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.
Keywords: DNA flexibility, DNA physical parameters, nucleosome positioning, replication origin, transcription start site,
transcription termination site.
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