Ephemeral protein binding to DNA shapes stable nuclear bodies and chromatin domains
Ephemeral protein binding to DNA shapes stable nuclear bodies and chromatin domains
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DOI：
10.1101/065664
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发表时间：
2016-07
期刊：
影响因子：
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通讯作者：
C. Brackley;B. Liebchen;D. Michieletto;Francois Mouvet;P. Cook;D. Marenduzzo
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文献类型：
--
作者：
C. Brackley;B. Liebchen;D. Michieletto;Francois Mouvet;P. Cook;D. Marenduzzo
荧光显微镜显示，许多(无膜)核“体”的内容物与可溶池快速交换，而底层结构保持不变；这种观察有待令人满意的生物物理解释。为了阐明这一点，我们对染色质纤维与一组(多价)DNA结合蛋白质相互作用进行了大规模的布朗动力学模拟；这些蛋白质在两种状态之间切换--活性(结合)和非活性(非结合)。这个系统为任何DNA结合蛋白提供了一个模型，这些蛋白可以在翻译后被修饰以改变其与DNA的亲和力(例如，像转录因子的磷酸化)。由于这种不平衡的过程，蛋白质自发地组装成大小自我限制的簇，因为簇中的单个蛋白质与可溶池以类似于光漂白实验中看到的动力学进行交换。这种行为与只以结合状态存在的“平衡”或非转换蛋白质的行为形成鲜明对比；当这些蛋白质非特定地与DNA结合时，它们会形成大小无限增长的簇。我们的结果表明，染色质桥蛋白的翻译后修饰是一种通用的机制，推动了具有核体特性的高度动态、非平衡的蛋白质簇的自组装。这种主动的修饰也重塑了染色质内的接触，使网络类似于拓扑相关结构域中的网络，因为开关明显有利于本地(短距离)接触而不是远程接触。
Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To shed light on this, we perform large-scale Brownian dynamics simulations of a chromatin fiber interacting with an ensemble of (multivalent) DNA-binding proteins; these proteins switch between two states – active (binding) and inactive (non-binding). This system provides a model for any DNA-binding protein that can be modified post-translationally to change its affinity for DNA (e.g., like the phosphorylation of a transcription factor). Due to this out-of-equilibrium process, proteins spontaneously assemble into clusters of self-limiting size, as individual proteins in a cluster exchange with the soluble pool with kinetics like those seen in photo-bleaching experiments. This behavior contrasts sharply with that exhibited by "equilibrium", or non-switching, proteins that exist only in the binding state; when these bind to DNA non-specifically, they form clusters that grow indefinitely in size. Our results point to post-translational modification of chromatin-bridging proteins as a generic mechanism driving the self-assembly of highly dynamic, non-equilibrium, protein clusters with the properties of nuclear bodies. Such active modification also reshapes intra-chromatin contacts to give networks resembling those seen in topologically-associating domains, as switching markedly favors local (short-range) contacts over distant ones.