Evaluation of DNA Intramolecular Interactions for Nucleosome Positioning in Yeast

Michael Fernandez[1] (re0701m@bio.kyutech.ac.jp)
Satoshi Fujii[1] (s.fujii@bio.kyutech.ac.jp)
Hidetoshi Kono[2] (kono.hidetoshi@jaea.go.jp)
Akinori Sarai[1] (sarai@bio.kyutech.ac.jp)

[1]Department of Bioscience and Bioinformatics, Kyushu Institute of Technology (KIT), Iizuka, 820-8502, Japan.
[2] Computational Biology Group, Japan Atomic Energy Agency, Kyoto, 619-0215, Japan


We calculated intramolecular interaction energies of DNA by threading DNA sequences around crystal structures of nucleosomes. The strength of the intramolecular energy oscillations at frequency ~10 bps for dinucleotides was in agreement with previous nucleosome models. The intramolecular energy calculated along yeast genome positively correlated with nucleosome positioning experimentally measured.

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Japanese Society for Bioinformatics