Department of Electronic, School of Information Science and Technology, Sun Yat-Sen University, Guangzhou 510006, China.
Bioinformatics. 2011 Jul 1;27(13):1758-64. doi: 10.1093/bioinformatics/btr290. Epub 2011 May 6.
The intrinsic DNA sequence is an important determinant of nucleosome positioning. Some DNA sequence patterns can facilitate nucleosome formation, while others can inhibit nucleosome formation. Nucleosome positioning influences the overall rate of sequence evolution. However, its impacts on specific patterns of sequence evolution are still poorly understood.
Here, we examined whether nucleosomal DNA and nucleosome-depleted DNA show distinct polymorphism patterns to maintain adequate nucleosome architecture on a genome scale in yeast. We found that sequence polymorphisms in nucleosomal DNA tend to facilitate nucleosome formation, whereas polymorphisms in nucleosome-depleted DNA tend to inhibit nucleosome formation, which is especially evident at nucleosome-disfavored sequences in nucleosome-free regions at both ends of genes. Sequence polymorphisms facilitating nucleosome positioning correspond to stable nucleosome positioning. These results reveal that sequence polymorphisms are under selective constraints to maintain nucleosome positioning.
固有 DNA 序列是核小体定位的重要决定因素。一些 DNA 序列模式可以促进核小体的形成，而另一些则可以抑制核小体的形成。核小体定位影响序列整体进化速度。然而，其对特定序列进化模式的影响仍知之甚少。
在这里，我们研究了在酵母中，核小体 DNA 和无核小体 DNA 是否表现出不同的多态性模式，以维持基因组范围内足够的核小体结构。我们发现，核小体 DNA 中的序列多态性倾向于促进核小体的形成，而无核小体 DNA 中的多态性倾向于抑制核小体的形成，这在基因两端无核小体区域的核小体非偏好序列中尤为明显。有利于核小体定位的序列多态性对应于稳定的核小体定位。这些结果表明，序列多态性受到选择性压力的限制，以维持核小体定位。
