The implication of DNA bending energy for nucleosome positioning and sliding.
The implication of DNA bending energy for nucleosome positioning and sliding.
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DNA弯曲能对核小体定位和滑动的影响
DOI：
10.1038/s41598-018-27247-x
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发表时间：
2018-06-11
影响因子：
4.6
通讯作者：
Wang J
中科院分区：
文献类型：
--
作者：
Liu G;Xing Y;Zhao H;Cai L;Wang J
核小体不仅直接影响细胞过程，如DNA复制、重组和转录，而且是表观遗传修饰的根本目标。我们先前的研究表明，DNA的弯曲特性在核小体的形成中很重要，特别是在预测核小体在DNA片段上的二联体位置时。在这里，我们研究了弯曲能在核小体定位和深度滑动中的作用，以破译序列导向机制。结果表明，弯曲能是预测核小体体外重组过程中自由能的一个很好的物理指标。我们的数据还表明，在发芽酵母中，至少有20%的核小体不采用规范定位，其中包裹在组蛋白周围的潜在序列在结构上是对称的。我们还揭示了明显组织的染色质结构的弯曲能量分布的不同模式，如定位良好的核小体、模糊的核小体和连接区，并从弯曲能量的角度讨论了核小体的滑动。我们认为，核小体的稳定性与DNA片段的弯曲各向异性的强度呈正相关，并且核小体滑动的可达性和方向性都可能受到不同模式的DNA弯曲能谱的调制。
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.
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DOI：
10.1080/07391102.2010.10507347
发表时间：
2010-08-01
影响因子：
4.4
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影响因子：
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作者：
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影响因子：
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