Electrostatic mechanism of nucleosomal array folding revealed by computer simulation

Abstract

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 ...

Topoisomerase II, not topoisomerase I, is the proficient relaxase of nucleosomal DNA

“…In the first place, chromatin structure may differently affect their substrate availability. Torsional elasticity of chromatin could be smaller than for naked DNA, leading to a smaller driving torque and thus to a low activity of topo I. Conversely, chromatin might favor DNA transport activity of topo II by increasing the juxtaposition probability of DNA segments (Sun et al, 2005). Such increase may be significant in ( þ ) supercoiled chromatin.…”

Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions

“…The modeling approach involves Monte Carlo simulations of a coarse-grained ''mesoscale'' chromatin model that accounts for important structural and energetic components whereas still making oligonucleosome simulations computationally feasible (26)(27)(28)(29). Because experimental observations emphasize the polymorphic and irregular nature of chromatin fiber in vitro and in vivostemming from linker DNA flexibility, rotational flexibility of DNA in the nucleosome core, and flexible histone tails that interact with the DNA and counterions within as well as between the nucleosomes (11, 30)-our mesoscale modeling approach uniquely takes into account histone-tail flexibility, linker-histone electrostatics and orientation, Mg 2ϩ -induced electrostatic screening, and linker-DNA bending at physiological conditions, as well as thermal fluctuations and entropic effects.…”

From Macroscopic to Mesoscopic Models of Chromatin Folding

“…The algorithms create designed to create an irregular surface for the nucleosome so that tail geometries (though rigid) are captured (top) [37]. This model captured the salt-dependent folding and unfolding of chromatin (bottom) at different univalent salt environment [38]. Figure 8: Mesoscopic oligonucleosome model.…”

“…Our first-generation "macroscopic" models treated the nucleosome and the wound DNA according to general mechanical and electrostatic properties, with the histone tails approximated as rigid bodies and linker histones neglected ( Fig. 3) [24,35,36,37,38]. As Fig.…”

“…Hence modeling fiber structure and motion requires specialized models that treat the system's electrostatics as accurately as possible -since these features are thought to be crucial for chromatin organization -while approximating others so as to make possible studies of nucleosome arrays (or oligonucleosomes) with sufficient configurational sampling (e.g., 100 million configurations) or simulation times of milliseconds and longer to be biologically relevant. In recent years, a variety of computational models have been developed (e.g., [22,23,24,25,26,27,28]). …”