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Nucleosome is the elementary structural unit of eukaryotic chromatin. The instability of nucleosome positioning participates in chromatin remodeling processes of the differentiation and disease. Although positions of nucleosomes have already been distinguished by experimental and computational methods, the interrogation of nucleosome dynamics remains of great interest. In this study, we focused on investigating the characteristic of nucleosome dynamics in Saccharomyces cerevisiae genome by a geometric model based on the Z curve theory. Our model describes the nucleosome sequence feature through one-to-one correspondence between the nucleotide composition of DNA sequences and curves in the three-dimensional space. We distinguished 52941 stable nucleosomes and 7607 dynamical nucleosomes, compiling into a genome-wide nucleosome dynamical positioning map. And a user-friendly visualization platform of this map was also constructed. Analysis revealed that nucleosomes covered almost 70% of the entire genome, and significantly enriched on the exons. Both categories of nucleosomes were depleted near the TSSs or TFBSs to regulate transcription. In our analysis, TFBSs were enriched by linkers. Meanwhile, among the little occupy of nucleosomes around TFBSs, it also a little preferred dynamical nucleosomes. TFBSs occupied by dynamical nucleosomes may relate with transcription activation and deactivation. GO enrichment analysis indicated that stable nucleosomes were enriched on basic biological processes, while dynamical nucleosomes were enriched on developmental and transcriptional regulation processes. Nucleosome dynamics facilitates the access of transcription factors to promoters and other regulatory elements, contributing to gene regulation and their regulatory functions. This study provides a strategy to comprehending chromatin remodeling and transcriptional regulation of genes.
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