Theory and computational modeling of the 30 nm chromatin fiber

New Comprehensive Biochemistry

Volumn 39, Issue , 2004, Pages 397-420

  Langowski, Jörg ^a   Schiessel, Helmut ^b  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^b MAX PLANCK INSTITUTE FOR POLYMER RESEARCH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 28744454727     PISSN: 01677306     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0167-7306(03)39015-5     Document Type: Review

References (109)

1. H. Zentgraf W.W. Franke Differences of supranucleosomal organization in different kinds of chromatin: cell type-specific globular subunits containing different numbers of nucleosomes J. Cell Biol. 99 1984 272 286
2. A.L. Olins D.E. Olins Spheroid chromatin units (v bodies) J. Cell Biol. 59 1973 252a
3. A.L. Olins D.E. Olins Spheroid chromatin units (v bodies) Science 183 1974 330 332
4. C.L.F. Woodcock Ultrastructure of inactive chromatin J. Cell Biol. 59 1973 368a
5. K. van Holde J. Zlatanova Chromatin higher order structure: Chasing a mirage? J. Biol. Chem. 270 1995 8373 8376
6. K. van Holde J. Zlatanova What determines the folding of the chromatin fiber Proc. Natl. Acad. Sci. USA 93 1996 10548 10555
7. K.E. van Holde Chromatin 1989 Springer Heidelberg
8. J. Widom Toward a unified model of chromatin folding Annu. Rev. Biophys. Biophys. Chem. 18 1989 365 395
9. J.T. Finch A. Klug Solenoidal model for superstructure in chromatin Proc. Natl. Acad. Sci. USA 73 1976 1897 1901
10. F. Thoma T. Koller A. Klug Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin J. Cell Biol. 83 1979 403 427
11. J. Widom A. Klug Structure of the 300A chromatin filament: X-ray diffraction from oriented samples Cell 43 1985 207 213
12. C.L. Woodcock S.A. Grigoryev R.A. Horowitz N. Whitaker A chromatin folding model that incorporates linker variability generates fibers resembling the native structures Proc. Natl. Acad. Sci. USA 90 1993 9021 9025
13. R.A. Horowitz D.A. Agard J.W. Sedat C.L. Woodcock The three-dimensional architecture of chromatin in situ: electron tomography reveals fibers composed of a continuously variable zig-zag nucleosomal ribbon J. Cell Biol. 125 1994 1 10
14. C.L. Woodcock S. Dimitrov Higher-order structure of chromatin and chromosomes Curr. Opin. Genet. Dev. 11 2001 130 135
15. S.H. Leuba G. Yang C. Robert B. Samori K. van Holde J. Zlatanova C. Bustamante Three-dimensional structure of extended chromatin fibers as revealed by tapping-mode scanning force microscopy Proc. Natl. Acad. Sci. USA 91 1994 11621 11625
16. J. Bednar R.A. Horowitz S.A. Grigoryev L.M. Carruthers J.C. Hansen A.J. Koster C.L. Woodcock Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin Proc. Natl. Acad. Sci. USA 95 1998 14173 14178
17. H. Schiessel W.M. Gelbart R. Bruinsma DNA folding: Structural and mechanical properties of the two-angle model for chromatin Biophys. J. 80 2001 1940 1956
18. D. Stigter Interactions of highly charged colloidal cylinders with applications to double stranded DNA Biopolymers 16 1977 1435 1448
19. K.V. Klenin M.D. Frank-Kamenetskii J. Langowski Modulation of intramolecular interactions in superhelical DNA by curved sequences: a Monte Carlo simulation study Biophys. J. 68 1995 81 88
20. J.J. Delrow J.A. Gebe J.M. Schurr Comparison of hard-cylinder and screened Coulomb interactions in the modeling of supercoiled DNAs Biopolymers 42 1997 455 470
21. K. Klenin H. Merlitz J. Langowski A Brownian dynamics program for the simulation of linear and circular DNA and other wormlike chain polyelectrolytes Biophys. J. 74 1998 780 788
22. H. Merlitz K. Rippe K.V. Klenin J. Langowski Looping dynamics of linear DNA molecules and the effect of DNA curvature: a study by Brownian dynamics simulation Biophys. J. 74 1998 773 779
23. V.V. Rybenkov N.R. Cozzarelli A.V. Vologodskii Probability of DNA knotting and the effective diameter of the DNA double helix Proc. Natl. Acad. Sci. USA 90 1993 5307 5311
24. V.V. Rybenkov A.V. Vologodskii N.R. Cozzarelli The effect of ionic conditions on DNA helical repeat, effective diameter and free energy of supercoiling Nucleic Acids Res. 25 1997 1412 1418
25. M. Hammermann C. Steinmaier H. Merlitz U. Kapp W. Waldeck G. Chirico J. Langowski Salt effects on the structure and internal dynamics of superhelical DNAs studied by light scattering and Brownian dynamics Biophys. J. 73 1997 2674 2687
26. M. Hammermann N. Brun K.V. Klenin R. May K. Toth J. Langowski Salt-dependent DNA superhelix diameter studied by small angle neutron scattering measurements and Monte Carlo simulations Biophys. J. 75 1998 3057 3063
27. Y. Lu B. Weers N.C. Stellwagen DNA persistence length revisited Biopolymers 61 2001 261 275
28. M.D. Barkley B.H. Zimm Theory of twisting and bending of chain macromolecules: analysis of the fluorescence depolarization of DNA J. Chem. Phys. 70 1979 2991 3007
29. B.S. Fujimoto J.M. Schurr Dependence of the torsional rigidity of DNA on base composition Nature 344 1990 175 177
30. J.M. Schurr B.S. Fujimoto P. Wu L. Song Fluorescence studies of nucleic acids: dynamics, rigidities and structures. J.R. Lakowicz Topics in Fluorescence Spectroscopy 3 1992 Plenum Press New York 137 229
31. D. Shore R.L. Baldwin Energetics of DNA twisting. I. Relation between twist and cyclization probability J. Mol. Biol. 179 1983 957 981
32. D.S. Horowitz J.C. Wang Torsonal Rigidity of DNA and Length Dependence of the Free Energy of DNA Supercoiling J. Mol. Biol. 173 1984 75 91
33. W.H. Taylor P.J. Hagerman Application of the method of phage T4 DNA ligase-catalyzed ring-closure to the study of DNA structure I.NaCl-dependence of DNA flexibility and helical repeat J. Mol. Biol. 212 1990 363 376
34. P. Cluzel A. Lebrun C. Heller R. Lavery J.-L. Viovy D. Chatenay F. Caron DNA: An extensible molecule Science 271 1996 792 794
35. S.B. Smith Y. Cui C. Bustamante Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules Science 271 1996 795 799
36. F. Lankas J. Sponer P. Hobza J. Langowski Sequence-dependent elastic properties of DNA J. Mol. Biol. 299 2000 695 709
37. F. Lankas I.T. Cheatham N. Spackova P. Hobza J. Langowski J. Sponer Critical effect of the N2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts Biophys. J. 82 2002 2592 2609
38. G. Arents R.W. Burlingame B.-C. Wang W.E. Love E.N. Moudrianakis The nucleosomal core histone octamer at 3.1 Å resolution: A triparatite protein assembly and a left-handed superhelix Proc. Natl. Acad. Sci. USA 88 1991 10148 10152
39. K. Luger A.W. Mäder R.K. Richmond D.F. Sargent T.J. Richmond Crystal structure of the nucleosome core particle at 2.8 Å resolution Nature 389 1997 251 260
40. A. Sivolob F. DeLucia B. Révet A. Prunell Nucleosome dynamics. II. High flexibility of nucleosome entering and exiting DNAs to positive crossing. An ethidium bromide fluorescence study of mononucleosomes on DNA minicircles J. Mol. Biol. 285 1999 1081 1099
41. A. Sivolob A. Prunell Nucleosome dynamics V. Ethidium bromide versus histone tails in modulating ethidium bromide-driven tetrasome chiral transition. A fluorescence study of tetrasomes on DNA minicircles J. Mol. Biol. 295 2000 41 53
42. B.D. Brower-Toland C.L. Smith R.C. Yeh J.T. Lis C.L. Peterson M.D. Wang Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA Proc. Natl. Acad. Sci. USA. 99 2002 1960 1965
43. M.L. Bennink S.H. Leuba G.H. Leno J. Zlatanova B.G. de Grooth J. Greve Unfolding individual nucleosomes by stretching single chromatin fibers with optical tweezers Nat. Struct. Biol. 8 2001 606 610
44. A. Leforestier F. Livolant Liquid crystalline ordering of nucleosome core particles under macromolecular crowding conditions: evidence for a discotic columnar hexagonal phase Biophys. J. 73 1997 1771 1776
45. F. Livolant A. Leforestier Chiral discotic columnar germs of nucleosome core particles Biophys. J. 78 2000 2716 2729
46. A. Leforestier J. Dubochet F. Livolant Bilayers of nucleosome core particles Biophys. J. 81 2001 2414 2421
47. S. Mangenot A. Leforestier D. Durand F. Livolant X-ray diffraction characterization of the dense phases formed by nucleosome core particles Biophys. J. 84 2003 2570 2584
48. S. Mangenot A. Leforestier P. Vachette D. Durand F. Livolant Salt-induced conformation and interaction changes of nucleosome core particles Biophys. J. 82 2002 345 356
49. S. Mangenot E. Raspaud C. Tribet L. Belloni F. Livolant Interactions between isolated nucleosome core particles: A tail-bridging effect? Eur. Phys. J. E 7 2002 221 231
50. G. Wedemann J. Langowski Computer simulation of the 30-nanometer chromatin fiber Biophys. J. 82 2002 2847 2859
51. D.A. Beard T. Schlick Modeling salt-mediated electrostatics of macromolecules: the discrete surface charge optimization algorithm and its application to the nucleosome Biopolymers 58 2001 106 115
52. A. Matsumoto N. Go Dynamic properties of double-stranded DNA by normal mode analysis J. Chem. Phys. 110 1999 11070 11075
53. A. Matsumoto W.K. Olson Sequence-dependent motions of DNA: a normal mode analysis at the base-pair level Biophys. J. 83 2002 22 41
54. T.E. Cheatham 3rd M.A. Young Molecular dynamics simulation of nucleic acids: successes, limitations, and promise Biopolymers 56 2000 232 256
55. K.V. Klenin A.V. Vologodskii V.V. Anshelevich A.M. Dykhne M.D. Frank-Kamenetskii Effect of excluded volume on topological properties of circular DNA J. Biomol. Struct. Dyn. 5 1988 1173 1185
56. A.V. Vologodskii S.D. Levene K.V. Klenin M. Frank-Kamenetskii N.R. Cozzarelli Conformational and thermodynamic properties of supercoiled DNA J. Mol. Biol. 227 1992 1224 1243
57. J. Langowski U. Kapp K. Klenin A. Vologodskii Solution structure and dynamics of DNA topoisomers. Dynamic light scattering studies and Monte-Carlo simulations Biopolymers 34 1994 639 646
58. V.V. Rybenkov A.V. Vologodskii N.R. Cozzarelli The effect of ionic conditions on the conformations of supercoiled DNA .1. Sedimentation analysis J. Mol. Biol. 267 1997 299 311
59. J. Huang T. Schlick A. Vologodskii Dynamics of site juxtaposition in supercoiled DNA Proc. Natl. Acad. Sci. USA 98 2001 968 973
60. B.S. Fujimoto J.M. Schurr Monte Carlo simulations of supercoiled DNAs confined to a plane Biophys. J. 82 2002 944 962
61. S.A. Allison J.A. McCammon Transport properties of rigid and flexible macromolecules by Brownian dynamics simulation Biopolymers 23 1984 167 187
62. S.A. Allison Brownian dynamics simulation of wormlike chains. Fluorescence depolarization and depolarized light scattering Macromolecules 19 1986 118 124
63. S.A. Allison S.S. Sorlie R. Pecora Brownian dynamics simulations of wormlike chains: Dynamic light scattering from a 2311 base pair DNA fragment Macromolecules 23 1990 1110 1118
64. J.A. Gebe S.A. Allison J.B. Clendenning J.M. Schurr Monte-Carlo simulations of supercoiling free-energies for unknotted and trefoil knotted DNAs Biophys. J. 68 1995 619 633
65. D.A. Beard T. Schlick Computational modeling predicts the structure and dynamics of chromatin fiber Structure 9 2001 105 114
66. Y. Cui C. Bustamante Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure Proc. Natl. Acad. Sci. USA 97 2000 127 132
67. H. Schiessel J. Widom R.F. Bruinsma W.M. Gelbart Polymer reptation and nucleosome repositioning Phys. Rev. Lett. 86 2001 4414 4417
68. T.C. Bishop J.E. Hearst Potential function describing the folding of the 30 nm fiber J. Phys. Chem. B 102 1998 6433 6439
69. T.C. Bishop O.O. Zhmudsky Mechanical model of the nucleosome and chromatin J. Biomol. Struct. Dyn. 19 2002 877 887
70. J. Zlatanova S.H. Leuba K. van Holde Chromatin fiber structure: morphology, molecular determinants, structural transitions Biophys. J. 74 1998 2554 2566
71. J. Widom A relationship between the helical twist of DNA and the ordered positioning of nucleosomes in all eukaryotic cells Proc. Natl. Acad. Sci. USA 89 1992 1095 1099
72. Schiessel, H. (2003) The physics of chromatin. J. Phys: Condens. Matter, in press
73. J.R. Daban Physical constraints in the condensation of eukaryotic chromosomes. Local concentration of DNA versus linear packing ratio in higher order chromatin structures Biochemistry 39 2000 3861 3866
74. K. vanHolde J. Zlatanova What determines the folding of the chromatin fiber? Proc. Natl. Acad. Sci. USA 93 1996 10548 10555
75. H. Schiessel How short-ranged electrostatics controls the chromatin structure on much larger scales Euro. Lett. 58 2002 140 146
76. E. Ben-Haim A. Lesne J.M. Victor Chromatin: a tunable spring at work inside chromosomes Phys. Rev. E Stat. Nonlin. Soft Matter. Phys. 64 2001 051921
77. F.B. Fuller The writhing number of a space curve Proc. Natl. Acad. Sci. USA 68 1971 815 819
78. C.J. Benham The statistics of superhelicity J. Mol. Biol. 123 1978 361 370
79. C.J. Benham Elastic model of supercoiling Proc. Natl. Acad. Sci. USA 74 1977 2397 2401
80. W.K. Olson V.B. Zhurkin Modeling DNA deformations Curr. Opin. Struct. Biol. 10 2000 286 297
81. J. Langowski W.K. Olson S.C. Pedersen I. Tobias T.P. Westcott Y. Yang DNA supercoiling, localized bending and thermal fluctuations Trends Biochem. Sci. 21 1996 50
82. N. Metropolis A.W. Rosenbluth M.N. Rosenbluth A.H. Teller E. Teller Equation of state calculations by fast computing machines J. Chem. Phys. 21 1953 1087 1092
83. D.L. Ermak J.A. McCammon Brownian dynamics with hydrodynamic interactions J. Chem. Phys. 69 1978 1352 1359
84. S.A. Allison R. Austin M. Hogan Bending and twisting dynamics of short linear DNAs-analysis of the triplet anisotropy decay of a 209-base pair fragment by Brownian simulation J. Chem. Phys. 90 1989 3843 3854
85. G. Chirico J. Langowski Calculating hydrodynamic properties of DNA through a second-order Brownian dynamics algorithm Macromolecules 25 1992 769 775
86. G. Chirico J. Langowski Kinetics of DNA supercoiling studied by Brownian dynamics simulation Biopolymers 34 1994 415 433
87. G. Chirico J. Langowski Brownian dynamics simulations of supercoiled DNA with bent sequences Biophys. J. 71 1996 955 971
88. J. Garcia de la Torre S. Navarro M.C. Lopez Martinez Hydrodynamic properties of a double-helical model for DNA Biophys. J. 66 1994 1573 1579
89. V. Katritch C. Bustamante V.K. Olson Pulling chromatin fibers: Computer simulations of direct physical micromanipulations J. Mol. Biol. 295 2000 29 40
90. J.G. Gay B.J. Berne Modification of the overlap potential to mimic a linear site–site potential J. Chem. Phys. 74 1981 3316 3319
91. S.E. Gerchman V. Ramakrishnan Chromatin higher-order structure studied by neutron scattering and scanning transmission electron microscopy Proc. Natl. Acad. Sci. USA 84 1987 7802 7806
92. S.I. Dimitrov V.L. Makarov I.G. Pashev The chromatin fiber: structure and conformational transitions as revealed by optical anisotropy studies J. Biomol. Struct. Dyn. 8 1990 23 35
93. H.R. Widlund J.M. Vitolo C. Thiriet J.J. Hayes DNA sequence-dependent contributions of core histone tails to nucleosome stability: Differential effects of acetylation and proteolytic tail removal Biochemistry 39 2000 3835 3841
94. A. Thastrom P.T. Lowary H.R. Widlund H. Cao M. Kubista J. Widom Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences J. Mol. Biol. 288 1999 213 229
95. G. Wedemann C. Münkel G. Schoppe J. Langowski Kinetics of structural changes in superhelical DNA Phys. Rev. E 58 1998 3537 3546
96. L. Ehrlich C. Munkel G. Chirico J. Langowski A Brownian dynamics model for the chromatin fiber Comput. Appl. Biosci. 13 1997 271 279
97. C. Münkel J. Langowski Chromosome structure described by a polymer model Phys. Rev. E 57 1998 5888 5896
98. J. Yao P.T. Lowary J. Widom Direct detection of linker DNA bending in defined-length oligomers of chromatin Proc. Natl. Acad. Sci. USA 87 1990 7603 7607
99. P.J. Butler J.O. Thomas Dinucleosomes show compaction by ionic strength, consistent with bending of linker DNA J. Mol. Biol. 281 1998 401 407
100. G. van den Engh R. Sachs B.J. Trask Estimating genomic distance from DNA sequence location in cell nuclei by a random walk model Science 257 1992 1410 1412
101. B.J. Trask S. Allen H. Massa A. Fertitta R. Sachs G. van den Engh M. Wu Studies of metaphase and interphase chromosomes using fluorescence in situ hybridization Cold Spring Harb. Symp. Quant. Biol. 58 1993 767 775
102. H. Yokota G. van den Engh J. Hearst R.K. Sachs B.J. Trask Evidence for the organization of chromatin in megabase pair-sized loops arranged along a random walk path in the human G0/G1 interphase nucleus J. Cell Biol. 130 1995 1239 1249
103. Castro, C. (1994). Measurement of the elasticity of single chromatin fibers: the effect of histone H1. PhD Thesis, University of Oregon, Eugene
104. B. Houchmandzadeh J.F. Marko D. Chatenay A. Libchaber Elasticity and structure of eukaryote chromosomes studied by micromanipulation and micropipette aspiration J. Cell. Biol. 139 1997 1 12
105. L. Ringrose S. Chabanis P.O. Angrand C. Woodroofe A.F. Stewart Quantitative comparison of DNA looping in vitro and in vivo : chromatin increases effective DNA flexibility at short distances EMBO J. 18 1999 6630 6641
106. J. Dekker K. Rippe M. Dekker N. Kleckner Capturing chromosome conformation Science 295 2002 1306 1311
107. J.Y. Ostashevsky C.S. Lange The 30 nm chromatin fiber as a flexible polymer J. Biomol. Struct. Dyn. 11 1994 813 820
108. R.K. Sachs G. van den Engh B. Trask H. Yokota J.E. Hearst A random-walk/giant-loop model for interphase chromosomes Proc. Natl. Acad. Sci. USA 92 1995 2710 2714
109. M. Bussiek N. Mücke J. Langowski Polylysine-coated mica can be used to observe systematic changes in the supercoiled DNA conformation by scanning force microscopy in solution Nucleic Acids Res. 31 2003 137