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池部 仁善; 桜庭 俊*; 河野 秀俊
no journal, ,
In eukaryotic cells, genome DNA forms nucleosomes composed of DNA wrapped around a histone octamer: two copies of H3, H4, H2A, and H2B histone proteins, and it is compactly stored in the nucleus. The nucleosomes fold into a higher order aggregate, called as chromatin. Although the highly condensed chromatin packing disturbs access of transcriptional factors to DNA, transcription is systematically regulated in vivo. Probably, acetylation will direct dissociation of the tails from DNA, which will result in allowing DNA-binding proteins to access DNA. However, the detailed mechanism has not yet been verified because the conformational information of histone tails is difficult to obtain experimentally and is missing. To elucidate the information, we performed conformational sampling for H3 histone tails with and without acetylation. The results showed that whether acetylated or not, the tails were almost always located nearby DNA and would not dissociate from DNA contrary to the conventional view. The acetylation slightly weakens interactions between the tail and DNA and enhances the alpha-helix formation. We infer that the tail compaction caused by the alpha-helix formation induces unwrapping of DNA at entry and exit regions more and increases the chance of DNA-binding proteins bind to DNA. The results give a new view of how acetylation affects chromatin conformation.
河野 秀俊; 池部 仁善; 桜庭 俊*; 石田 恒
no journal, ,
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.
立和名 博昭*; 有村 泰宏*; 松本 亮平*; 滝沢 由政*; 堀 哲也*; 松本 淳; 小田 隆*; 佐藤 衛*; 河野 秀俊; 深川 竜郎*; et al.
no journal, ,
Centromeres are specific region of chromosomes, which ensure equal chromosome segregation in mitosis. The histone H3 variant, CENP-A, is a key protein for the establishment and maintenance of centromeres. However, little is known about how the incorporation of CENP-A into the chromatin leads to the centromere formation. We reported that a nucleosome containing human CENP-A (CENP-A nucleosome) has different structural feature, by which the CENP-A nucleosome may contribute to organize a unique chromatin structure in centromeres1. Then, we further analysed whether CENP-A nucleosome affects the poly-nucleosome structure using reconstituted tri-nucleosomes. To enable this, we reconstituted the tri-nucleosome, in which single CENP-A nucleosome is arranged at the centre, and two H3 nucleosomes are arranged on the both sides (H3-CA-H3 nucleosomes), by anucleosome-ligation method. Then, we analyzed structures of H3-CA-H3 nucleosomes and control H3-H3-H3 nucleosomes by dynamic light scattering, small angle X-ray scattering, and electron microscopic analyses. We found that single CENP-A nucleosome significantly alters higher order chromatin configuration. Based on these analyses, we propose a chromatin structure containing CENP-A nucleosomes and discuss the advantage of this structure in centromere formation and maintenance.