A deformation energy model reveals sequence-dependent property of nucleosome positioning.

IF 2.5 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Chromosoma Pub Date : 2021-03-01 Epub Date: 2021-01-16 DOI:10.1007/s00412-020-00750-9

Guoqing Liu, Hongyu Zhao, Hu Meng, Yongqiang Xing, Lu Cai

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Abstract

We present a deformation energy model for predicting nucleosome positioning, in which a position-dependent structural parameter set derived from crystal structures of nucleosomes was used to calculate the DNA deformation energy. The model is successful in predicting nucleosome occupancy genome-wide in budding yeast, nucleosome free energy, and rotational positioning of nucleosomes. Our model also indicates that the genomic regions underlying the MNase-sensitive nucleosomes in budding yeast have high deformation energy and, consequently, low nucleosome-forming ability, while the MNase-sensitive non-histone particles are characterized by much lower DNA deformation energy and high nucleosome preference. In addition, we also revealed that remodelers, SNF2 and RSC8, are likely to act in chromatin remodeling by binding to broad nucleosome-depleted regions that are intrinsically favorable for nucleosome positioning. Our data support the important role of position-dependent physical properties of DNA in nucleosome positioning.

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变形能模型揭示了核小体定位的序列依赖特性。

我们提出了一种预测核小体定位的形变能模型，该模型利用从核小体晶体结构中获得的与位置相关的结构参数集来计算DNA形变能。该模型成功地预测了芽殖酵母中全基因组的核小体占据率、核小体自由能以及核小体的旋转定位。我们的模型还表明，芽殖酵母中对 MNase 敏感的核小体所处的基因组区域具有较高的形变能，因此核小体形成能力较低；而对 MNase 不敏感的非组蛋白颗粒则具有更低的 DNA 形变能和较高的核小体偏好性。此外，我们还发现重塑因子 SNF2 和 RSC8 很可能通过与宽泛的核糖体缺失区域结合而在染色质重塑中发挥作用，这些区域本质上有利于核糖体定位。我们的数据支持 DNA 的位置依赖性物理特性在核小体定位中的重要作用。

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来源期刊

Chromosoma 生物-生化与分子生物学

CiteScore

3.30

自引率

6.20%

发文量

审稿时长

1 months

期刊介绍： Chromosoma publishes research and review articles on the functional organization of the eukaryotic cell nucleus, with a particular emphasis on the structure and dynamics of chromatin and chromosomes; the expression and replication of genomes; genome organization and evolution; the segregation of genomes during meiosis and mitosis; the function and dynamics of subnuclear compartments; the nuclear envelope and nucleocytoplasmic interactions, and more. The scope of Chromosoma encompasses genetic, biophysical, molecular and cell biological studies. Average time from receipt of contributions to first decision: 22 days Publishes research and review articles on the functional organization of the eukaryotic cell nucleus Topics include structure and dynamics of chromatin and chromosomes; the expression and replication of genomes; genome organization and evolution; the segregation of genomes during meiosis and mitosis and more Encompasses genetic, biophysical, molecular and cell biological studies.