ヌクレオソームポジショニングにおける間接認識の役割

Role of indirect recognition in nucleosome positioning

Fernandez, M.*; 藤井 聡*; 河野 秀俊; 皿井 明倫*

Fernandez, M.*; Fujii, Satoshi*; Kono, Hidetoshi; Sarai, Akinori*

Nucleosomes are the primary organizational units of chromatin in Eukaryotic chromosomes. They are composed of about 147 DNA base pairs wrapped around a histone octamer. Classical computational methods have limitations to analyze nucleosomes because of the weak sequence-dependent signal for nucleosome positioning. In general, proteins can recognize specific DNA sequences not only by direct contacts between amino acids and bases (direct readout) but also through conformational properties of DNA (indirect readout). Because of peculiar conformation of DNA in the nucleosome structure, indirect readout may play important role in nucleosome positioning along the genome. We calculated conformation energies of DNA by threading DNA sequences around crystal structures of nucleosomes. The strength of the conformation energy oscillates at frequency 10 bps for dinucleotides, in agreement with the previous nucleosome models, in which distinctive sequence motifs recurring periodically at the DNA helical repeat are known to facilitate the sharp bending of DNA around the nucleosome. The DNA conformation energy calculated along yeast genome positively correlated with nucleosome positioning experimentally measured.