Calculation of nucleosomal DNA deformation energy: its implication for nucleosome positioning

Nucleosome positioning plays an essential role in various fundamental cellular processes by modulating the accessibility of DNA to binding proteins. Understanding the mechanisms and precise recognition of nucleosome positioning along genomic sequences are substantially important for elucidating regulations of cellular processes such as DNA replication, recombination, and gene transcription. In this report, we present a knowledge-based model for calculation of deformational energy of nucleosomal DNA and apply the model to the prediction of nucleosome positioning along the genome of Saccharomyces cerevisiae accurately. The model successfully predicted genome-wide in vitro nucleosome positions. When combined with quadratic discriminant classifier, the model achieved an accuracy of 92.9 % in discriminating in vitro nucleosome forming sequences from nucleosome inhibiting sequences. Our result supports the debated notion that the nucleosome positioning in the genomic sequences is guided primarily by deformational properties of DNA.