DNA Folding: Structural and Mechanical Properties of the Two-Angle Model for Chromatin

Schiessel, Helmut; Gelbart, William M.; Bruinsma, Robijn

doi:10.1016/s0006-3495(01)76164-4

Cited by 106 publications

(147 citation statements)

References 36 publications

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“…Simulations showed that the nucleosome-nucleosome interaction played a major role in determining the mechanical properties of chromatin (29). A similar conclusion regarding the internucleosome attraction also was obtained in a theoretical analysis (30) of a two-angle model of chromatin (17).…”

supporting

confidence: 74%

Electrostatic mechanism of nucleosomal array folding revealed by computer simulation

Sun

Zhang

Schlick

2005

Proc. Natl. Acad. Sci. U.S.A.

106

113

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Although numerous experiments indicate that the chromatin fiber displays salt-dependent conformations, the associated molecular mechanism remains unclear. Here, we apply an irregular Discrete Surface Charge Optimization (DiSCO) model of the nucleosome with all histone tails incorporated to describe by Monte Carlo simulations salt-dependent rearrangements of a nucleosomal array with 12 nucleosomes. The ensemble of nucleosomal array conformations display salt-dependent condensation in good agreement with hydrodynamic measurements and suggest that the array adopts highly irregular 3D zig-zag conformations at high (physiological) salt concentrations and transitions into the extended ''beads-on-a-string'' conformation at low salt. Energy analyses indicate that the repulsion among linker DNA leads to this extended form, whereas internucleosome attraction drives the folding at high salt. The balance between these two contributions determines the salt-dependent condensation. Importantly, the internucleosome and linker DNA-nucleosome attractions require histone tails; we find that the H3 tails, in particular, are crucial for stabilizing the moderately folded fiber at physiological monovalent salt.chromatin modeling ͉ irregular 3D zig-zag ͉ Discrete Surface Charge Optimization model C hromatin folding and the dynamic interplay between chromatin structures and various cellular factors directly regulate fundamental gene expression and silencing processes (1-4). Extensive studies have probed the structural and dynamic properties of chromatin and the molecular mechanisms that determine these properties (5-8). Nonetheless, questions remain concerning how a chain of nucleosomes connected by linker DNA folds into a condensed 30-nm chromatin fiber under physiological conditions (9) and what the exact arrangements of nucleosomes in the 30-nm fiber are (6). Two principal architectures of fiber arrangement proposed are the solenoid and zig-zag models. They differ significantly in how the linker DNA is arranged within the condensed chromatin fiber. In the solenoid model, the linker DNA is bent such that the consecutive nucleosomes interact with each other and form a helix (10-14); in the zig-zag model, the linker DNA remains straight and crosses the fiber axis so that the consecutive nucleosomes appear at the opposite side of the fiber axis (5, 15-18).The structure of chromatin strongly depends on the salt environment, both in terms of the valence of the ions and their concentration in solution (1). At low salt concentrations, chromatin adopts the extended ''beads-on-a-string'' conformation, whereas at high salt concentrations it folds into compact forms. In the presence of linker histones (H1 or H5) under physiological salt conditions, chromatin forms the folded 30-nm fiber. The histone tails are known to be crucial for the folding of chromatin fibers (19-21; reviewed in ref. 22). The tail domains, accounting for Ϸ50% of the positive charges of the histone octamer, are located at the N-terminal portions of H2A, H2B, H3, and H4, and ...

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supporting

confidence: 74%

Electrostatic mechanism of nucleosomal array folding revealed by computer simulation

Sun

Zhang

Schlick

2005

Proc. Natl. Acad. Sci. U.S.A.

106

113

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“…This works for DNA [22] but not in the case of chromatin. The discrete and complex nature of the chromatin assembly leads to difficult and cumbersome computations in order to determine the linker shape, as it can be seen in the work of Schiessel et al [7]. Moreover, this approach fails to give an analytical solution except when the relaxed fiber exhibits a special geometry, for example a ribbon-like flat structure.…”

Section: Discussionmentioning

confidence: 99%

“…A second approach has been performed recently by Schiessel et al [7]. As discussed below (VII.B), its basic step is to relate the strains at the DNA and fiber scales (instead of the stresses, as performed here in Section IV).…”

Section: F Comparison With Chromatin Fiber Pulling Experimentsmentioning

confidence: 99%

Chromatin: A tunable spring at work inside chromosomes

2001

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This paper focuses on mechanical aspects of chromatin biological functioning. Within a basic geometric modeling of the chromatin assembly, we give for the first time the complete set of elastic constants (twist and bend persistence lengths, stretch modulus and twist-stretch coupling constant) of the so-called 30-nm chromatin fiber, in terms of DNA elastic properties and geometric properties of the fiber assembly. The computation naturally embeds the fiber within a current analytical model known as the "extensible worm-like rope", allowing a straightforward prediction of the forceextension curves. We show that these elastic constants are strongly sensitive to the linker length, up to 1 bp, or equivalently to its twist, and might locally reach very low values, yielding a highly flexible and extensible domain in the fiber. In particular, the twist-stretch coupling constant, reflecting the chirality of the chromatin fiber, exhibits steep variations and sign changes when the linker length is varied. We argue that this tunable elasticity might be a key feature for chromatin function, for instance in the initiation and regulation of transcription.

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“…The geometrical wedge-shape of NCPs 344,363 and interaction-mediated 364 constraints anticipated for isolated NCPs will interfere with constraints of continuous DNA ''wrapping'' through the fiber structure. Looping and bending of linker DNAs 365 influenced by binding of linker H1/H5 histones is another stabilization mechanisms of a particular forms of ''30 nm'' chromatin fibers.…”

Section: Implications For the Fiber Structurementioning

confidence: 99%

Electrostatic interactions in biological DNA-related systems

Cherstvy

2011

Phys. Chem. Chem. Phys.

153

141

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In this perspective article, we focus on recent developments in the theory of charge effects in biological DNA-related systems. The electrostatic effects on different levels of DNA organization are considered, including the DNA-DNA interactions, DNA complexation with cationic lipid membranes, DNA condensates and DNA-dense cholesteric phases, protein-DNA recognition, DNA wrapping in nucleosomes, and inter-nucleosomal interactions. For these systems, we develop a theoretical framework to describe the physical-chemical mechanisms of structure formation and anticipate some biological consequences. General biophysical principles of DNA compaction in chromatin fibers and DNA spooling inside viral capsids are discussed in the end, with emphasis on electrostatic aspects.

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DNA Folding: Structural and Mechanical Properties of the Two-Angle Model for Chromatin

Cited by 106 publications

References 36 publications

Electrostatic mechanism of nucleosomal array folding revealed by computer simulation

Electrostatic mechanism of nucleosomal array folding revealed by computer simulation

Chromatin: A tunable spring at work inside chromosomes

Electrostatic interactions in biological DNA-related systems

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