3558-3568
    • (2009) Nucleic Acids Res , vol.37 , pp. 3558-3568
    • De Nooijer, S.1    Wellink, J.2    Mulder, B.3    Bisseling, T.4
  • 59
    • 71049147905 scopus 로고    scopus 로고
    • Topological origins of chromosomal territories
    • Dorier J. and Stasiak A. (2009) Topological origins of chromosomal territories. Nucleic Acids Res., 37, 6316-6322
    • (2009) Nucleic Acids Res , vol.37 , pp. 6316-6322
    • Dorier, J.1    Stasiak, A.2


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