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Positional variations among heterogeneous nucleosome maps give dynamical information on chromatin.

Tanaka Y, Yoshimura I, Nakai K - Chromosoma (2010)

Bottom Line: Taken together, our map shows the general information of nucleosome dynamics reasonably well.The "nucleosome dynamics" map provides the new significant correlation with the degree of expression variety instead of their intensity.Furthermore, the associations with gene function and histone modification were also discussed here.

View Article: PubMed Central - PubMed

Affiliation: Department of Medical Genome Sciences, University of Tokyo, Minato-ku, Japan.

ABSTRACT
Although nucleosome remodeling is essential to transcriptional regulation in eukaryotes, little is known about its genome-wide behavior. Since a number of nucleosome positioning maps in vivo have been recently determined, we examined if their comparisons might be used for obtaining a genome-wide profile of nucleosome remodeling. Using seven yeast maps, the local variability of nucleosomes, measured by the entropy, was significantly higher in a set of reported unstable nucleosomes. The binding sites of four transcription factors, known as the remodeling factors, were distinctively high both in entropy and linker ratio, whereas those of Yhp1, their potential inhibitor, showed the lowest values in both of them. Taken together, our map shows the general information of nucleosome dynamics reasonably well. The "nucleosome dynamics" map provides the new significant correlation with the degree of expression variety instead of their intensity. Furthermore, the associations with gene function and histone modification were also discussed here.

Show MeSH
Nucleosome dynamics and histone modifications with the dataset of Pokholok et al., 2005. The asterisk indicates significant difference (P < 0.01 from Wilcoxon test)
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Fig6: Nucleosome dynamics and histone modifications with the dataset of Pokholok et al., 2005. The asterisk indicates significant difference (P < 0.01 from Wilcoxon test)

Mentions: From the comparison with the ChIP–chip data, we found significant differences in entropy for five out of eight modifications (Fig. 6). In monomethylation of H3 lysine 4 (H3K4me1) and trimethylation of H3 lysine 36 (H3K36me3), the entropies in hyper-modified sites were significantly higher than those in hypo-modified sites (P < 1.3e-7 from Wilcoxon test). On the other hand, hyper-acetylation of H3 lysine 14 (H3K14ac) and H4 (H4ac) as well as trimethylation of H3 lysine 4 (H3K4me3) showed significantly lower entropies than their hypo-modifications (P < 2.6e-6). For the linker ratio, small differences were observed in H3K36me3, H3K4me3, and H3K14ac (P < 5.0e-3; Supplementary Fig. 8).Fig. 6


Positional variations among heterogeneous nucleosome maps give dynamical information on chromatin.

Tanaka Y, Yoshimura I, Nakai K - Chromosoma (2010)

Nucleosome dynamics and histone modifications with the dataset of Pokholok et al., 2005. The asterisk indicates significant difference (P < 0.01 from Wilcoxon test)
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2926881&req=5

Fig6: Nucleosome dynamics and histone modifications with the dataset of Pokholok et al., 2005. The asterisk indicates significant difference (P < 0.01 from Wilcoxon test)
Mentions: From the comparison with the ChIP–chip data, we found significant differences in entropy for five out of eight modifications (Fig. 6). In monomethylation of H3 lysine 4 (H3K4me1) and trimethylation of H3 lysine 36 (H3K36me3), the entropies in hyper-modified sites were significantly higher than those in hypo-modified sites (P < 1.3e-7 from Wilcoxon test). On the other hand, hyper-acetylation of H3 lysine 14 (H3K14ac) and H4 (H4ac) as well as trimethylation of H3 lysine 4 (H3K4me3) showed significantly lower entropies than their hypo-modifications (P < 2.6e-6). For the linker ratio, small differences were observed in H3K36me3, H3K4me3, and H3K14ac (P < 5.0e-3; Supplementary Fig. 8).Fig. 6

Bottom Line: Taken together, our map shows the general information of nucleosome dynamics reasonably well.The "nucleosome dynamics" map provides the new significant correlation with the degree of expression variety instead of their intensity.Furthermore, the associations with gene function and histone modification were also discussed here.

View Article: PubMed Central - PubMed

Affiliation: Department of Medical Genome Sciences, University of Tokyo, Minato-ku, Japan.

ABSTRACT
Although nucleosome remodeling is essential to transcriptional regulation in eukaryotes, little is known about its genome-wide behavior. Since a number of nucleosome positioning maps in vivo have been recently determined, we examined if their comparisons might be used for obtaining a genome-wide profile of nucleosome remodeling. Using seven yeast maps, the local variability of nucleosomes, measured by the entropy, was significantly higher in a set of reported unstable nucleosomes. The binding sites of four transcription factors, known as the remodeling factors, were distinctively high both in entropy and linker ratio, whereas those of Yhp1, their potential inhibitor, showed the lowest values in both of them. Taken together, our map shows the general information of nucleosome dynamics reasonably well. The "nucleosome dynamics" map provides the new significant correlation with the degree of expression variety instead of their intensity. Furthermore, the associations with gene function and histone modification were also discussed here.

Show MeSH