School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China.
Inner Mongolia Key Laboratory for Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, 014010, China.
Sci Rep. 2018 Jun 11;8(1):8853. doi: 10.1038/s41598-018-27247-x.
Nucleosome not only directly affects cellular processes, such as DNA replication, recombination, and transcription, but also severs as a fundamentally important target of epigenetic modifications. Our previous study indicated that the bending property of DNA is important in nucleosome formation, particularly in predicting the dyad positions of nucleosomes on a DNA segment. Here, we investigated the role of bending energy in nucleosome positioning and sliding in depth to decipher sequence-directed mechanism. The results show that bending energy is a good physical index to predict the free energy in the process of nucleosome reconstitution in vitro. Our data also imply that there are at least 20% of the nucleosomes in budding yeast do not adopt canonical positioning, in which underlying sequences wrapped around histones are structurally symmetric. We also revealed distinct patterns of bending energy profile for distinctly organized chromatin structures, such as well-positioned nucleosomes, fuzzy nucleosomes, and linker regions and discussed nucleosome sliding in terms of bending energy. We proposed that the stability of a nucleosome is positively correlated with the strength of the bending anisotropy of DNA segment, and both accessibility and directionality of nucleosome sliding is likely to be modulated by diverse patterns of DNA bending energy profile.
核小体不仅直接影响细胞过程，如 DNA 复制、重组和转录，而且还作为表观遗传修饰的一个基本重要靶标。我们之前的研究表明，DNA 的弯曲性质对于核小体的形成很重要，特别是在预测 DNA 片段上核小体的二分位置方面。在这里，我们深入研究了弯曲能在核小体定位和滑动中的作用，以深入了解序列导向的机制。结果表明，弯曲能是预测体外核小体重建过程中自由能的一个很好的物理指标。我们的数据还表明，在芽殖酵母中，至少有 20%的核小体不采用经典的定位方式，其中围绕组蛋白包裹的潜在序列在结构上是对称的。我们还揭示了不同组织形式的染色质结构的弯曲能图谱的明显模式，如定位良好的核小体、模糊核小体和连接区，并根据弯曲能讨论了核小体滑动。我们提出，核小体的稳定性与 DNA 片段弯曲各向异性的强度呈正相关，核小体滑动的可及性和方向性可能受到不同的 DNA 弯曲能图谱模式的调节。
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