Nucleosomes are the most abundant protein–DNA complexes in eukaryotes that provide compaction of genomic DNA and are implicated in regulation of transcription, DNA replication and repair. The details of DNA positioning on the nucleosome and the DNA conformation can provide key regulatory signals. Hydroxyl-radical footprinting (HRF) of protein–DNA complexes is a chemical technique that probes nucleosome organization in solution with a high precision unattainable by other methods. In this work we propose an integrative modeling method for constructing high-resolution atomistic models of nucleosomes based on HRF experiments. Our method precisely identifies DNA positioning on nucleosome by combining HRF data for both DNA strands with the pseudo-symmetry constraints. We performed high-resolution HRF for Saccharomyces cerevisiae centromeric nucleosome of unknown structure and characterized it using our integrative modeling approach. Our model provides the basis for further understanding the cooperative engagement and interplay between Cse4p protein and the A-tracts important for centromere function.

中文翻译：

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羟基自由基足迹与分子建模相结合可识别DNA构象和核小体定位的独特特征

核小体是真核生物中含量最丰富的蛋白质-DNA复合物，可提供基因组DNA的紧实性，并参与转录，DNA复制和修复的调控。DNA在核小体上的定位细节和DNA构象可以提供关键的调控信号。蛋白质-DNA复合物的羟自由基足迹（HRF）是一种化学技术，可以高精度地探测溶液中的核小体组织，这是其他方法无法达到的。在这项工作中，我们提出了一种基于HRF实验构建核小体高分辨率原子模型的综合建模方法。我们的方法通过将两条DNA链的HRF数据与伪对称约束相结合，精确地鉴定了DNA在核小体上的定位。我们对酿酒酵母进行了高分辨率HRF未知结构的着丝粒核小体，并使用我们的整合建模方法对其进行了表征。我们的模型为进一步了解Cse4p蛋白与着丝粒功能重要的A区之间的合作参与和相互作用提供了基础。