Translational nucleosome positioning: A computational study
Physical review. E, vol. 101, pp. 022405
Abstract
About three-quarters of eukaryotic DNA is wrapped into nucleosomes; DNA spools with a protein core. The affinity of a given DNA stretch to be incorporated into a nucleosome is known to depend on the base-pair sequence-dependent geometry and elasticity of the DNA double helix. This causes the rotational and translational positioning of nucleosomes. In this study we ask the question whether the latter can be predicted by a simple coarse-grained DNA model with sequence-dependent elasticity, the rigid base-pair model. Whereas this model is known to be rather robust in predicting rotational nucleosome positioning, we show that the translational positioning is a rather subtle effect that is dominated by the guanine-cytosine content dependence of entropy rather than energy. A correct qualitative prediction within the rigid base-pair framework can only be achieved by assuming that DNA elasticity effectively changes on complexation into the nucleosome complex. With that extra assumption we arrive at a model which gives an excellent quantitative agreement to experimental in vitro nucleosome maps, under the additional assumption that nucleosomes equilibrate their positions only locally.
Authors 3
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Leiden University · Ludwig-Maximilians-Universität München · Max Planck Institute for the Physics of Complex Systems
Affiliation as printed
Faculty of Physics, Ludwig-Maximilians-Universität München, 80333 München, Germany
Instituut-Lorentz, Universiteit Leiden, Postbus 9506, 2300 RA Leiden, The Netherlands
Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
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Affiliation as printed
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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Affiliation as printed
Instituut-Lorentz, Universiteit Leiden, Postbus 9506, 2300 RA Leiden, The Netherlands
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