Theory of Active Chromatin Remodeling
Theory of Active Chromatin Remodeling
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DOI：
10.1103/physrevlett.123.208102
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发表时间：
2019-11-13
影响因子：
8.6
通讯作者：
Zhang, Bin
中科院分区：
文献类型：
--
作者：
Jiang, Zhongling;Zhang, Bin
核小体定位控制染色质的可及区域，并在DNA模板化过程中起重要作用。ATP驱动的重塑酶是其在体内建立的关键，但它们的非平衡性质阻碍了核小体定位的统一理论框架的发展。使用微扰理论，我们表明，这些酶的效果可以很好地近似与重新缩放的温度和相互作用的有效平衡模型。数值模拟支持的理论在预测动力学和稳态量，包括有效温度和径向分布函数，在生物相关的制度的准确性。从我们的研究中出现的能量景观视图提供了一个直观的理解重塑酶的影响，无论是加强或抑制核小体定位的内在信号，并可能有助于提高计算机模型预测的准确性。
Nucleosome positioning controls the accessible regions of chromatin and plays essential roles in DNA-templated processes. ATP driven remodeling enzymes are known to be crucial for its establishment in vivo, but their nonequilibrium nature has hindered the development of a unified theoretical framework for nucleosome positioning. Using a perturbation theory, we show that the effect of these enzymes can be well approximated by effective equilibrium models with rescaled temperatures and interactions. Numerical simulations support the accuracy of the theory in predicting both kinetic and steady-state quantities, including the effective temperature and the radial distribution function, in biologically relevant regimes. The energy landscape view emerging from our study provides an intuitive understanding for the impact of remodeling enzymes in either reinforcing or overwriting intrinsic signals for nucleosome positioning, and may help improve the accuracy of computational models for its prediction in silico.