메뉴 건너뛰기




Volumn 75, Issue 7, 2012, Pages

Physical descriptions of the bacterial nucleoid at large scales, and their biological implications

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN;

EID: 84863534788     PISSN: 00344885     EISSN: None     Source Type: Journal    
DOI: 10.1088/0034-4885/75/7/076602     Document Type: Review
Times cited : (71)

References (144)
  • 2
    • 0037381991 scopus 로고    scopus 로고
    • Increased bending rigidity of single DNA molecules by H-NS, a temperature and osmolarity sensor
    • Amit R, Oppenheim A B and Stavans J 2003 Increased bending rigidity of single DNA molecules by H-NS, a temperature and osmolarity sensor Biophys. J. 84 246773 (Pubitemid 36373568)
    • (2003) Biophysical Journal , vol.84 , Issue.4 , pp. 2467-2473
    • Amit, R.1    Oppenheim, A.B.2    Stavans, J.3
  • 3
    • 34848860442 scopus 로고    scopus 로고
    • Time scale of entropic segregation of flexible polymers in confinement: Implications for chromosome segregation in filamentous bacteria
    • DOI 10.1103/PhysRevE.76.031901
    • Arnold A and Jun S 2007 Time scale of entropic segregation of flexible polymers in confinement: implications for chromosome segregation in filamentous bacteria Phys. Rev. E 76 031901 (Pubitemid 47507103)
    • (2007) Physical Review E - Statistical, Nonlinear, and Soft Matter Physics , vol.76 , Issue.3 , pp. 031901
    • Arnold, A.1    Jun, S.2
  • 5
    • 74149085645 scopus 로고    scopus 로고
    • Coordination of genomic structure and transcription by the main bacterial nucleoid-associated protein HU
    • 10.1038/embor.2009.232 1469-221X
    • Berger M, Farcas A, Geertz M, Zhelyazkova P, Brix K, Travers A and Muskhelishvili G 2010 Coordination of genomic structure and transcription by the main bacterial nucleoid-associated protein HU EMBO Rep. 11 5964
    • (2010) EMBO Rep. , vol.11 , Issue.1 , pp. 59-64
    • Berger, M.1    Farcas, A.2    Geertz, M.3    Zhelyazkova, P.4    Brix, K.5    Travers, A.6    Muskhelishvili, G.7
  • 6
    • 52949111871 scopus 로고    scopus 로고
    • Spatial organization of a replicating bacterial chromosome
    • 10.1073/pnas.0804982105 0027-8424
    • Berlatzky I A, Rouvinski A and Ben-Yehuda S 2008 Spatial organization of a replicating bacterial chromosome Proc. Natl Acad. Sci. USA 105 1413640
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , Issue.37 , pp. 14136-14140
    • Berlatzky, I.A.1    Rouvinski, A.2    Ben-Yehuda, S.3
  • 8
    • 33745612978 scopus 로고    scopus 로고
    • Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome
    • DOI 10.1038/sj.embor.7400729, PII 7400729
    • Blot N, Mavathur R, Geertz M, Travers A and Muskhelishvili G 2006 Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome Embo. Rep. 7 71015 (Pubitemid 43986268)
    • (2006) EMBO Reports , vol.7 , Issue.7 , pp. 710-715
    • Blot, N.1    Mavathur, R.2    Geertz, M.3    Travers, A.4    Muskhelishvili, G.5
  • 9
    • 34948885665 scopus 로고    scopus 로고
    • Effects of Fis on Escherichia coli gene expression during different growth stages
    • DOI 10.1099/mic.0.2007/008565-0
    • Bradley M D, Beach M B, de Koning A P J, Pratt T S and Osuna R 2007 Effects of Fis on Escherichia coli gene expression during different growth stages Microbiology 153 292240 (Pubitemid 47517054)
    • (2007) Microbiology , vol.153 , Issue.9 , pp. 2922-2940
    • Bradley, M.D.1    Beach, M.B.2    De Koning, A.P.J.3    Pratt, T.S.4    Osuna, R.5
  • 11
    • 78149484750 scopus 로고    scopus 로고
    • A geometrical model for DNA organization in bacteria
    • 10.1371/journal.pone.0013806 1932-6203 e13806
    • Buenemann M and Lenz P 2010 A geometrical model for DNA organization in bacteria PLoS One 5 e13806
    • (2010) PLoS One , vol.5 , Issue.11
    • Buenemann, M.1    Lenz, P.2
  • 12
    • 51849083802 scopus 로고    scopus 로고
    • Fractional langevin equation: Overdamped, underdamped, and critical behaviors
    • 10.1103/PhysRevE.78.031112 1539-3755 E 031112
    • Burov S and Barkai E 2008 Fractional langevin equation: overdamped, underdamped, and critical behaviors Phys. Rev. E 78 031112
    • (2008) Phys. Rev. , vol.78 , Issue.3
    • Burov, S.1    Barkai, E.2
  • 14
    • 67649394401 scopus 로고    scopus 로고
    • Active transcription of rRNA operons condenses the nucleoid in Escherichia coli: Examining the effect of transcription on nucleoid structure in the absence of transertion
    • 10.1128/JB.01707-08 0021-9193
    • Cabrera J E, Cagliero C, Quan S, Squires C L and Jin D J 2009 Active transcription of rRNA operons condenses the nucleoid in Escherichia coli: examining the effect of transcription on nucleoid structure in the absence of transertion J. Bacteriol. 191 41805
    • (2009) J. Bacteriol. , vol.191 , Issue.13 , pp. 4180-4185
    • Cabrera, J.E.1    Cagliero, C.2    Quan, S.3    Squires, C.L.4    Jin, D.J.5
  • 15
    • 79952741894 scopus 로고    scopus 로고
    • Nucleoid occlusion factor SlmA is a DNA-activated FtsZ polymerization antagonist
    • 10.1073/pnas.1018674108 0027-8424
    • Cho H, McManus H R, Dove S L and Bernhardt T G 2011 Nucleoid occlusion factor SlmA is a DNA-activated FtsZ polymerization antagonist Proc. Natl Acad. Sci. USA 108 37738
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , Issue.9 , pp. 3773-3778
    • Cho, H.1    McManus, H.R.2    Dove, S.L.3    Bernhardt, T.G.4
  • 18
    • 77956155529 scopus 로고    scopus 로고
    • Dimerization and DNA-dependent aggregation of the Escherichia coli nucleoid protein and chaperone CbpA
    • 10.1111/j.1365-2958.2010.07292.x 0950-382X
    • Cosgriff S, Chintakayala K, Chim Y T A, Chen X, Allen S, Lovering A L and Grainger D C 2010 Dimerization and DNA-dependent aggregation of the Escherichia coli nucleoid protein and chaperone CbpA Mol. Microbiol. 77 1289300
    • (2010) Mol. Microbiol. , vol.77 , Issue.5 , pp. 1289-1300
    • Cosgriff, S.1    Chintakayala, K.2    Chim, Y.T.A.3    Chen, X.4    Allen, S.5    Lovering, A.L.6    Grainger, D.C.7
  • 19
    • 0035084721 scopus 로고    scopus 로고
    • Isolation of the Escherichia coli nucleoid
    • DOI 10.1016/S0300-9084(01)01245-7
    • Cunha S, Odijk T, Suleymanoglu E and Woldringh C L 2001 Isolation of the Escherichia coli nucleoid Biochimie 83 14954 (Pubitemid 32243558)
    • (2001) Biochimie , vol.83 , Issue.2 , pp. 149-154
    • Cunha, S.1    Odijk, T.2    Suleymanoglu, E.3    Woldringh, C.L.4
  • 20
    • 18144393456 scopus 로고    scopus 로고
    • Restricted diffusion of DNA segments within the isolated Escherichia coli nucleoid
    • DOI 10.1016/j.jsb.2005.02.004
    • Cunha S, Woldringh C L and Odijk T 2005 Restricted diffusion of DNA segments within the isolated Escherichia coli nucleoid J. Struct. Biol. 150 22632 (Pubitemid 40615747)
    • (2005) Journal of Structural Biology , vol.150 , Issue.2 , pp. 226-232
    • Cunha, S.1    Woldringh, C.L.2    Odijk, T.3
  • 21
    • 33751098486 scopus 로고    scopus 로고
    • Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation
    • DOI 10.1038/nature05283, PII NATURE05283
    • Dame R T, Noom M C and Wuite G J L 2006 Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation Nature 444 38790 (Pubitemid 44764116)
    • (2006) Nature , vol.444 , Issue.7117 , pp. 387-390
    • Dame, R.T.1    Noom, M.C.2    Wuite, G.J.L.3
  • 22
    • 79959843457 scopus 로고    scopus 로고
    • Chromosomal macrodomains and associated proteins: Implications for DNA organization and replication in gram negative bacteria
    • 10.1371/journal.pgen.1002123 1553-7404 e1002123
    • Dame R T, Kalmykowa O J and Grainger D C 2011 Chromosomal macrodomains and associated proteins: implications for DNA organization and replication in gram negative bacteria PLoS Genet. 7 e1002123
    • (2011) PLoS Genet. , vol.7 , Issue.6
    • Dame, R.T.1    Kalmykowa, O.J.2    Grainger, D.C.3
  • 23
    • 77649261823 scopus 로고    scopus 로고
    • Compartmentalization by directional gene expression
    • 10.1073/pnas.0908919107 0027-8424
    • Daube S S, Bracha D, Buxboim A and Bar-Ziv R H 2010 Compartmentalization by directional gene expression Proc. Natl Acad. Sci. USA 107 283641
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , Issue.7 , pp. 2836-2841
    • Daube, S.S.1    Bracha, D.2    Buxboim, A.3    Bar-Ziv, R.H.4
  • 24
    • 19944406574 scopus 로고
    • Dynamics of entangled polymer solutions: I. The Rouse model
    • 10.1021/ma60052a011 0024-9297
    • DeGennes P G 1976 Dynamics of entangled polymer solutions: I. The Rouse model Macromolecules 9 587
    • (1976) Macromolecules , vol.9 , Issue.4 , pp. 587
    • Degennes, P.G.1
  • 26
    • 38849141628 scopus 로고    scopus 로고
    • Intracellular mobility of plasmid DNA is limited by the para family of partitioning systems
    • DOI 10.1111/j.1365-2958.2007.06066.x
    • Derman A I, Lim-Fong G and Pogliano J 2008 Intracellular mobility of plasmid DNA is limited by the parA family of partitioning systems Mol. Microbiol. 67 93546 (Pubitemid 351207325)
    • (2008) Molecular Microbiology , vol.67 , Issue.5 , pp. 935-946
    • Derman, A.I.1    Lim-Fong, G.2    Pogliano, J.3
  • 27
    • 78649882848 scopus 로고    scopus 로고
    • DNA condensation in bacteria: Interplay between macromolecular crowding and nucleoid proteins
    • 10.1016/j.biochi.2010.06.024 0300-9084
    • de Vries R 2010 DNA condensation in bacteria: Interplay between macromolecular crowding and nucleoid proteins Biochimie 92 171521
    • (2010) Biochimie , vol.92 , Issue.12 , pp. 1715-1721
    • De Vries, R.1
  • 28
    • 0034195169 scopus 로고    scopus 로고
    • Binding of molecules to DNA and other semiflexible polymers
    • 10.1103/PhysRevE.61.6740 1063-651X E
    • Diamant H and Andelman D 2000 Binding of molecules to DNA and other semiflexible polymers Phys. Rev. E 61 67409
    • (2000) Phys. Rev. , vol.61 , Issue.6 , pp. 6740-6749
    • Diamant, H.1    Andelman, D.2
  • 29
    • 76949089832 scopus 로고    scopus 로고
    • Bacterial nucleoid-associated proteins, nucleoid structure and gene expression
    • 10.1038/nrmicro2261 1740-1526
    • Dillon S C and Dorman C J 2010 Bacterial nucleoid-associated proteins, nucleoid structure and gene expression Nature Rev. Microbiol. 8 18595
    • (2010) Nature Rev. Microbiol. , vol.8 , Issue.3 , pp. 185-195
    • Dillon, S.C.1    Dorman, C.J.2
  • 30
    • 68249087576 scopus 로고    scopus 로고
    • Dynamics of semiflexible treelike polymeric networks
    • 10.1063/1.3184797 0021-9606 044905
    • Dolgushev M and Blumen A 2009 Dynamics of semiflexible treelike polymeric networks J. Chem. Phys. 131 044905
    • (2009) J. Chem. Phys. , vol.131 , Issue.4
    • Dolgushev, M.1    Blumen, A.2
  • 31
    • 0344851112 scopus 로고
    • The entropy of a confined polymer: I
    • 10.1088/0305-4470/2/2/001 0022-3689
    • Edwards S F and Freed K F 1969 The entropy of a confined polymer: I. J. Phys. A: Gen. Phys. 2 145
    • (1969) J. Phys. A: Gen. Phys. , vol.2 , Issue.2 , pp. 145
    • Edwards, S.F.1    Freed, K.F.2
  • 33
    • 33750495828 scopus 로고    scopus 로고
    • Organization of the Escherichia coli chromosome into macrodomains and its possible functional implications
    • DOI 10.1016/j.jsb.2006.07.010, PII S104784770600219X
    • Espéli O and Boccard F 2006 Organization of the Escherichia coli chromosome into macrodomains and its possible functional implications J. Struct. Biol. 156 30410 (Pubitemid 44666450)
    • (2006) Journal of Structural Biology , vol.156 , Issue.2 , pp. 304-310
    • Espeli, O.1    Boccard, F.2
  • 34
    • 44249103292 scopus 로고    scopus 로고
    • DNA dynamics vary according to macrodomain topography in the E. coli chromosome
    • DOI 10.1111/j.1365-2958.2008.06239.x
    • Espéli O, Mercier R and Boccard F 2008 DNA dynamics vary according to macrodomain topography in the E. coli chromosome Mol. Microbiol. 68 141827 (Pubitemid 351725253)
    • (2008) Molecular Microbiology , vol.68 , Issue.6 , pp. 1418-1427
    • Espeli, O.1    Mercier, R.2    Boccard, F.3
  • 35
    • 79960808394 scopus 로고    scopus 로고
    • DNA compaction: Fundamentals and applications
    • 10.1039/c1sm05373f 1744-683X
    • Estevez-Torres A and Baigl D 2011 DNA compaction: fundamentals and applications Soft Matter 7 674656
    • (2011) Soft Matter , vol.7 , Issue.15 , pp. 6746-6756
    • Estevez-Torres, A.1    Baigl, D.2
  • 37
    • 84863117103 scopus 로고    scopus 로고
    • A model for Escherichia coli chromosome packaging supports transcription factor-induced DNA domain formation
    • 10.1093/nar/gkr779 0305-1048
    • Fritsche M, Li S, Heermann D W and Wiggins P A 2011 A model for Escherichia coli chromosome packaging supports transcription factor-induced DNA domain formation Nucl. Acids Res. 40 97280
    • (2011) Nucl. Acids Res. , vol.40 , Issue.3 , pp. 972-980
    • Fritsche, M.1    Li, S.2    Heermann, D.W.3    Wiggins, P.A.4
  • 38
    • 0001966018 scopus 로고
    • Linear viscoelasticity in Gaussian networks
    • 10.1021/ma60074a032 0024-9297
    • Graessley W W 1980 Linear viscoelasticity in Gaussian networks Macromolecules 13 3726
    • (1980) Macromolecules , vol.13 , Issue.2 , pp. 372-376
    • Graessley, W.W.1
  • 40
    • 33750000118 scopus 로고    scopus 로고
    • Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome
    • DOI 10.1093/nar/gkl542
    • Grainger D C, Hurd D, Goldberg M D and Busby S J W 2006 Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome Nucl. Acids Res. 34 464252 (Pubitemid 44567058)
    • (2006) Nucleic Acids Research , vol.34 , Issue.16 , pp. 4642-4652
    • Grainger, D.C.1    Hurd, D.2    Goldberg, M.D.3    Busby, S.J.W.4
  • 41
    • 33846659467 scopus 로고    scopus 로고
    • Transcription factor distribution in Escherichia coli: Studies with FNR protein
    • DOI 10.1093/nar/gkl1023
    • Grainger D C, Aiba H, Hurd D, Browning D F and Busby S J 2007 Transcription factor distribution in Escherichia coli: studies with FNR protein Nucl. Acids Res. 35 26978 (Pubitemid 46189851)
    • (2007) Nucleic Acids Research , vol.35 , Issue.1 , pp. 269-278
    • Grainger, D.C.1    Aiba, H.2    Hurd, D.3    Browning, D.F.4    Busby, S.J.W.5
  • 42
    • 44249126516 scopus 로고    scopus 로고
    • Selective repression by Fis and H-NS at the Escherichia coli dps promoter
    • DOI 10.1111/j.1365-2958.2008.06253.x
    • Grainger D C, Goldberg M D, Lee D J and Busby S J 2008 Selective repression by Fis and H-NS at the Escherichia coli dps promoter Mol. Microbiol. 68 136677 (Pubitemid 351725264)
    • (2008) Molecular Microbiology , vol.68 , Issue.6 , pp. 1366-1377
    • Grainger, D.C.1    Goldberg, M.D.2    Lee, D.J.3    Busby, S.J.W.4
  • 44
    • 84956136196 scopus 로고
    • Crumpled globule model of the three-dimensional structure of DNA
    • 10.1209/0295-5075/23/5/012 0295-5075 012
    • Grosberg A, Rabin Y, Havlin S and Neer A 1993 Crumpled globule model of the three-dimensional structure of DNA Europhys. Lett. 23 3738
    • (1993) Europhys. Lett. , vol.23 , Issue.5 , pp. 373-378
    • Grosberg, A.1    Rabin, Y.2    Havlin, S.3    Neer, A.4
  • 45
    • 0031751368 scopus 로고    scopus 로고
    • Fused nucleoids resegregate faster than cell elongation in Escherichia coli pbpB(Ts) filaments after release from chloramphenicol inhibition
    • Helvoort J M V, Huls P G, Vischer N O and Woldringh C L 1998 Fused nucleoids resegregate faster than cell elongation in Escherichia coli pbpB(Ts) filaments after release from chloramphenicol inhibition Microbiology 144 130917 (Pubitemid 28233835)
    • (1998) Microbiology , vol.144 , Issue.5 , pp. 1309-1317
    • Helvoort, J.M.V.1    Huls, P.G.2    Vischer, N.O.E.3    Woldringh, C.L.4
  • 46
    • 48849092363 scopus 로고    scopus 로고
    • Random time-scale invariant diffusion and transport coefficients
    • 10.1103/PhysRevLett.101.058101 0031-9007 058101
    • He Y, Burov S, Metzler R and Barkai E 2008 Random time-scale invariant diffusion and transport coefficients Phys. Rev. Lett. 101 058101
    • (2008) Phys. Rev. Lett. , vol.101 , Issue.5
    • He, Y.1    Burov, S.2    Metzler, R.3    Barkai, E.4
  • 47
    • 35349030892 scopus 로고    scopus 로고
    • Dynamic conformational behavior and molecular interaction discrimination of DNA/binder complexes by single-chain stretching in a microdevice
    • DOI 10.1002/cbic.200700229
    • Huang W-H, Zinchenko A A, Pawlak C, Chen Y and Baigl D 2007 Dynamic conformational behavior and molecular interaction discrimination of DNA/binder complexes by single-chain stretching in a microdevice Chembiochem 8 17714 (Pubitemid 47612863)
    • (2007) ChemBioChem , vol.8 , Issue.15 , pp. 1771-1774
    • Huang, W.-H.1    Zinchenko, A.A.2    Pawlak, C.3    Chen, Y.4    Baigl, D.5
  • 48
    • 79961062430 scopus 로고    scopus 로고
    • Collapse transition of randomly branched polymers: Renormalized field theory
    • 10.1103/PhysRevE.83.051126 1539-3755 E 051126
    • Janssen H-K and Stenull O 2011 Collapse transition of randomly branched polymers: renormalized field theory Phys. Rev. E 83 051126
    • (2011) Phys. Rev. , vol.83 , Issue.5
    • Janssen, H.-K.1    Stenull, O.2
  • 49
    • 0942300123 scopus 로고    scopus 로고
    • Dynamics of randomly branched polymers: Configuration averages and solvable models
    • 10.1103/PhysRevE.68.051106 1063-651X E 051106
    • Jasch F, von Ferber Ch and Blumen A 2003 Dynamics of randomly branched polymers: configuration averages and solvable models Phys. Rev. E 68 051106
    • (2003) Phys. Rev. , vol.68 , Issue.5
    • Jasch, F.1    Von Ferber, Ch.2    Blumen, A.3
  • 50
    • 0035801637 scopus 로고    scopus 로고
    • A moving DNA replication factory in Caulobacter crescentus
    • DOI 10.1093/emboj/20.17.4952
    • Jensen R B, Wang S C and Shapiro L 2001 A moving DNA replication factory in Caulobacter crescentus EMBO J. 20 495263 (Pubitemid 32848647)
    • (2001) EMBO Journal , vol.20 , Issue.17 , pp. 4952-4963
    • Jensen, R.B.1    Wang, S.C.2    Shapiro, L.3
  • 51
    • 33750529760 scopus 로고    scopus 로고
    • Coupling the distribution of RNA polymerase to global gene regulation and the dynamic structure of the bacterial nucleoid in Escherichia coli
    • DOI 10.1016/j.jsb.2006.07.005, PII S1047847706002139
    • Jin D J and Cabrera J E 2006 Coupling the distribution of RNA polymerase to global gene regulation and the dynamic structure of the bacterial nucleoid in Escherichia coli J. Struct. Biol. 156 28491 (Pubitemid 44666448)
    • (2006) Journal of Structural Biology , vol.156 , Issue.2 , pp. 284-291
    • Jin, D.J.1    Cabrera, J.E.2
  • 52
    • 79952591477 scopus 로고    scopus 로고
    • Escherichia coli sister chromosome separation includes an abrupt global transition with concomitant release of late-splitting intersister snaps
    • 10.1073/pnas.1019593108 0027-8424
    • 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 276570
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , Issue.7 , 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
  • 53
    • 78651347562 scopus 로고    scopus 로고
    • Overlapping two self-avoiding polymers in a closed cylindrical pore: Implications for chromosome segregation in a bacterial cell
    • 10.1103/PhysRevE.82.051926 1539-3755 E
    • 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 82 5192631
    • (2010) Phys. Rev. , vol.82 , Issue.5 , pp. 51926-51931
    • Jung, Y.1    Ha, B.-Y.2
  • 54
    • 77649198707 scopus 로고    scopus 로고
    • Spatial and topological organization of DNA chains induced by gene co-localization
    • 10.1371/journal.pcbi.1000678 1553-7358 e1000678
    • Junier I, Martin O and Képès F 2010 Spatial and topological organization of DNA chains induced by gene co-localization PLoS Comput. Biol. 6 e1000678
    • (2010) PLoS Comput. Biol. , vol.6 , Issue.2
    • Junier, I.1    Martin, O.2    Képès, F.3
  • 55
    • 77954719357 scopus 로고    scopus 로고
    • Entropy as the driver of chromosome segregation
    • 10.1038/nrmicro2391 1740-1526
    • Jun S and Wright A 2010 Entropy as the driver of chromosome segregation Nature Rev. Micro. 8 6007
    • (2010) Nature Rev. Micro. , vol.8 , Issue.8 , pp. 600-607
    • Jun, S.1    Wright, A.2
  • 59
    • 0017045430 scopus 로고
    • Electron microscopy of membrane free folded chromosomes from Escherichia coli
    • DOI 10.1007/BF00328479
    • Kavenoff R and Bowen B C 1976 Electron microscopy of membrane-free folded chromosomes from Escherichia coli Chromosoma 59 89101 (Pubitemid 8002265)
    • (1976) Chromosoma , vol.59 , Issue.2 , pp. 89-101
    • Kavenoff, R.1    Bowen, B.C.2
  • 60
    • 17444389603 scopus 로고    scopus 로고
    • Transcription-based solenoidal model of chromosome
    • 10.1159/000082184 1424-8492
    • Képès F and Valliant C 2003 Transcription-based solenoidal model of chromosome ComPlexUs 1 17180
    • (2003) ComPlexUs , vol.1 , Issue.4 , pp. 171-180
    • Képès, F.1    Valliant, C.2
  • 61
    • 3042660143 scopus 로고    scopus 로고
    • Fundamental structural units of the Escherichia coli nucleoid revealed by atomic force microscopy
    • DOI 10.1093/nar/gkh512
    • Kim J, Yoshimura S H, Hizume K, Ohniwa R L, Ishihama A and Takeyasu K 2004 Fundamental structural units of the Escherichia coli nucleoid revealed by atomic force microscopy Nucl. Acids Res. 32 198292 (Pubitemid 38842538)
    • (2004) Nucleic Acids Research , vol.32 , Issue.6 , pp. 1982-1992
    • Kim, J.1    Yoshimura, S.H.2    Hizume, K.3    Ohniwa, R.L.4    Ishihama, A.5    Takeyasu, K.6
  • 62
    • 53449099613 scopus 로고    scopus 로고
    • Bacterial partitioning proteins affect the subcellular location of broad-host-range plasmid RK2
    • 10.1099/mic.0.2008/018762-0 1350-0872
    • Kolatka K, Witosinska M, Pierechod M and Konieczny I 2008 Bacterial partitioning proteins affect the subcellular location of broad-host-range plasmid RK2 Microbiology 154 284756
    • (2008) Microbiology , vol.154 , Issue.9 , pp. 2847-2856
    • Kolatka, K.1    Witosinska, M.2    Pierechod, M.3    Konieczny, I.4
  • 64
    • 33645717867 scopus 로고    scopus 로고
    • Mass fractal dimension of the ribosome and implication of its dynamic characteristics
    • 10.1103/PhysRevE.73.042901 1539-3755 E 042901
    • Lee C-Y 2006 Mass fractal dimension of the ribosome and implication of its dynamic characteristics Phys. Rev. E 73 042901
    • (2006) Phys. Rev. , vol.73 , Issue.4
    • Lee, C.-Y.1
  • 65
    • 22144463194 scopus 로고    scopus 로고
    • Roles for replichores and macrodomains in segregation of the Escherichia coli chromosome
    • DOI 10.1038/sj.embor.7400428
    • Lesterlin C, Mercier R, Boccard F, Barre F X and Cornet F 2005 Roles for replichores and macrodomains in segregation of the Escherichia coli chromosome EMBO Rep. 6 55762 (Pubitemid 40973965)
    • (2005) EMBO Reports , vol.6 , Issue.6 , pp. 557-562
    • Lesterlin, C.1    Mercier, R.2    Boccard, F.3    Barre, F.-X.4    Cornet, F.5
  • 66
    • 70349873824 scopus 로고    scopus 로고
    • Comprehensive mapping of long-range interactions reveals folding principles of the human genome
    • 10.1126/science.1181369 0036-8075
    • Lieberman-Aiden E et al 2009 Comprehensive mapping of long-range interactions reveals folding principles of the human genome Science 326 28993
    • (2009) Science , vol.326 , Issue.5950 , pp. 289-293
    • Lieberman-Aiden, E.1
  • 67
    • 84860359300 scopus 로고    scopus 로고
    • Gene silencing H-NS paralogue StpA forms a rigid protein filament along DNA that blocks DNA accessibility
    • 10.1093/nar/gkr1247 0305-1048
    • Lim C J, Whang Y R, Kenney L J and Yan J 2011 Gene silencing H-NS paralogue StpA forms a rigid protein filament along DNA that blocks DNA accessibility Nucl. Acids Res. 40 331628
    • (2011) Nucl. Acids Res. , vol.40 , Issue.8 , pp. 3316-3328
    • Lim, C.J.1    Whang, Y.R.2    Kenney, L.J.3    Yan, J.4
  • 68
    • 77349104369 scopus 로고    scopus 로고
    • Replication-directed sister chromosome alignment in Escherichia coli
    • 10.1111/j.1365-2958.2009.06791.x 0950-382X
    • Liu X, Wang X, Reyes-Lamothe R and Sherratt D 2010 Replication-directed sister chromosome alignment in Escherichia coli Mol. Microbiol. 75 10907
    • (2010) Mol. Microbiol. , vol.75 , Issue.5 , pp. 1090-1097
    • Liu, X.1    Wang, X.2    Reyes-Lamothe, R.3    Sherratt, D.4
  • 69
    • 33750527566 scopus 로고    scopus 로고
    • The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: A molecular perspective
    • DOI 10.1016/j.jsb.2006.05.006, PII S1047847706001614
    • Luijsterburg M S, Noom M C, Wuite G J and Dame R T 2006 The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective J. Struct. Biol. 156 26272 (Pubitemid 44666444)
    • (2006) Journal of Structural Biology , vol.156 , Issue.2 , pp. 262-272
    • Luijsterburg, M.S.1    Noom, M.C.2    Wuite, G.J.L.3    Dame, R.Th.4
  • 70
    • 33845295824 scopus 로고    scopus 로고
    • The depletion attraction: An underappreciated force driving cellular organization
    • DOI 10.1083/jcb.200609066
    • Marenduzzo D, Finan K and Cook P R 2006a The depletion attraction: an underappreciated force driving cellular organization J. Cell. Biol. 175 6816 (Pubitemid 44878499)
    • (2006) Journal of Cell Biology , vol.175 , Issue.5 , pp. 681-686
    • Marenduzzo, D.1    Finan, K.2    Cook, P.R.3
  • 71
    • 33646195227 scopus 로고    scopus 로고
    • Entropy-driven genome organization
    • 10.1529/biophysj.105.077685 0006-3495
    • Marenduzzo D, Micheletti C and Cook P R 2006b Entropy-driven genome organization Biophys. J. 90 371221
    • (2006) Biophys. J. , vol.90 , Issue.10 , pp. 3712-3721
    • Marenduzzo, D.1    Micheletti, C.2    Cook, P.R.3
  • 73
    • 66749191436 scopus 로고    scopus 로고
    • Linking topology of tethered polymer rings with applications to chromosome segregation and estimation of the knotting length
    • 10.1103/PhysRevE.79.051905 1539-3755 E 051905
    • Marko J F 2009 Linking topology of tethered polymer rings with applications to chromosome segregation and estimation of the knotting length Phys. Rev. E 79 051905
    • (2009) Phys. Rev. , vol.79 , Issue.5
    • Marko, J.F.1
  • 74
    • 0037336483 scopus 로고    scopus 로고
    • The micromechanics of DNA
    • 0953-8585
    • Marko J F and Cocco S 2003 The micromechanics of DNA Phys. World 3741 http://www.phys.ens.fr/cocco/Art/24physworld.pdf
    • (2003) Phys. World , pp. 37-41
    • Marko, J.F.1    Cocco, S.2
  • 75
    • 40649089205 scopus 로고    scopus 로고
    • Dissecting the logical types of network control in gene expression profiles
    • DOI 10.1186/1752-0509-2-18
    • Marr C, Geertz M, Hütt M T and Muskhelishvili G 2008 Dissecting the logical types of network control in gene expression profiles BMC Syst. Biol. 2 18 (Pubitemid 351372426)
    • (2008) BMC Systems Biology , vol.2 , pp. 18
    • Marr, C.1    Geertz, M.2    Hutt, M.-T.3    Muskhelishvili, G.4
  • 76
    • 62649137535 scopus 로고    scopus 로고
    • Spatially confined folding of chromatin in the interphase nucleus
    • 10.1073/pnas.0809501106 0027-8424
    • Mateos-Langerak J et al 2009 Spatially confined folding of chromatin in the interphase nucleus Proc. Natl Acad. Sci. USA 106 38127
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , Issue.10 , pp. 3812-3817
    • Mateos-Langerak, J.1
  • 77
    • 77952268971 scopus 로고    scopus 로고
    • Chromosomal periodicity and positional networks of genes in Escherichia coli
    • 10.1038/msb.2010.21 1744-4292
    • Mathelier A and Carbone A 2010 Chromosomal periodicity and positional networks of genes in Escherichia coli Mol. Syst. Biol. 6 366
    • (2010) Mol. Syst. Biol. , vol.6 , pp. 366
    • Mathelier, A.1    Carbone, A.2
  • 78
    • 63449089710 scopus 로고    scopus 로고
    • A systematic in vitro study of nucleoprotein complexes formed by bacterial nucleoid-associated proteins revealing novel types of DNA organization
    • 10.1016/j.jmb.2009.02.050 0022-2836
    • Maurer S, Fritz J and Muskhelishvili G 2009 A systematic in vitro study of nucleoprotein complexes formed by bacterial nucleoid-associated proteins revealing novel types of DNA organization J. Mol. Biol. 387 126176
    • (2009) J. Mol. Biol. , vol.387 , Issue.5 , pp. 1261-1276
    • Maurer, S.1    Fritz, J.2    Muskhelishvili, G.3
  • 79
    • 79251604784 scopus 로고    scopus 로고
    • The terminal region of theE. coli chromosome localises at the periphery of the nucleoid
    • 10.1186/1471-2180-11-28 1471-2180
    • Meile J-C, Mercier R, Stouf M, Pages C, Bouet J-Y and Cornet F 2011 The terminal region of theE. coli chromosome localises at the periphery of the nucleoid BMC Microbiol. 11 28
    • (2011) BMC Microbiol. , vol.11 , Issue.1 , pp. 28
    • Meile, J.-C.1    Mercier, R.2    Stouf, M.3    Pages, C.4    Bouet, J.-Y.5    Cornet, F.6
  • 80
    • 54949146519 scopus 로고    scopus 로고
    • The MatP/matS site-specific system organizes the terminus region of theE. coli chromosome into a macrodomain
    • 10.1016/j.cell.2008.08.031 0092-8674
    • Mercier R, Petit M-A, Schbath S, Robin S, Karoui M El, Boccard F and Espéli O 2008 The MatP/matS site-specific system organizes the terminus region of theE. coli chromosome into a macrodomain Cell 135 47585
    • (2008) Cell , vol.135 , Issue.3 , pp. 475-485
    • Mercier, R.1    Petit, M.-A.2    Schbath, S.3    Robin, S.4    El, K.M.5    Boccard, F.6    Espéli, O.7
  • 81
    • 79952279926 scopus 로고    scopus 로고
    • The fractal globule as a model of chromatin architecture in the cell
    • 10.1007/s10577-010-9177-0 0967-3849
    • Mirny L A 2011 The fractal globule as a model of chromatin architecture in the cell Chromosome Res. 19 3751
    • (2011) Chromosome Res. , vol.19 , Issue.1 , pp. 37-51
    • Mirny, L.A.1
  • 82
    • 13144257718 scopus 로고    scopus 로고
    • Topological insulators inhibit diffusion of transcription-induced positive supercoils in the chromosome of Escherichia coli
    • DOI 10.1111/j.1365-2958.2004.04411.x
    • Moulin L, Rahmouni A R and Boccard F 2005 Topological insulators inhibit diffusion of transcription-induced positive supercoils in the chromosome of Escherichia coli Mol. Microbiol. 55 60110 (Pubitemid 40179390)
    • (2005) Molecular Microbiology , vol.55 , Issue.2 , pp. 601-610
    • Moulin, L.1    Rahmouni, A.R.2    Boccard, F.3
  • 83
    • 77949706153 scopus 로고    scopus 로고
    • General organisational principles of the transcriptional regulation system: A tree or a circle?
    • 10.1039/b909192k 1742-206X
    • Muskhelishvili G, Sobetzko P, Geertz M and Berger M 2010 General organisational principles of the transcriptional regulation system: a tree or a circle? Mol. Biosyst. 6 66276
    • (2010) Mol. Biosyst. , vol.6 , Issue.4 , pp. 662-676
    • Muskhelishvili, G.1    Sobetzko, P.2    Geertz, M.3    Berger, M.4
  • 84
    • 66149104488 scopus 로고    scopus 로고
    • Thermodynamic pathways to genome spatial organization in the cell nucleus
    • 10.1016/j.bpj.2008.12.3919 0006-3495
    • Nicodemi M and Prisco A 2009 Thermodynamic pathways to genome spatial organization in the cell nucleus Biophys. J. 96 216877
    • (2009) Biophys. J. , vol.96 , Issue.6 , pp. 2168-2177
    • Nicodemi, M.1    Prisco, A.2
  • 85
    • 33749177128 scopus 로고    scopus 로고
    • The Escherichia coli chromosome is organized with the left and right chromosome arms in separate cell halves
    • DOI 10.1111/j.1365-2958.2006.05346.x
    • Nielsen H J, Ottesen J R, Youngren B, Austin S J and Hansen F G 2006 The Escherichia coli chromosome is organized with the left and right chromosome arms in separate cell halves Mol. Microbiol. 62 3318 (Pubitemid 44477225)
    • (2006) Molecular Microbiology , vol.62 , Issue.2 , pp. 331-338
    • Nielsen, H.J.1    Ottesen, J.R.2    Youngren, B.3    Austin, S.J.4    Hansen, F.G.5
  • 86
    • 36749101359 scopus 로고    scopus 로고
    • Dynamics of Escherichia coli chromosome segregation during multifork replication
    • DOI 10.1128/JB.01212-07
    • Nielsen H J, Youngren B, Hansen F G and Austin S 2007 Dynamics of Escherichia coli chromosome segregation during multifork replication J. Bacteriol. 189 86606 (Pubitemid 350210036)
    • (2007) Journal of Bacteriology , vol.189 , Issue.23 , pp. 8660-8666
    • Nielsen, H.J.1    Youngren, B.2    Hansen, F.G.3    Austin, S.4
  • 87
    • 0034650256 scopus 로고    scopus 로고
    • Dynamic organization of chromosomal DNA in Escherichia coli
    • 0890-9369
    • Niki H, Yamaichi Y and Hiraga S 2000 Dynamic organization of chromosomal DNA in Escherichia coli Genes Dev. 14 21223
    • (2000) Genes Dev.
    • Niki, H.1    Yamaichi, Y.2    Hiraga, S.3
  • 88
    • 0029165965 scopus 로고
    • Hypothesis: Chromosome separation in Escherichia coli involves autocatalytic gene expression, transertion and membrane-domain formation
    • 10.1111/j.1365-2958.1995.tb02330.x 0950-382X
    • Norris V 1995 Hypothesis: chromosome separation in Escherichia coli involves autocatalytic gene expression, transertion and membrane-domain formation Mol. Microbiol. 16 10517
    • (1995) Mol. Microbiol. , vol.16 , Issue.6 , pp. 1051-1057
    • Norris, V.1
  • 89
    • 0028697888 scopus 로고
    • The origin evolution of species differences in Escherichia coli and salmonella typhimurium
    • 1023-294X
    • Ochman H and Groisman E A 1994 The origin evolution of species differences in Escherichia coli and salmonella typhimurium EXS 69 47993
    • (1994) EXS
    • Ochman, H.1    Groisman, E.A.2
  • 90
    • 0032050083 scopus 로고    scopus 로고
    • Dimensions of a plectonemic DNA supercoil under fairly general perturbations
    • PII S0378437197005888
    • Odijk T and Ubbink J 1998 Dimensions of a plectonemic DNA supercoil under fairly general perturbations Physica A 252 616 (Pubitemid 128417612)
    • (1998) Physica A: Statistical Mechanics and its Applications , vol.252 , Issue.1-2 , pp. 61-66
    • Odijk, T.1    Ubbink, J.2
  • 91
    • 0032514107 scopus 로고    scopus 로고
    • Osmotic compaction of supercoiled DNA into a bacterial nucleoid
    • DOI 10.1016/S0301-4622(98)00115-X, PII S030146229800115X
    • Odijk T 1998 Osmotic compaction of supercoiled DNA into a bacterial nucleoid Biophys. Chem. 73 239 (Pubitemid 28325691)
    • (1998) Biophysical Chemistry , vol.73 , Issue.1-2 , pp. 23-29
    • Odijk, T.1
  • 92
    • 79955588726 scopus 로고    scopus 로고
    • Proteomic analyses of nucleoid-associated proteins in Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, and Staphylococcus aureus
    • 10.1371/journal.pone.0019172 1932-6203
    • Ohniwa R L, Ushijima Y, Saito S and Morikawa K 2011 Proteomic analyses of nucleoid-associated proteins in Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, and Staphylococcus aureus PLoS One 6 e19172
    • (2011) PLoS One , vol.6 , Issue.4 , pp. 19172
    • Ohniwa, R.L.1    Ushijima, Y.2    Saito, S.3    Morikawa, K.4
  • 93
    • 33751580332 scopus 로고    scopus 로고
    • Dynamic state of DNA topology is essential for genome condensation in bacteria
    • DOI 10.1038/sj.emboj.7601414, PII 7601414
    • Ohniwa R L, Morikawa K, Kim J, Ohta T, Ishihama A, Wada C and Takeyasu K 2006 Dynamic state of DNA topology is essential for genome condensation in bacteria EMBO J. 25 5591602 (Pubitemid 44847199)
    • (2006) EMBO Journal , vol.25 , Issue.23 , pp. 5591-5602
    • Ohniwa, R.L.1    Morikawa, K.2    Kim, J.3    Ohta, T.4    Ishihama, A.5    Wada, C.6    Takeyasu, K.7
  • 94
    • 33750898424 scopus 로고    scopus 로고
    • Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase
    • DOI 10.1093/dnares/dsl009
    • Oshima T, Ishikawa S, Kurokawa K, Aiba H and Ogasawara N 2006 Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase DNA Res. 13 14153 (Pubitemid 44726365)
    • (2006) DNA Research , vol.13 , Issue.4 , pp. 141-153
    • Oshima, T.1    Ishikawa, S.2    Kurokawa, K.3    Aiba, H.4    Ogasawara, N.5
  • 95
    • 0032519183 scopus 로고    scopus 로고
    • Dynamics of the swelling or collapse of a homopolymer
    • 10.1209/epl/i1998-00175-8 0295-5075 467
    • Pitard E and Orland H 1998 Dynamics of the swelling or collapse of a homopolymer Europhys. Lett. 41 46772
    • (1998) Europhys. Lett. , vol.41 , Issue.4 , pp. 467-472
    • Pitard, E.1    Orland, H.2
  • 96
    • 3142774839 scopus 로고    scopus 로고
    • Topological domain structure of the Escherichia coli chromosome
    • DOI 10.1101/gad.1207504
    • Postow L, Hardy C D, Arsuaga J and Cozzarelli N R 2004 Topological domain structure of the Escherichia coli chromosome Genes Dev. 18 176679 (Pubitemid 38938191)
    • (2004) Genes and Development , vol.18 , Issue.14 , pp. 1766-1779
    • Postow, L.1    Hardy, C.D.2    Arsuaga, J.3    Cozzarelli, N.R.4
  • 97
    • 77956363480 scopus 로고    scopus 로고
    • Anomalies in the vibrational dynamics of proteins are a consequence of fractal-like structure
    • 10.1073/pnas.1002018107 0027-8424
    • Reuveni S, Granek R and Klafter J 2010 Anomalies in the vibrational dynamics of proteins are a consequence of fractal-like structure Proc. Natl Acad. Sci. USA 107 13696700
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , Issue.31 , pp. 13696-13700
    • Reuveni, S.1    Granek, R.2    Klafter, J.3
  • 98
    • 41149121779 scopus 로고    scopus 로고
    • Independent Positioning and Action of Escherichia coli Replisomes in Live Cells
    • DOI 10.1016/j.cell.2008.01.044, PII S0092867408002092
    • Reyes-Lamothe R, Possoz C, Danilova O and Sherratt D J 2008 Independent positioning and action of Escherichia coli replisomes in live cells Cell 133 90102 (Pubitemid 351442987)
    • (2008) Cell , vol.133 , Issue.1 , pp. 90-102
    • Reyes-Lamothe, R.1    Possoz, C.2    Danilova, O.3    Sherratt, D.J.4
  • 100
    • 58449118337 scopus 로고    scopus 로고
    • The organization of the bacterial genome
    • 10.1146/annurev.genet.42.110807.091653 0066-4197
    • Rocha E P C 2008 The organization of the bacterial genome Annu. Rev. Genet. 42 21133
    • (2008) Annu. Rev. Genet. , vol.42 , Issue.1 , pp. 211-233
    • Rocha, E.P.C.1
  • 101
    • 34147130136 scopus 로고    scopus 로고
    • Internal structure and dynamics of isolated Escherichia coli nucleoids assessed by fluorescence correlation spectroscopy
    • DOI 10.1529/biophysj.106.095729
    • Romantsov T, Fishov I and Krichevsky O 2007 Internal structure and dynamics of isolated Escherichia coli nucleoids assessed by fluorescence correlation spectroscopy Biophys. J. 92 287584 (Pubitemid 46557861)
    • (2007) Biophysical Journal , vol.92 , Issue.8 , pp. 2875-2884
    • Romantsov, T.1    Fishov, I.2    Krichevsky, O.3
  • 102
    • 78649639015 scopus 로고    scopus 로고
    • Dynamic distribution of SeqA protein across the chromosome of Escherichia coli K-12
    • 10.1128/mBio.00012-10 2150-7511
    • Sánchez-Romero M A, Busby S J W, Dyer N P, Ott S, Millard A D and Grainger D C 2010 Dynamic distribution of SeqA protein across the chromosome of Escherichia coli K-12 MBio 1 e0012-1
    • (2010) MBio , vol.1 , Issue.1
    • Sánchez-Romero, M.A.1    Busby, S.J.W.2    Dyer, N.P.3    Ott, S.4    Millard, A.D.5    Grainger, D.C.6
  • 104
    • 79951661202 scopus 로고    scopus 로고
    • Gene clusters reflecting macrodomain structure respond to nucleoid perturbations
    • 10.1039/c0mb00213e 1742-206X
    • Scolari V F, Bassetti B, Sclavi B and Lagomarsino M C 2011 Gene clusters reflecting macrodomain structure respond to nucleoid perturbations Mol. Biosyst. 7 87888
    • (2011) Mol. Biosyst. , vol.7 , Issue.3 , pp. 878-888
    • Scolari, V.F.1    Bassetti, B.2    Sclavi, B.3    Lagomarsino, M.C.4
  • 105
    • 79960943853 scopus 로고    scopus 로고
    • Bacterial growth laws and their applications
    • 10.1016/j.copbio.2011.04.014 0958-1669
    • Scott M and Hwa T 2011 Bacterial growth laws and their applications Curr. Opin. Biotechnol. 22 55965
    • (2011) Curr. Opin. Biotechnol. , vol.22 , Issue.4 , pp. 559-565
    • Scott, M.1    Hwa, T.2
  • 106
    • 78449268845 scopus 로고    scopus 로고
    • Interdependence of cell growth and gene expression: Origins and consequences
    • 10.1126/science.1192588 0036-8075
    • Scott M, Gunderson C W, Mateescu E M, Zhang Z and Hwa T 2010 Interdependence of cell growth and gene expression: origins and consequences Science 330 1099102
    • (2010) Science , vol.330 , Issue.6007 , pp. 1099-1102
    • Scott, M.1    Gunderson, C.W.2    Mateescu, E.M.3    Zhang, Z.4    Hwa, T.5
  • 107
    • 0041853574 scopus 로고    scopus 로고
    • Bacterial chromosome dynamics
    • DOI 10.1126/science.1084780
    • Sherratt D J 2003 Bacterial chromosome dynamics Science 301 7805 (Pubitemid 36962608)
    • (2003) Science , vol.301 , Issue.5634 , pp. 780-785
    • Sherratt, D.J.1
  • 109
    • 33750954891 scopus 로고    scopus 로고
    • Mechanism of Chromosome Compaction and Looping by the Escherichia coli Nucleoid Protein Fis
    • DOI 10.1016/j.jmb.2006.09.043, PII S0022283606012496
    • Skoko D, Yoo D, Bai H, Schnurr B, Yan J, McLeod S M, Marko J F and Johnson R C 2006 Mechanism of chromosome compaction and looping by the Escherichia coli nucleoid protein fis J. Mol. Biol. 364 77798 (Pubitemid 44737831)
    • (2006) Journal of Molecular Biology , vol.364 , Issue.4 , pp. 777-798
    • Skoko, D.1    Yoo, D.2    Bai, H.3    Schnurr, B.4    Yan, J.5    McLeod, S.M.6    Marko, J.F.7    Johnson, R.C.8
  • 110
    • 0000873404 scopus 로고
    • On the statistics of generalized Gaussian structures: Collapse and random external fields
    • 10.1088/0305-4470/28/23/018 0305-4470
    • Sommer J U and Blumen A 1995 On the statistics of generalized Gaussian structures: collapse and random external fields J. Phys. A: Math. Gen. 28 6669
    • (1995) J. Phys. A: Math. Gen. , vol.28 , Issue.23 , pp. 6669
    • Sommer, J.U.1    Blumen, A.2
  • 111
    • 34247517469 scopus 로고    scopus 로고
    • DNA-protein interactions and bacterial chromosome architecture
    • 1478-3975 R01
    • Stavans J and Oppenheim A 2006 DNA-protein interactions and bacterial chromosome architecture Phys. Biol. 3 R110
    • (2006) Phys. Biol. , vol.3 , Issue.4 , pp. 1-10
    • Stavans, J.1    Oppenheim, A.2
  • 113
    • 65549143001 scopus 로고    scopus 로고
    • A thermodynamic model for the agglomeration of DNA-looping proteins
    • 1742-5468 P11005
    • Sumedha and Weigt M 2008 A thermodynamic model for the agglomeration of DNA-looping proteins J. Stat. Mech. Theory Exp. 2008 P11005
    • (2008) J. Stat. Mech. Theory Exp. , vol.2008 , Issue.11
    • Sumedha1    Weigt, M.2
  • 114
    • 33750531252 scopus 로고    scopus 로고
    • Chromosome organization and segregation in bacteria
    • DOI 10.1016/j.jsb.2006.05.007, PII S1047847706001869
    • Thanbichler M and Shapiro L 2006 Chromosome organization and segregation in bacteria J. Struct. Biol. 156 292303 (Pubitemid 44666446)
    • (2006) Journal of Structural Biology , vol.156 , Issue.2 , pp. 292-303
    • Thanbichler, M.1    Shapiro, L.2
  • 115
    • 27144448812 scopus 로고    scopus 로고
    • The bacterial nucleoid: A highly organized and dynamic structure
    • DOI 10.1002/jcb.20519
    • Thanbichler M, Wang S C and Shapiro L 2005 The bacterial nucleoid: a highly organized and dynamic structure J. Cell. Biochem. 96 50621 (Pubitemid 41504649)
    • (2005) Journal of Cellular Biochemistry , vol.96 , Issue.3 , pp. 506-521
    • Thanbichler, M.1    Wang, S.C.2    Shapiro, L.3
  • 117
    • 77957262402 scopus 로고    scopus 로고
    • Bacterial chromosome organization and segregation
    • 10.1101/cshperspect.a000349 1943-0264 a000349
    • Toro E and Shapiro L 2010 Bacterial chromosome organization and segregation Cold Spring Harb Perspect Biol. 2 a000349
    • (2010) Cold Spring Harb Perspect Biol. , vol.2 , Issue.2
    • Toro, E.1    Shapiro, L.2
  • 118
    • 0000457477 scopus 로고    scopus 로고
    • Architecture of a bacterial chromosome (review)
    • Trun N J and Marko J F 1998 Architecture of a bacterial chromosome (review) Am. Soc. Microbiol. News 64 276
    • (1998) Am. Soc. Microbiol. News , vol.64 , pp. 276
    • Trun, N.J.1    Marko, J.F.2
  • 119
    • 0033062960 scopus 로고    scopus 로고
    • Electrostatic-undulatory theory of plectonemically supercoiled DNA
    • Ubbink J and Odijk T 1999 Electrostatic-undulatory theory of plectonemically supercoiled DNA Biophys. J. 76 250219 (Pubitemid 29264612)
    • (1999) Biophysical Journal , vol.76 , Issue.5 , pp. 2502-2519
    • Ubbink, J.1    Odijk, T.2
  • 120
    • 81255146230 scopus 로고    scopus 로고
    • The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation
    • 10.1016/j.molcel.2011.09.010 1097-2765
    • Umbarger M A et al 2011 The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation Mol. Cell. 44 25264
    • (2011) Mol. Cell. , vol.44 , Issue.2 , pp. 252-264
    • Umbarger, M.A.1
  • 121
    • 9144264275 scopus 로고    scopus 로고
    • Macrodomain organization of the Escherichia coli chromosome
    • DOI 10.1038/sj.emboj.7600434
    • Valens M, Penaud S, Rossignol M, Cornet F and Boccard F 2004 Macrodomain organization of the Escherichia coli chromosome EMBO J. 23 433041 (Pubitemid 39546170)
    • (2004) EMBO Journal , vol.23 , Issue.21 , pp. 4330-4341
    • Valens, M.1    Penaud, S.2    Rossignol, M.3    Cornet, F.4    Boccard, F.5
  • 122
    • 0029978680 scopus 로고    scopus 로고
    • Chloramphenicol causes fusion of separated nucleoids in Escherichia coli K-12 cells and filaments
    • van Helvoort J M, Kool J and Woldringh C L 1996 Chloramphenicol causes fusion of separated nucleoids in Escherichia coli K-12 cells and filaments J. Bacteriol. 178 428993
    • (1996) J. Bacteriol.
    • Van Helvoort, J.M.1    Kool, J.2    Woldringh, C.L.3
  • 124
    • 68349150613 scopus 로고    scopus 로고
    • Statistics of polymer rings in the melt: A numerical simulation study
    • 1478-3975 025013
    • 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 , Issue.2
    • Vettorel, T.1    Grosberg, A.Y.2    Kremer, K.3
  • 126
    • 67651102745 scopus 로고    scopus 로고
    • Protein occupancy landscape of a bacterial genome
    • 10.1016/j.molcel.2009.06.035 1097-2765
    • Vora T, Hottes A K and Tavazoie S 2009 Protein occupancy landscape of a bacterial genome Molecular Cell 35 24753
    • (2009) Molecular Cell , vol.35 , Issue.2 , pp. 247-253
    • Vora, T.1    Hottes, A.K.2    Tavazoie, S.3
  • 127
    • 34250619055 scopus 로고    scopus 로고
    • Genomic analysis of protein-DNA interactions in bacteria: Insights into transcription and chromosome organization
    • DOI 10.1111/j.1365-2958.2007.05781.x
    • Wade J T, Struhl K, Busby S J and Grainger D C 2007 Genomic analysis of protein-DNA interactions in bacteria: insights into transcription and chromosome organization Mol. Microbiol. 65 216 (Pubitemid 46934493)
    • (2007) Molecular Microbiology , vol.65 , Issue.1 , pp. 21-26
    • Wade, J.T.1    Struhl, K.2    Busby, S.J.W.3    Grainger, D.C.4
  • 128
    • 80052643394 scopus 로고    scopus 로고
    • Chromosome organization by a nucleoid-associated protein in live bacteria
    • 10.1126/science.1204697 0036-8075
    • Wang W, Li G-W, Chen C, Xie X S and Zhuang X 2011a Chromosome organization by a nucleoid-associated protein in live bacteria Science 333 14459
    • (2011) Science , vol.333 , Issue.6048 , pp. 1445-1449
    • Wang, W.1    Li, G.-W.2    Chen, C.3    Xie, X.S.4    Zhuang, X.5
  • 129
    • 79960584723 scopus 로고    scopus 로고
    • Replication and segregation of an Escherichia coli chromosome with two replication origins
    • 10.1073/pnas.1100874108 0027-8424
    • Wang X, Lesterlin C, Reyes-Lamothe R, Ball G and Sherratt D J 2011b Replication and segregation of an Escherichia coli chromosome with two replication origins Proc. Natl Acad. Sci. USA 108 E24350
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , Issue.26
    • Wang, X.1    Lesterlin, C.2    Reyes-Lamothe, R.3    Ball, G.4    Sherratt, D.J.5
  • 130
    • 33745603713 scopus 로고    scopus 로고
    • The two Escherichia coli chromosome arms locate to separate cell halves
    • DOI 10.1101/gad.388406
    • Wang X, Liu X, Possoz C and Sherratt D J 2006 The two Escherichia coli chromosome arms locate to separate cell halves Genes Dev. 20 172731 (Pubitemid 43992881)
    • (2006) Genes and Development , vol.20 , Issue.13 , pp. 1727-1731
    • Wang, X.1    Liu, X.2    Possoz, C.3    Sherratt, D.J.4
  • 131
    • 4444340534 scopus 로고    scopus 로고
    • Statistical analysis of the spatial distribution of operons in the transcriptional regulation network of Escherichia coli
    • DOI 10.1016/j.jmb.2004.07.074, PII S0022283604009155
    • Warren P B and ten Wolde P R 2004 Statistical analysis of the spatial distribution of operons in the transcriptional regulation network of Escherichia coli J. Mol. Biol. 342 137990 (Pubitemid 39208666)
    • (2004) Journal of Molecular Biology , vol.342 , Issue.5 , pp. 1379-1390
    • Warren, P.B.1    Ten Wolde, P.R.2
  • 132
    • 77953494844 scopus 로고    scopus 로고
    • Bacterial chromosomal loci move subdiffusively through a viscoelastic cytoplasm
    • 10.1103/PhysRevLett.104.238102 0031-9007 238102
    • Weber S C, Spakowitz A J and Theriot J A 2010a Bacterial chromosomal loci move subdiffusively through a viscoelastic cytoplasm Phys. Rev. Lett. 104 238102
    • (2010) Phys. Rev. Lett. , vol.104 , Issue.23
    • Weber, S.C.1    Spakowitz, A.J.2    Theriot, J.A.3
  • 133
    • 77954819972 scopus 로고    scopus 로고
    • Subdiffusive motion of a polymer composed of subdiffusive monomers
    • 10.1103/PhysRevE.82.011913 1539-3755 E 011913
    • Weber S C, Theriot J A and Spakowitz A J 2010b Subdiffusive motion of a polymer composed of subdiffusive monomers Phys. Rev. E 82 011913
    • (2010) Phys. Rev. , vol.82 , Issue.1
    • Weber, S.C.1    Theriot, J.A.2    Spakowitz, A.J.3
  • 134
    • 0031633272 scopus 로고    scopus 로고
    • Dynamics of selfavoiding tethered membranes. I. Model A dynamics (Rouse model)
    • Wiese K J 1998 Dynamics of selfavoiding tethered membranes I Model A Dynamics (Rouse Model) Eur. Phys. J. B1 26972 (Pubitemid 128437435)
    • (1998) European Physical Journal B , vol.1 , Issue.3 , pp. 269-272
    • Wiese, K.J.1
  • 135
    • 77950455981 scopus 로고    scopus 로고
    • Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament
    • 10.1073/pnas.0912062107 0027-8424
    • 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. 107 49915
    • (2010) Proc. Natl Acad. Sci. , vol.107 , Issue.11 , pp. 4991-4995
    • Wiggins, P.A.1    Cheveralls, K.C.2    Martin, J.S.3    Lintner, R.4    Kondev, J.5
  • 136
    • 70349957921 scopus 로고    scopus 로고
    • Protein-mediated molecular bridging: A key mechanism in biopolymer organization
    • 10.1016/j.bpj.2009.06.051 0006-3495
    • Wiggins P A, Dame R Th, Noom M C and Wuite G J L 2009 Protein-mediated molecular bridging: a key mechanism in biopolymer organization Biophys. J. 97 19972003
    • (2009) Biophys. J. , vol.97 , Issue.7 , pp. 1997-2003
    • Wiggins, P.A.1    Th, D.R.2    Noom, M.C.3    Wuite, G.J.L.4
  • 137
    • 33750504444 scopus 로고    scopus 로고
    • Structural and physical aspects of bacterial chromosome segregation
    • DOI 10.1016/j.jsb.2006.04.013, PII S1047847706001560
    • Woldringh C L and Nanninga N 2006 Structural and physical aspects of bacterial chromosome segregation J. Struct. Biol. 156 27383 (Pubitemid 44666441)
    • (2006) Journal of Structural Biology , vol.156 , Issue.2 , pp. 273-283
    • Woldringh, C.L.1    Nanninga, N.2
  • 138
    • 84863406341 scopus 로고    scopus 로고
    • Polymer-monovalent salt-induced DNA compaction studied via single-molecule microfluidic trapping
    • 10.1039/c2lc20880f 1473-0197
    • Xu W and Muller S J 2012 Polymer-monovalent salt-induced DNA compaction studied via single-molecule microfluidic trapping Lab Chip 12 64751
    • (2012) Lab Chip , vol.12 , Issue.3 , pp. 647-651
    • Xu, W.1    Muller, S.J.2
  • 140
    • 70349728576 scopus 로고    scopus 로고
    • Macromolecular crowding induced elongation and compaction of single DNA molecules confined in a nanochannel
    • 10.1073/pnas.0904741106 0027-8424
    • Zhang C, Shao P G, van Kan J A and van der Maarel J R C 2009 Macromolecular crowding induced elongation and compaction of single DNA molecules confined in a nanochannel Proc. Natl Acad. Sci. USA 106 166516
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , Issue.39 , pp. 16651-16656
    • Zhang, C.1    Shao, P.G.2    Van Kan, J.A.3    Van Der Maarel, J.R.C.4
  • 141
    • 2942515131 scopus 로고    scopus 로고
    • Studies on the compaction of isolated nucleoids from Escherichia coli
    • DOI 10.1016/j.jsb.2004.02.003, PII S1047847704000401
    • Zimmerman S B 2004 Studies on the compaction of isolated nucleoids from Escherichia coli J. Struct. Biol. 147 14658 (Pubitemid 38757510)
    • (2004) Journal of Structural Biology , vol.147 , Issue.2 , pp. 146-158
    • Zimmerman, S.B.1
  • 142
    • 31344453142 scopus 로고    scopus 로고
    • Cooperative transitions of isolated Escherichia coli nucleoids: Implications for the nucleoid as a cellular phase
    • DOI 10.1016/j.jsb.2005.10.011, PII S1047847705002327
    • Zimmerman S B 2006a Cooperative transitions of isolated Escherichia coli nucleoids: implications for the nucleoid as a cellular phase J. Struct. Biol. 153 16075 (Pubitemid 43139695)
    • (2006) Journal of Structural Biology , vol.153 , Issue.2 , pp. 160-175
    • Zimmerman, S.B.1
  • 143
    • 33750510057 scopus 로고    scopus 로고
    • Shape and compaction of Escherichia coli nucleoids
    • DOI 10.1016/j.jsb.2006.03.022, PII S1047847706001274
    • Zimmerman S B 2006b Shape and compaction of Escherichia coli nucleoids J. Struct. Biol. 156 25561 (Pubitemid 44666440)
    • (2006) Journal of Structural Biology , vol.156 , Issue.2 , pp. 255-261
    • Zimmerman, S.B.1
  • 144
    • 33646941247 scopus 로고
    • The dimensions of chain molecules containing branches and rings
    • 10.1063/1.1747157 0021-9606
    • Zimm B H and Stockmayer W H 1949 The dimensions of chain molecules containing branches and rings J. Chem. Phys. 17 1301
    • (1949) J. Chem. Phys. , vol.17 , Issue.12 , pp. 1301
    • Zimm, B.H.1    Stockmayer, W.H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.