Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany.
Faculty of Physics, Ludwig-Maximilians-Universität München, 80333 München, Germany.
Phys Rev E. 2020 Feb;101(2-1):022405. doi: 10.1103/PhysRevE.101.022405.
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.
大约四分之三的真核生物 DNA 被包裹在核小体中；DNA 缠绕在带有蛋白质核心的核小体上。已知特定 DNA 片段被纳入核小体的亲和力取决于 DNA 双螺旋的碱基对序列依赖性几何形状和弹性。这导致了核小体的旋转和平移定位。在这项研究中，我们提出了这样一个问题，即后者是否可以通过具有序列依赖性弹性的简单粗粒 DNA 模型，即刚性碱基对模型来预测。虽然该模型在预测旋转核小体定位方面非常稳健，但我们表明，平移定位是一种相当微妙的效应，主要由熵而不是能量的鸟嘌呤-胞嘧啶含量依赖性决定。在刚性碱基对框架内进行正确的定性预测，只能通过假设 DNA 弹性在与核小体复合物复合时会有效改变来实现。通过这个额外的假设，我们得到了一个模型，该模型在假设核小体仅在局部平衡其位置的额外假设下，与实验体外核小体图谱非常吻合。
