A statistical model of intra-chromosome contact maps

Soft Matter

Volumn 11, Issue 5, 2015, Pages 1019-1025

  Nazarov, Leonid I ^a   Tamm, Mikhail V ^a,e   Avetisov, Vladik A ^b,e   Nechaev, Sergei K ^c,d,e  

^a MOSCOW STATE UNIVERSITY   (Russian Federation)

^b SEMENOV INSTITUTE OF CHEMICAL PHYSICS   (Russian Federation)

^c UNIVERSITÉ PARIS SACLAY   (France)

^d LEBEDEV PHYSICAL INSTITUTE   (Russian Federation)

^e NATIONAL RESEARCH UNIVERSITY HIGHER SCHOOL OF ECONOMICS   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

GENES;

CHAIN FOLDING; CONTACT MAPS; FINE STRUCTURES; HIERARCHICAL ELEMENTS; INTERMITTENCY; PRIMARY STRUCTURES; STATISTICAL AVERAGE; STATISTICAL MODELING;

CHROMOSOMES;

CHEMISTRY; CHROMOSOME; CHROMOSOME MAP; GENETICS; PROCEDURES; STATISTICAL MODEL;

CHROMOSOME MAPPING; CHROMOSOMES; MODELS, STATISTICAL;

EID: 84921529141     PISSN: 1744683X     EISSN: 17446848     Source Type: Journal    
DOI: 10.1039/c4sm02519a     Document Type: Article

References (36)

1. J. Dekker, K. Rippe, M. Dekker and N. Kleckner, Science, 2002, 295, 1306.
2. E. Lieberman-Aiden, N. L. van Berkum, L. Williams, M. Imakaev, T. Ragoczy, A. Telling, I. Amit, B. R. Lajoie, P. J. Sabo, M. O. Dorschner, et al., Science, 2009, 326, 289.
3. J. E. Dixon, S. Selvaraj, F. Yue, A. Kim, Y. Li, Y. Shen, M. Hu, J. S. Liu and B. Ren, Nature, 2012, 485, 376.
4. T. Sexton, E. Yaffe, E. Kenigsberg, F. Bantignies, B. Leblanc, M. Hoichman, H. Parrinello, A. Tanay and G. Cavalli, Cell, 2012, 148, 458.
5. Y. Zhang, R. P. McCord, Y.-J. Ho, B. R. Lajoie, D. G. Hildebrand, A. C. Simon, M. S. Becker, F. W. Alt and J. Dekker, Cell, 2012, 148, 908.
6. S. Sofueva, E. Yaffe, W.-C. Chan, D. Georgopoulou, M. V. Rudan, H. Mira-Bontenbal, S. M. Pollard, G. P. Schroth, A. Tanay and S. Hadjur, EMBO J., 2013, 32, 3119.
7. T. B. K. Le, M. V. Imakaev, L. A. Mirny and M. T. Laub, Science, 2013, 342, 731.
8. J. Dekker, M. A. Marti-Renom and L. A. Mirny, Nat. Rev. Genet., 2013, 14, 390.
9. R. K. Sachs, G. van der Engh, B. Trask, H. Yokota and J. E. Hearst, Proc. Natl. Acad. Sci. U. S. A., 1995, 92, 2710.
10. C. Münkel and J. Langowski, Phys. Rev. E: Stat. Phys., Plasmas, Fluids, Relat. Interdiscip. Top., 1998, 57, 5888.
11. J. Ostashevsky, Mol. Biol. Cell, 1998, 9, 3031.
12. J. Mateos-Langerak, M. Bohn, W. de Leeuw, O. Giromus, E. M. M. Manders, P. J. Verschure, M. H. G. Indemans, H. J. Gierman, D. W. Heerman, R. van Driel and S. Goetze, Proc. Natl. Acad. Sci. U. S. A., 2009, 106, 3812.
13. B. V. S. Iyer and G. Arya, Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys., 2012, 86, 011911.
14. M. Barbieri, M. Chotalia, J. Fraser, L.-M. Lavitas, J. Dostie, A. Pombo and M. Nicodemi, Proc. Natl. Acad. Sci. U. S. A., 2012, 109, 16173.
15. C. C. Fritsch and J. Longowski, Chromosome Res., 2011, 19, 63.
16. A. Y. Grosberg, Y. Rabin, S. Havlin and A. Neer, Europhys. Lett., 1993, 23, 373.
17. A. Rosa and R. Everaers, PLoS Comput. Biol., 2008, 4, e1000153.
18. L. A. Mirny, Chromosome Res., 2011, 19, 37.
19. J. D. Halverson, J. Smrek, K. Kremer and A. Yu. Grosberg, Rep. Prog. Phys., 2014, 77, 022601.
20. A. Yu. Grosberg, Soft Matter, 2014, 10, 560.
21. A. Rosa and R. Everaers, Phys. Rev. Lett., 2014, 112, 118302.
22. M. Imakaev, K. Tchourine, S. Nechaev and L. Mirny, Soft Matter, 2015, DOI: 10.1039/C4SM02099E.
23. M. Tamm, L. Nazarov, A. Gavrilov and A. Chertovich, arXiv:1404.2558.
24. A. Yu. Grosberg, S. K. Nechaev and E. I. Shakhnovich, J. Phys., 1988, 49, 2095.
25. A. Cournac, H. Marie-Nelly, M. Marbouty, R. Koszul and J. Mozziconacci, BMC Genomics, 2012, 13, 436.
26. M. Barbieri, A. Scialdone, A. Gamba, A. Pombo and M. Nicodemi, Soft Matter, 2013, 9, 8631.
27. J. D. Halverson, W. B. Lee, G. S. Grest, A. Y. Grosberg and K. Kremer, J. Chem. Phys., 2011, 134, 204905.
28. G. J. Filion, J. G. van Bemmel, U. Braunschweig, W. Talhout, J. Kind, L. D. Ward, W. Brugman, I. de Castro Genebra de Jesus, R. M. Kerkhoven, H. J. Bussemaker and B. van Steensel, Cell, 2010, 143, 212.
29. P.-G. de Gennes, Scaling Concepts in Polymer Physics, Cornell University Press, NY, 1979.
30. S. Nechaev and O. Vasilyev, Thermodynamics and topology of disordered knots: correlations in trivial lattice knot diagrams, in Physical and Numerical Models in Knot Theory, Series on Knots and Everything, WSPC, Singapore, 2005, ch. 22, pp. 421-472.
31. E. I. Shakhnovich and A. M. Gutin, J. Phys. A: Math. Gen., 1989, 22, 1647.
32. L. D. Landau and E. M. Lifshitz, Statistical Physics, Part 1, Elsevier, Oxford, 1980.
33. C. D. Sfatos, A. M. Gutin and E. I. Shakhnovich, Phys. Rev. E: Stat. Phys., Plasmas, Fluids, Relat. Interdiscip. Top., 1993, 48, 465.
34. M. Mezard, G. Parisi and M. Virasoro, Spin glass theory and beyond, World Scientific, Singapore, 1987.
35. G. H. Golub and C. F. Van Loan, Matrix Computations, Johns Hopkins Studies in Math. Sciences, 4th edn, 1996.
36. E. Yaffe and A. Tanay, Nat. Genet., 2011, 43, 1059.