变形能模型揭示了核小体定位的序列依赖性。

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

机构信息

School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China.

Inner Mongolia Key Lab of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, 014010, China.

出版信息

Chromosoma. 2021 Mar;130(1):27-40. doi: 10.1007/s00412-020-00750-9. Epub 2021 Jan 16.

DOI:10.1007/s00412-020-00750-9

PMID:33452566

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7889546/

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.

摘要

我们提出了一个用于预测核小体定位的变形能模型，该模型使用来自核小体晶体结构的位置相关结构参数集来计算 DNA 变形能。该模型成功地预测了出芽酵母中的全基因组核小体占有率、核小体自由能和核小体的旋转定位。我们的模型还表明，在出芽酵母中，MNase 敏感核小体下的基因组区域具有较高的变形能，因此核小体形成能力较低，而 MNase 敏感的非组蛋白颗粒的特点是 DNA 变形能低得多，核小体偏好性高。此外，我们还揭示了 SNF2 和 RSC8 等重塑因子可能通过结合内在有利于核小体定位的广泛核小体耗尽区域来发挥染色质重塑的作用。我们的数据支持 DNA 位置相关物理特性在核小体定位中的重要作用。