实验解析的核小体阵列数据分析揭示异质性特征
Data analysis of experimentally solved nucleosome arrays reveals heterogeneous features
对实验解析的原子分辨率核小体阵列结构进行系统分析，发现其几何特征兼具稳健性与异质性，并给出了适用于粗粒化建模的平均参数。异质性体现在相邻核小体的相对取向与定位以及 linker DNA 的开放程度上，其变化范围取决于 linker DNA 长度、核心组蛋白变体、辅助蛋白结合和纤维互穿。作者同时提供了配套网络资源，汇集这些结构系统并附分析工具。用中尺度模型对规则纤维的模拟表明，采用平均参数即可合理重现实验纤维几何，该结果与另文报道的带表观遗传标记的类生命系统一致。该结构表征为染色质架构调控提供新认识，并有助于染色质纤维的模块化设计。
来源：Nucleic Acids Research · doi.org
Atomic-resolution nucleosome array structures have provided invaluable information on eukaryotic genome packing. Although these arrays are often obtained for regular fibers with designed sequences, such information complements in vivo genome organization data and modeling studies. Here, we analyze such systems with a focus on chromatin organization. We highlight both robust and unique features, as well as suitable average values for coarse-grained modeling, such as the relative orientation and positioning of neighboring nucleosomes, and opening of the linker DNA. Our associated web resource (https://www.biomath.nyu.edu/chromstruct/) shares these collected systems and provides tools for their analysis. The heterogeneous features exhibit a wide range of geometrical properties that depend on linker DNA length, core histone protein variants, auxiliary protein binding, and fiber interdigitation. Yet experimental fiber geometries can be reproduced reasonably using average parameters, as demonstrated here by simulations with our mesoscale model for regular fibers and as reported separately for life-like systems with epigenetic marks. Such analysis may also be useful for modular design of chromatin fibers. The structural characterization of these chromatin building blocks provides new insights into the regulation of chromatin architecture and has implications for the modular design of chromatin fibers.