Lawrimore Josh, He Yunyan, Forest Gregory M, Bloom Kerry
Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Methods Mol Biol. 2019;2004:291-318. doi: 10.1007/978-1-4939-9520-2_21.
Chromatin dynamics and organization can be altered by condensin complexes. In turn, the molecular behavior of a condensin complex changes based on the tension of the substrate to which condensin is bound. This interplay between chromatin organization and condensin behavior demonstrates the need for tools that allows condensin complexes to be observed on a variety of chromatin organizations. We provide a method for simulating condensin complexes on a dynamic polymer substrate using the polymer dynamics simulator ChromoShake and the condensin simulator RotoStep. These simulations can be converted into simulated fluorescent images that are able to be directly compared to experimental images of condensin and fluorescently labeled chromatin. Our pipeline enables users to explore how changes in condensin behavior alters chromatin dynamics and vice versa while providing simulated image datasets that can be directly compared to experimental observations.
凝聚素复合体可改变染色质动力学和组织。反过来，凝聚素复合体的分子行为会根据其结合底物的张力而变化。染色质组织与凝聚素行为之间的这种相互作用表明，需要有工具能够在各种染色质组织上观察凝聚素复合体。我们提供了一种使用聚合物动力学模拟器ChromoShake和凝聚素模拟器RotoStep在动态聚合物底物上模拟凝聚素复合体的方法。这些模拟可以转换为模拟荧光图像，能够直接与凝聚素和荧光标记染色质的实验图像进行比较。我们的流程使用户能够探索凝聚素行为的变化如何改变染色质动力学，反之亦然，同时提供可直接与实验观察结果进行比较的模拟图像数据集。
