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首页> 外文期刊>Genomics >DNA physical properties outperform sequence compositional information in classifying nucleosome-enriched and -depleted regions
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DNA physical properties outperform sequence compositional information in classifying nucleosome-enriched and -depleted regions

机译：DNA物理特性优于分类核小体和 - 封闭区域的序列组成信息

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摘要

The nucleosome is the fundamental structural unit of eukaryotic chromatin and plays an essential role in the epigenetic regulation of cellular processes, such as DNA replication, recombination, and transcription. Hence, it is important to identify nucleosome positions in the genome. Our previous model based on DNA deformation energy, in which a set of DNA physical descriptors was used, performed well in predicting nucleosome dyad positions and occupancy. In this study, we established a machine-learning model for predicting nucleosome occupancy in order to further verify the physical descriptors. Results showed that (1) our model outperformed several other sequence compositional information-based models, indicating a stronger dependence of nucleosome positioning on DNA physical properties; (2) nucleosome-enriched and -depleted regions have distinct features in terms of DNA physical descriptors like sequence-dependent flexibility and equilibrium structure parameters; (3) gene transcription start sites and termination sites can be well characterized with the distribution patterns of the physical descriptors, indicating the regulatory role of DNA physical properties in gene transcription. In addition, we developed a web server for the model, which is freely accessible at http://lin-group.cn/server/iNuc-force/.
机译：核小核心是真核染色质的基本结构单元，在细胞过程的表观遗传调节中起重要作用，例如DNA复制，重组和转录。因此，重要的是鉴定基因组中的核心位置。我们基于DNA变形能量的先前模型，其中使用了一组DNA物理描述符，在预测核小体Dyad位置和占用时表现良好。在这项研究中，我们建立了一种用于预测核小体占用的机器学习模型，以进一步验证物理描述符。结果表明，（1）我们的模型表现出几种基于序列组成信息的模型，表明核小体定位对DNA物理性质的依赖性更强; （2）富含核心的富含和预定的区域在DNA物理描述符中具有不同的特征，如序列依赖性灵活性和平衡结构参数; （3）基因转录起始位点和终止位点可以利用物理描述符的分布模式，表明DNA物理性质在基因转录中的调节作用。此外，我们为模型开发了一个Web服务器，可在http://lin-group.cn/server/inuc-force/上自由访问。

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