Institute Lorentz for Theoretical Physics, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands.
Univ Lyon, ENS de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique and Centre Blaise Pascal, F-69342 Lyon, France.
Phys Rev E. 2017 Nov;96(5-1):052412. doi: 10.1103/PhysRevE.96.052412. Epub 2017 Nov 28.
The positions along DNA molecules of nucleosomes, the most abundant DNA-protein complexes in cells, are influenced by the sequence-dependent DNA mechanics and geometry. This leads to the "nucleosome positioning code", a preference of nucleosomes for certain sequence motives. Here we introduce a simplified model of the nucleosome where a coarse-grained DNA molecule is frozen into an idealized superhelical shape. We calculate the exact sequence preferences of our nucleosome model and find it to reproduce qualitatively all the main features known to influence nucleosome positions. Moreover, using well-controlled approximations to this model allows us to come to a detailed understanding of the physics behind the sequence preferences of nucleosomes.
DNA 分子上核小体的位置受序列依赖的 DNA 力学和几何形状的影响，核小体是细胞中最丰富的 DNA-蛋白质复合物。这导致了“核小体定位密码”，即核小体对某些序列基序的偏好。在这里，我们引入了一个简化的核小体模型，其中粗粒化的 DNA 分子被冻结成理想化的超螺旋形状。我们计算了我们的核小体模型的精确序列偏好，并发现它定性地再现了所有已知影响核小体位置的主要特征。此外，使用对此模型的精心控制的近似，使我们能够深入了解核小体序列偏好背后的物理原理。
