Chromosome dynamics, molecular crowding, and diffusion in the interphase cell nucleus: A Monte Carlo lattice simulation study

Chromosome Research

Volumn 19, Issue 1, 2011, Pages 63-81

  Fritsch, Christian C ^a   Langowski, Jörg ^a  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

Chromosome dynamics; Diffusion; Molecular crowding

Indexed keywords

BIOPOLYMER; DNA TOPOISOMERASE;

ARTICLE; CHROMATIN; CHROMATIN STRUCTURE; CHROMOSOME CONDENSATION; CONFOCAL LASER MICROSCOPY; DIFFUSION; DNA CROSS LINKING; ELASTICITY; HUMAN; INTERPHASE; MACROMOLECULE; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; MONTE CARLO METHOD; PRIORITY JOURNAL; VISCOSITY;

CHROMATIN; CHROMOSOMES; COMPUTER SIMULATION; DIFFUSION; ELASTICITY; INTERPHASE; MODELS, BIOLOGICAL; MOLECULAR DYNAMICS SIMULATION; MONTE CARLO METHOD; PROTEIN CONFORMATION; VISCOSITY;

EID: 79952282147     PISSN: 09673849     EISSN: 15736849     Source Type: Journal    
DOI: 10.1007/s10577-010-9168-1     Document Type: Article

References (37)

1. A Bancaud S Huet N Daigle J Mozziconacci J Beaudouin J Ellenberg 2009 Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin EMBO J 28 24 3785 3798 1:CAS:528:DC%2BD1MXhsVSmu7rN 10.1038/emboj.2009.340 19927119
2. R Biehl X Guo RK Prud'homme M Monkenbusch J Allgeier D Richter 2004 Diffusion of compact macromolecules through polymer meshes: mesh dynamics and probe dynamics Phys B Condens Matter 350 1-3 76 78 1:CAS:528: DC%2BD2cXlvFCrs7w%3D 10.1016/j.physb.2004.03.258 Proceedings of the third European conference on neutron scattering
3. M Bohn DW Heermann R van Driel 2007 Random loop model for long polymers Phys Rev E (Statistical, Nonlinear, and Soft Matter Physics) 76 5 051805 10.1103/PhysRevE.76.051805 (Pubitemid 350205871)
4. I Carmesin K Kremer 1988 The bond fluctuation method: a new effective algorithm for the dynamics of polymers in all spatial dimensions Macromolecules 21 2819 2823 1:CAS:528:DyaL1cXltFWitbc%3D 10.1021/ma00187a030
5. C Cremer Ch Münkel M Granzow A Jauch S Dietzel R Eils XY Guan PS Meltzer JM Trent J Langowski T Cremer 1996 Nuclear architecture and the induction of chromosomal aberrations Mutat Res Rev Genet Toxicol 366 2 97 116 1:CAS:528:DyaK28Xnt1OitL4%3D (Pubitemid 27008349)
6. JA Dix AS Verkman 2008 Crowding effects on diffusion in solutions and cells Annu Rev Biophys 37 247 263 1:CAS:528:DC%2BD1cXnsVGlur4%3D 10.1146/annurev.biophys.37.032807.125824 18573081
7. Doi M, Edwards SF (1986) The theory of polymer dynamics. Clarendon, Oxford
8. N Dross C Spriet M Zwerger G Müller W Waldeck J Langowski 2009 Mapping eGFP oligomer mobility in living cell nuclei PLoS ONE 4 4 5041, 04 10.1371/journal.pone.0005041
9. R Ellis A Minton 2003 Cell biology: join the crowd Nature 425 27 28 1:CAS:528:DC%2BD3sXmvFaguro%3D 10.1038/425027a 12955122 (Pubitemid 37101701)
10. E Farge AC Maggs 1993 Dynamic scattering from semiflexible polymers Macromolecules 26 19 5041 5044 1:CAS:528:DyaK3sXlsVShsLg%3D 10.1021/ma00071a009
11. CC Fritsch J Langowski 2010 Anomalous diffusion in the interphase cell nucleus: the effect of spatial correlations of chromatin J Chem Phys 133 025101 10.1063/1.3435345 20632774
12. SM Görisch M Wachsmuth C Ittrich CP Bacher K Rippe P Lichter 2004 Nuclear body movement is determined by chromatin accessibility and dynamics Proc Natl Acad Sci U S A 101 13221 13226 10.1073/pnas.0402958101 15331777 (Pubitemid 39209646)
13. SM Görisch P Lichter K Rippe 2005 Mobility of multi-subunit complexes in the nucleus: accessibility and dynamics of chromatin subcompartments Histochem Cell Biol 123 3 217 228 10.1007/s00418-005-0752-y 15830242 (Pubitemid 40674673)
14. SM Görisch M Wachsmuth KF Toth P Lichter K Rippe 2005 Histone acetylation increases chromatin accessibility J Cell Sci 118 24 5825 5834 10.1242/jcs.02689 16317046 (Pubitemid 43079275)
15. G Guigas M Weiss 2008 Sampling the cell with anomalous diffusion-the discovery of slowness Biophys J 94 1 90 94 1:CAS:528:DC%2BD1cXkvVY%3D 10.1529/biophysj.107.117044 17827216
16. D Jacobs H Nakanishi 1990 Autocorrelation functions for discrete random walks on disordered lattice Phys Rev A 41 2 706 719 1:CAS:528:DyaK3cXhsVGktr8%3D 10.1103/PhysRevA.41.706 9903153
17. TA Klar SW Hell 1999 Subdiffraction resolution in far-field fluorescence microscopy Opt Lett 24 954 956 1:CAS:528:DyaK1MXltFSgurw%3D 10.1364/OL.24.000954 18073907 (Pubitemid 129308287)
18. E Lieberman-Aiden NL van Berkum L Williams M Imakaev T Ragoczy A Telling I Amit BR Lajoie PJ Sabo MO Dorschner R Sandstrom B Bernstein MA Bender M Groudine A Gnirke J Stamatoyannopoulos LA Mirny ES Lander J Dekker 2009 Comprehensive mapping of long-range interactions reveals folding principles of the human genome Science 326 5950 289 293 1:CAS:528:DC%2BD1MXht1agsbjM 10.1126/science.1181369 19815776
19. TG Mason DA Weitz 1995 Optical measurements of frequency-dependent linear viscoelastic moduli of complex fluids Phys Rev Lett 74 7 1250 1253 1:CAS:528:DyaK2MXjs1KitL8%3D 10.1103/PhysRevLett.74.1250 10058972
20. N Metropolis AW Rosenbluth MN Rosenbluth AH Teller E Teller 1953 Equation of state calculations by fast computing machines J Chem Phys 21 1087 1092 1:CAS:528:DyaG3sXltlKhsw%3D%3D 10.1063/1.1699114
21. R Metzler J Klafter 2000 The random walk's guide to anomalous diffusion: a fractional dynamics approach Phys Rep 339 1 77 1:CAS:528:DC%2BD3cXovFSku7g%3D 10.1016/S0370-1573(00)00070-3
22. WG Müller D Walker GL Hager JG Mcnally 2001 Large-scale chromatin decondensation and recondensation regulated by transcription from a natural promoter J Cell Biol 154 1 33 48 10.1083/jcb.200011069 11448988 (Pubitemid 34289276)
23. C Münkel J Langowski 1998 Chromosome structure predicted a by polymer model Phys Rev E 57 5 5888 5896 10.1103/PhysRevE.57.5888 (Pubitemid 128579512)
24. JC Politz RA Tuft T Pederson 2003 Diffusion-based transport of nascent ribosomes in the nucleus Mol Biol Cell 14 12 4805 4812 1:CAS:528: DC%2BD3sXpsFakt78%3D 10.1091/mbc.E03-06-0395 12960421 (Pubitemid 37484797)
25. A Rosa R Everaers 2008 Structure and dynamics of interphase chromosomes PLoS Comput Biol 4 8 1000153 10.1371/journal.pcbi.1000153
26. Rubinstein M, Colby RH (2003) Polymer physics. Oxford University Press, Oxford
27. MJ Saxton 1994 Anomalous diffusion due to obstacles: a Monte Carlo study Biophys J 66 2, Part 1 394 401 1:CAS:528:DyaK2cXivVSrtr8%3D 10.1016/S0006- 3495(94)80789-1 8161693 (Pubitemid 24058459)
28. JP Siebrasse U Kubitscheck 2009 Single molecule tracking for studying nucleocytoplasmic transport and intranuclear dynamics Methods Mol Biol 464 343 61 10.1007/978-1-60327-461-6-19 18951194
29. JL Sikorav G Jannink 1994 Kinetics of chromosome condensation in the presence of topoisomerases-a phantom chain model Biophys J 66 3 827 837 1:CAS:528:DyaK2cXitlyns74%3D 10.1016/S0006-3495(94)80859-8 8011915 (Pubitemid 24083003)
30. Y Tseng J Lee T Kole I Jiang D Wirtz 2004 Micro-organization and visco-elasticity of the interphase nucleus revealed by particle nanotracking J Cell Sci 117 2159 2167 1:CAS:528:DC%2BD2cXksVyrs7s%3D 10.1242/jcs.01073 15090601 (Pubitemid 38745148)
31. M Wachsmuth W Waldeck J Langowski 2000 Anomalous diffusion of fluorescent probes inside living cell nuclei investigated by spatially-resolved fluorescence correlation spectroscopy J Mol Biol 298 4 677 689, 05 1:CAS:528:DC%2BD3cXivVSksLo%3D 10.1006/jmbi.2000.3692 10788329
32. Waigh TA (2007) Applied biophysics. Wiley, Chichester
33. A Wedemeier H Merlitz C-X Wu J Langowski 2007 Modeling diffusional transport in the interphase cell nucleus J Chem Phys 127 4 045102 10.1063/1.2753158 17672725 (Pubitemid 47192081)
34. A Wedemeier T Zhang H Merlitz C-X Wu J Langowski 2008 The role of chromatin conformations in diffusional transport of chromatin-binding proteins: Cartesian lattice simulations J Chem Phys 128 15 155101 10.1063/1.2895048 18433282 (Pubitemid 351574700)
35. A Wedemeier H Merlitz C-X Wu J Langowski 2009 How proteins squeeze through polymer networks: a Cartesian lattice study J Chem Phys 131 6 064905 10.1063/1.3205100 19691409
36. T Weidemann M Wachsmuth TA Knoch G Müller W Waldeck J Langowski 2003 Counting nucleosomes in living cells with a combination of fluorescence correlation spectroscopy and confocal imaging J Mol Biol 334 2 229 240 1:CAS:528:DC%2BD3sXos1Chtrk%3D 10.1016/j.jmb.2003.08.063 14607115 (Pubitemid 37357263)
37. IY Wong L MGardel R DReichman ER Weeks MT Valentine AR Bausch DA Weitz 2004 Anomalous diffusion probes microstructure dynamics of entangled F-actin networks Phys Rev Lett 92 17 178101 1:STN:280:DC%2BD2c3ntVSktg%3D%3D 10.1103/PhysRevLett.92.178101 15169197