Brownian dynamics simulations reveal regulatory properties of higher-order chromatin structures

Jens Odenheimer1, Dieter W. Heermann1, Gregor Kreth2
1Institute for Theoretical Physics, Heidelberg University, Heidelberg, Germany
2Kirchhoff Institute for Physics, Heidelberg University, Heidelberg, Germany

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Betzig E, Patterson GH et al (2006) Imaging intracellular fluorescent proteins at nanometer resolution. Science 313:1642–1645

Bohn M, Heermann DW et al (2007) A random loop model for long polymers. Phys Rev E Stat Nonlin Soft Matter Phys 76:051805. doi: 10.1103/PhysRevE.76.051805

Bon M, Marenduzzo D et al (2006) Modelling a self-avoiding chromatin loop: relation to the packing problem, action-at-a-distance, and nuclear context. J Cell Sci 14(2):197–204

Cremer T, Cremer C (2001) Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2(4):292–301. doi: 10.1038/35066075

Donnert G, Keller J et al (2006) Macromolecular-scale resolution in biological fluorescence microscopy. Proc Natl Acad Sci USA 103:11440–11445. doi: 10.1073/pnas.0604965103

Esa A, Edelmann P et al (2000) Three-dimensional spectral precision distance microscopy of chromatin nanostructures after triple-colour DNA labelling: a study of the BCR region on chromosome 22 and the Philadelphia chromosome. J Microsc 199(2):96–105. doi: 10.1046/j.1365-2818.2000.00707.x

Frenkel D, Smit B (2002) Understanding molecular simulation from algorithms to applications. Computational science from theory to applications, vol 1, 2nd edn. Academic Press, San diego

Gorisch SM, Wachsmuth M et al (2005) Histone acetylation increases chromatin accessibility. J Cell Sci 118(24):5825–5834. doi: 10.1242/jcs.02689

Grünwald D, Martin RM et al (2008) Probing intranuclear environments at the single-molecule level. Biophys J 94:2847–2858. doi: 10.1529/biophysj.107.115014

Marenduzzo D, Faro-Trindade I et al (2007) What are the molecular ties that maintain genomic loops? Trends Genet 23(3):126–133. doi: 10.1016/j.tig.2007.01.007

Münkel C, Langowski J (1998) Chromosome structure predicted by a polymer model. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 57:5888–5896. doi: 10.1103/PhysRevE.57.5888

Nicodemi M, Prisco A (2009) Thermodynamic pathways to genome spatial organization in the cell nucleus. Biophys J 96:2168–2177. doi: 10.1016/j.bpj.2008.12.3919

Odenheimer J, Kreth G et al (2005) Dynamic simulation of active/inactive chromatin domains. J Biol Phys 31(3):351–163. doi: 10.1007/s10867-005-7286-3

Ostashevsky J (1998) A polymer model for the structural organization of chromatin loops and minibands in interphase chromosomes. Mol Biol Cell 9(11):3031–3040

Politz JC, Tuft RA et al (2003) Diffusion-based transport of nascent ribosomes in the nucleus. Mol Biol Cell 14(12):4805–4812. doi: 10.1091/mbc.E03-06-0395

Roh TY, Cuddapah S et al (2005) Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Genes Dev 19(5):542–552. doi: 10.1101/gad.1272505

Schöppe G, Heermann DW (1999) Alternative off-lattice model with continuous backbone mass for polymers. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 59:636–641. doi: 10.1103/PhysRevE.59.636

Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403(6765):41–45. doi: 10.1038/47412

Verschure PJ, van der Kraan I et al (2003) Condensed chromatin domains in the mammalian nucleus are accessible to large macromolecules. EMBO Rep 4(9):861–866. doi: 10.1038/sj.embor.embor922