Brownian dynamics simulation of the cross-talking effect among modified histones on conformations of nucleosomes

doi:10.1088/1674-1056/19/4/048701

中国物理B ›› 2010, Vol. 19 ›› Issue (4): 48701-048701.doi: 10.1088/1674-1056/19/4/048701

Brownian dynamics simulation of the cross-talking effect among modified histones on conformations of nucleosomes

段兆文, 李伟, 谢平, 窦硕星, 王鹏业

Key Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China

收稿日期:2009-11-16 修回日期:2010-01-04 出版日期:2010-04-15 发布日期:2010-04-15
基金资助:
Project supported by the National Natural Science Foundation of China (Grants Nos.~10834014 and 10674173) and the National Basic Research Program of China (Grant No.~2009CB930704).

Brownian dynamics simulation of the cross-talking effect among modified histones on conformations of nucleosomes

Duan Zhao-Wen(段兆文), Li Wei(李伟), Xie Ping(谢平), Dou Shuo-Xing(窦硕星), and Wang Peng-Ye(王鹏业)^†

Key Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China

Received:2009-11-16 Revised:2010-01-04 Online:2010-04-15 Published:2010-04-15
Supported by:
Project supported by the National Natural Science Foundation of China (Grants Nos.~10834014 and 10674173) and the National Basic Research Program of China (Grant No.~2009CB930704).

摘要/Abstract

摘要： Using Brownian dynamics simulation, we studied the effect of histone modifications on conformations of an array of nucleosomes in a segment of chromatin. The simulation demonstrated that the segment of chromatin shows the dynamic behaviour that its conformation can switch between a state with nearly all of the histones being wrapped by DNA and a state with nearly all of the histones being unwrapped by DNA, thus involving the ``cross-talking'' interactions among the histones. Each state can stay for a sufficiently long time. These conformational states are essential for gene expression or gene silence. The simulation also shows that these conformational states can be inherited by the daughter DNAs during DNA replication, giving a theoretical explanation of the epigenetic phenomenon.

Abstract: Using Brownian dynamics simulation, we studied the effect of histone modifications on conformations of an array of nucleosomes in a segment of chromatin. The simulation demonstrated that the segment of chromatin shows the dynamic behaviour that its conformation can switch between a state with nearly all of the histones being wrapped by DNA and a state with nearly all of the histones being unwrapped by DNA, thus involving the ``cross-talking'' interactions among the histones. Each state can stay for a sufficiently long time. These conformational states are essential for gene expression or gene silence. The simulation also shows that these conformational states can be inherited by the daughter DNAs during DNA replication, giving a theoretical explanation of the epigenetic phenomenon.

Key words: nucleosome, histone modification, DNA, Brownian dynamics

中图分类号: (Nucleic acids)

87.14.G-

87.15.B- (Structure of biomolecules) 87.15.H- (Dynamics of biomolecules) 87.15.K- (Molecular interactions; membrane-protein interactions) 87.17.-d (Cell processes)

段兆文, 李伟, 谢平, 窦硕星, 王鹏业. Brownian dynamics simulation of the cross-talking effect among modified histones on conformations of nucleosomes[J]. 中国物理B, 2010, 19(4): 48701-048701.

Duan Zhao-Wen(段兆文), Li Wei(李伟), Xie Ping(谢平), Dou Shuo-Xing(窦硕星), and Wang Peng-Ye(王鹏业). Brownian dynamics simulation of the cross-talking effect among modified histones on conformations of nucleosomes[J]. Chin. Phys. B, 2010, 19(4): 48701-048701.

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Brownian dynamics simulation of the cross-talking effect among modified histones on conformations of nucleosomes

Brownian dynamics simulation of the cross-talking effect among modified histones on conformations of nucleosomes

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