Topological origins of chromosomal territories

Nucleic Acids Research

Volumn 37, Issue 19, 2009, Pages 6316-6322

  Dorier, Julien ^a   Stasiak, Andrzej ^a  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

DNA TOPOISOMERASE (ATP HYDROLYSING); POLYMER;

ARTICLE; CELL COMPARTMENTALIZATION; CELL NUCLEUS; CELL PERMEABILIZATION; CELLULAR DISTRIBUTION; CHROMATIN; CHROMATIN CONDENSATION; CHROMOSOMAL LOCALIZATION; CONTROLLED STUDY; ENZYME SUBSTRATE; INTERPHASE; MOLECULAR MODEL; PRIORITY JOURNAL;

BIOPOLYMERS; CHROMOSOMES; MODELS, MOLECULAR;

EID: 71049147905     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp702     Document Type: Article

References (36)

1. Cremer,T. and Cremer,C. (2001) Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat. Rev. Genet. 2, 292-301.
2. Tanabe,H., Muller,S., Neusser,M., von Hase,J., Calcagno,E., Cremer,M., Solovei,I., Cremer,C. and Cremer,T. (2002) Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates. Proc. Natl Acad. Sci. USA, 99, 4424-4429.
3. Cremer,T., Cremer,M., Dietzel,S., Muller,S., Solovei,I. and Fakan,S. (2006) Chromosome territories - a functional nuclear landscape. Curr. Opin. Cell Biol., 18, 307-316.
4. Branco,M.R. and Pombo,A. (2006) Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol., 4, e138.
5. Gasser,S.M. (2002) Visualizing chromatin dynamics in interphase nuclei. Science, 296, 1412-1416.
6. Rosa,A. and Everaers,R. (2008) Structure and dynamics of interphase chromosomes. PLoS Comput. Biol., 4, e1000153.
7. 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.
8. Vettorel,T., Grosberg,A.Y. and Kremer,K. (2009) Statistics of polymer rings in the melt: A numerical study. Phys. Biol., 6, 25013.
9. Cates,M.E. and Deutsch,J.M. (1986) Conjectures on the statistics of ring polymers. J. Physique, 47, 2121-2128.
10. Müller,M., Wittmer,J.P. and Cates,M.E. (1996) Topological effects in ring polymers: A computer simulation study. Phys. Rev. E, 53 5063-5074.
11. Suzuki,J., Takano,A. and Matsushita,Y. (2008) Topological effect in ring polymers investigated with Monte Carlo simulation. J. Chem. Phys., 129, 034903.
12. Deutsch,J.M. (1999) Equilibrium size of large ring molecules. Phys. Rev. E, 59, R2539-R2541.
13. Dobay,A., Dubochet,J., Millett,K., Sottas,P.E. and Stasiak,A. (2003) Scaling behavior of random knots. Proc. Natl Acad. Sci. USA, 100, 5611-5615.
14. Moore,N.T., Lua,R.C. and Grosberg,A.Y. (2004) Topologically driven swelling of a polymer loop. Proc. Natl Acad. Sci. USA, 101, 13431-13435.
15. Shaw,S.Y. and Wang,J.C. (1993) Knotting of a DNA chain during ring closure. Science, 260, 533-536.
16. Bednar,J., Furrer,P., Stasiak,A., Dubochet,J., Egelman,E.H. and Bates,A.D. (1994) The twist, writhe and overall shape of supercoiled DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix. Possible implications for DNA structure in vivo. J. Mol. Biol., 235, 825-847.
17. Portugal,J. and Rodriguez-Campos,A. (1996) T7 RNA polymerase cannot transcribe through a highly knotted DNA template. Nucleic Acids Res. 24, 4890-4894.
18. Deibler,R.W., Mann,J.K., Sumners,D.W. and Zechiedrich,L. (2007) Hin-mediated DNA knotting and recombining promote replicon dysfunction and mutation. BMC Mol. Biol., 8, 44.
19. Sikorav,J.L. and Jannink,G. (1994) Kinetics of chromosome condensation in the presence of topoisomerases: A phantom chain model. Biophys. J. 66, 827-837.
20. Schvartzman,J.B. and Stasiak,A. (2004) A topological view of the replicon. EMBO Rep., 5, 256-261.
21. Nitiss,J.L. (2009) DNA topoisomerase II and its growing repertoire of biological functions. Nat. Rev. Cancer, 9, 327-337.
22. Gasser,R., Koller,T. and Sogo,J.M. (1996) The stability of nucleosomes at the replication fork. J. Mol. Biol., 258, 224-239.
23. Krude,T. (1999) Chromatin assembly during DNA replication in somatic cells. Eur. J. Biochem., 263, 1-5.
24. Bermejo,R., Doksani,Y., Capra,T., Katou,Y.M., Tanaka,H., Shirahige,K. and Foiani,M. (2007) Top1- and Top2-mediated topological transitions at replication forks ensure fork progression and stability and prevent DNA damage checkpoint activation. Genes Dev., 21, 1921-1936.
25. Dekker,J. (2008) Mapping in vivo chromatin interactions in yeast suggests an extended chromatin fiber with regional variation in compaction. J. Biol. Chem., 283, 34532-34540.
26. Vologodskii,A.V., Levene,S.D., Klenin,K.V., Frank-Kamenetskii,M. and Cozzarelli,N.R. (1992) Conformational and thermodynamic properties of supercoiled DNA. J. Mol. Biol., 227, 1224-1243.
27. Burnier,Y., Dorier,J. and Stasiak,A. (2008) DNA supercoiling inhibits DNA knotting. Nucleic Acids Res., 36, 4956-4963.
28. Burnier,Y., Weber,C., Flammini,A. and Stasiak,A. (2007) Local selection rules that can determine specific pathways of DNA unknotting by type II DNA topoisomerases. Nucleic Acids Res., 35, 5223-5231.
29. Wedemann,G. and Langowski,J. (2002) Computer simulation of the 30-nanometer chromatin fiber. Biophys. J., 82, 2847-2859.
30. Bolzer,A., Kreth,G., Solovei,I., Koehler,D., Saracoglu,K., Fauth,C., Muller,S., Eils,R., Cremer,C., Speicher,M.R. et al. (2005) Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol., 3, e157.
31. Munkel,C., Eils,R., Dietzel,S., Zink,D., Mehring,C., Wedemann,G., Cremer,T. and Langowski,J. (1999) Compartmentalization of interphase chromosomes observed in simulation and experiment. J. Mol. Biol., 285, 1053-1065.
32. Rosa,A., Maddocks,J.H., Neumann,F.R., Gasser,S.M. and Stasiak,A. (2006) Measuring limits of telomere movement on nuclear envelope. Biophys. J., 90, L24-L26.
33. Lavelle,C. (2008) DNA torsional stress propagates through chromatin fiber and participates in transcriptional regulation. Nat. Struct. Mol. Biol., 15, 123-125.
34. Kouzine,F., Sanford,S., Elisha-Feil,Z. and Levens,D. (2008) The functional response of upstream DNA to dynamic supercoiling in vivo. Nat. Struct. Mol. Biol., 15, 146-154.
35. Jakob,B., Splinter,J., Durante,M. and Taucher-Scholz,G. (2009) Live cell microscopy analysis of radiation-induced DNA double-strand break motion. Proc. Natl Acad. Sci. USA, 106, 3172-3177.
36. Kruhlak,M.J., Celeste,A., Dellaire,G., Fernandez-Capetillo,O., Muller,W.G., McNally,J.G., Bazett-Jones,D.P. and Nussenzweig,A. (2006) Changes in chromatin structure and mobility in living cells at sites of DNA double-strand breaks. J. Cell Biol., 172, 823-834.