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Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae

机译：酿酒酵母基因组中一致的核小体位置揭示了结构限制

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Background Recent advances in the field of high-throughput genomics have rendered possible the performance of genome-scale studies to define the nucleosomal landscapes of eukaryote genomes. Such analyses are aimed towards providing a better understanding of the process of nucleosome positioning, for which several models have been suggested. Nevertheless, questions regarding the sequence constraints of nucleosomal DNA and how they may have been shaped through evolution remain open. In this paper, we analyze in detail different experimental nucleosome datasets with the aim of providing a hypothesis for the emergence of nucleosome-forming sequences. Results We compared the complete sets of nucleosome positions for the budding yeast (Saccharomyces cerevisiae) as defined in the output of two independent experiments with the use of two different experimental techniques. We found that Conclusion Our findings may be combined into a hypothesis for the emergence of a weak nucleosome-positioning code. According to this hypothesis, consistent nucleosomes may be partly guided by nearby nucleosome-free regions through statistical positioning. Once established, a set of well-positioned consistent nucleosomes may impose secondary constraints that further shape the structure of the underlying DNA. We were able to capture these constraints through the application of a recently introduced structural property that is related to the symmetry of DNA curvature. Furthermore, we found that both consistently positioned nucleosomes and their adjacent nucleosome-free regions show an increased tendency towards conservation of this structural feature.
机译：背景技术高通量基因组学领域的最新进展使得进行基因组规模的研究以定义真核生物基因组的核小体景观成为可能。此类分析旨在更好地了解核小体定位过程，为此提出了几种模型。然而，关于核小体DNA的序列限制以及如何通过进化来塑造它们的问题仍然悬而未决。在本文中，我们详细分析了不同的实验核小体数据集，目的是为核小体形成序列的出现提供一个假设。结果我们使用两种不同的实验技术，比较了两个独立实验的输出中定义的出芽酵母（酿酒酵母）的完整核小体位置。我们发现结论结论我们的发现可能与关于弱核小体定位代码出现的假设结合在一起。根据该假设，一致的核小体可以通过统计定位部分地由附近的无核小体区域引导。一旦建立，一组位置良好的一致核小体可能会施加次级约束，从而进一步塑造基础DNA的结构。我们能够通过应用最近引入的与DNA曲率对称性相关的结构特性来捕获这些约束。此外，我们发现一致定位的核小体及其相邻的无核小体的区域均显示出这种结构特征保守的趋势。

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