Instituut-Lorentz for Theoretical Physics, Leiden University, P.O. Box 9506, 2300 RA Leiden, The Netherlands.
Section de Mathématiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
Phys Rev E. 2017 May;95(5-1):052402. doi: 10.1103/PhysRevE.95.052402. Epub 2017 May 8.
About three quarters of our DNA is wrapped into nucleosomes: DNA spools with a protein core. It is well known that the affinity of a given DNA stretch to be incorporated into a nucleosome depends on the geometry and elasticity of the basepair sequence involved, causing the positioning of nucleosomes. Here we show that DNA elasticity can have a much deeper effect on nucleosomes than just their positioning: it affects their "identities". Employing a recently developed computational algorithm, the mutation Monte Carlo method, we design nucleosomes with surprising physical characteristics. Unlike any other nucleosomes studied so far, these nucleosomes are short-lived when put under mechanical tension whereas other physical properties are largely unaffected. This suggests that the nucleosome, the most abundant DNA-protein complex in our cells, might more properly be considered a class of complexes with a wide array of physical properties, and raises the possibility that evolution has shaped various nucleosome species according to their genomic context.
大约四分之三的 DNA 被包裹在核小体中：带有蛋白质核心的 DNA 线轴。众所周知，给定的 DNA 片段与核小体结合的亲和力取决于涉及的碱基序列的几何形状和弹性，从而导致核小体的定位。在这里，我们表明 DNA 的弹性对核小体的影响远不止于它们的定位：它会影响它们的“身份”。我们采用最近开发的计算算法——突变蒙特卡罗方法，设计出具有惊人物理特性的核小体。与迄今为止研究过的任何其他核小体不同，这些核小体在受到机械张力时寿命很短，而其他物理性质则基本不受影响。这表明核小体，即我们细胞中最丰富的 DNA-蛋白质复合物，可能更应该被视为具有广泛物理性质的一类复合物，并提出了这样一种可能性，即进化根据基因组背景塑造了各种核小体物种。
