In-depth analysis of the recent five experimental nucleosome datasets reveals the broad disagreements between the final nucleosome positions detected by the previous studies. Using signal processing methods, we found two distinct nucleosome distribution domains which evidently emerge from promoter and coding regions. We calculated and confirmed that the fuzzy nucleosomes fall into the dynamic domain, and well-positioned nucleosomes fall into the stable one. By combining the domains information with gene properties, transcription factors binding sites (TFBs) and DNA bendability, we revealed the relationship between the two domains with TATA and TATA_less genes. Then, investigating the link between the two domains and the histone H3 modifications, we observed that the extremely rapid-replacing histone H3 occurs at the immediate downstream of transcription start sites (TSS) rather than +1 nucleosome position. Finally, we presented a slots model for nucleosome assembly in the yeast genome to explain the mechanism of nucleosome forming in the genes promoter regions.
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