Sivolob A V, Khrapunov S N
Department of General Molecular Genetics, Shevchenko University of Kiev, Ukraine.
J Mol Biol. 1995 Apr 14;247(5):918-31. doi: 10.1006/jmbi.1994.0190.
A model has been derived that accounts for the nucleosome translational position in terms of the bending free energy that depends on the nearest-neighbor interactions between base-pairs. The available data on the nucleosome positioning on defined DNA sequences in the reconstituted systems have been analyzed. It has been shown that the model allows one to predict the preferred nucleosome translational positioning with an accuracy of about one turn of the double helix. The conclusion is made that the isotropic elastic properties of the DNA molecule are very important for nucleosome translational positioning. The anisotropic flexibility modulates the sequence-dependent preference and defines the precise rotational placement. The analysis points to a possible involvement of DNA bendability in nucleosome structural transitions. To model the nucleosome positioning within the chromatin fiber, the derived algorithm has been applied to random DNA sequences. The nucleosome distribution obtained is close to random, but nucleosomes, according to calculations, are placed on sites with a low value of bending free energy and decreased G+C-content. Relations with other work and some implications are discussed.
已经推导了一个模型，该模型根据取决于碱基对之间最近邻相互作用的弯曲自由能来解释核小体的平移位置。对重构系统中定义的DNA序列上核小体定位的现有数据进行了分析。结果表明，该模型能够以约双螺旋一圈的精度预测核小体的首选平移定位。得出的结论是，DNA分子的各向同性弹性特性对核小体的平移定位非常重要。各向异性柔韧性调节序列依赖性偏好并定义精确的旋转位置。分析指出DNA弯曲性可能参与核小体结构转变。为了模拟染色质纤维内的核小体定位，已将推导的算法应用于随机DNA序列。获得的核小体分布接近随机，但根据计算，核小体位于弯曲自由能值低且G+C含量降低的位点上。讨论了与其他工作的关系和一些启示。
