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

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

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.

Keywords: nucleosome histone modification DNA Brownian dynamics

Received: 16 November 2009
Revised: 04 January 2010
Accepted manuscript online:

PACS:	87.14.G-	(Nucleic acids)
	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)

Fund: 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).

Cite this article:

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 2010 Chin. Phys. B 19 048701

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

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