Nucleosome interactions in chromatin: fiber stiffening and hairpin formation

Abstract

We use Monte Carlo simulations to study attractive and excluded volume interactions between nucleosome core particles in 30 nm-chromatin fibers. The nucleosomes are treated as disk-like objects having an excluded volume and short range attraction modelled by a variant of the Gay-Berne potential. The nucleosomes are connected via bendable and twistable linker DNA in the crossed linker fashion. We investigate the influence of the nucleosomal excluded volume on the stiffness of the fiber. For parameter values that correspond to chicken erythrocyte chromatin we find that the persistence length is governed to a large extent by that excluded volume whereas the soft linker backbone elasticity plays only a minor role. We further find that internucleosomal attraction can induce the formation of hairpin configurations. Tension-induced opening of such configurations into straight fibers manifests itself in a quasi-plateau in the force-extension curve that resembles results from recent micromanipulation experiments. Such hairpins may play a role in the formation of higher order structures in chromosomes like chromonema fibers.

11 pages, 5 figures, Phys. Rev. E, in press

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Cited by in corpus (6)

• Thermodynamic pathways to genome spatial organization in the cell nucleus
• Controlled DNA compaction within chromatin: the tail-bridging effect
• The two-angle model and the phase diagram for Chromatin
• The influence of the cylindrical shape of the nucleosomes and H1 defects on properties of chromatin
• Condensation of circular DNA
• Conditions for positioning of nucleosomes on DNA