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Report No.

Dynamics of nucleosomes and impact of acetylation

Kono, Hidetoshi; Ikebe, Kimiyoshi; Sakuraba, Shun*; Ishida, Hisashi

Dynamics of the nucleosome and accessibility of nucleosomal DNA play critical roles in many nuclear processes. Nucleosomes themselves are highly dynamic and the nucleosomal DNA is spontaneously unwrapped to make it accessible to various DNA-binding proteins. Histone variants are known for each of histone proteins and are supposed to have different roles in the regulation of nuclear processes. In addition, post-translational modifications of histones have been known to affect the regulation, but it is still unknown how they affect changes of the structure and dynamics of chromatin. Through computer simulations, we are investigating the following topics to understand the dynamics of nucleosomes: (1) how much it costs for unwrapping nucleosomal DNA from the histone core, (2) how different the dynamics are among nucleosomes composed of histone variants and (3) how acetylation of histone tails impacts on nucleosome structures. Our simulations suggest that the cost for unwrapping 1bp of DNA from histone core is 0.1 to 0.4 kcal/mol and it changes according to nucleosome types. In the dissociation of nucleosomal DNA, asymmetric unwrapping (unwrapping either end of DNA) became remarkable when the DNA unwrapping reached the inner turn, probably because DNA-DNA repulsion disappeared at this stage, thereby histone-DNA interactions were stabilized. Acetylation of K14 of H3 tail enhanced the DNA flexibility.



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