DNA Physical Parameters Modulate Nucleosome Positioning in the Saccharomyces cerevisiae Genome

Nucleosome positioning plays essential roles in various cellular processes. Although many efforts have been made in this area, the rules defining nucleosome positioning is still elusive. In the present study, DNA physical parameters derived from atomistic molecular dynamic simulations were introduced to analyze nucleosomal and linker DNA sequences. The distinct structural patterns between nucleosomal and linker sequences indicate that DNA physical parameters are suitable to describe nucleosomal DNA sequences and to reveal physical mechanisms of nucleosome positioning. Further analysis of DNA flexibility around regulatory regions indicates that nucleosome positioning is closely correlated with sequence flexibility. These results demonstrate that DNA physical parameters are useful for the in silico nucleosome positioning prediction.