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Nucleosomal Context of Binding Sites Influences Transcription Factor Binding Affinity and Gene Regulation

Genomics, Proteomics & Bioinformatics 2009年第4期7卷 155-162页

作者： zhiming dai xianhua dai qian xiang jihua feng Electronic Department Sun Yat-Sen University Guangzhou 510006 China.

Transcription factor （TF） binding to its DNA target site plays an essential role in gene regulation. The location, orientation and spacing of transcription factor binding sites （TFBSs） also affect regulatory function of the TF. However, how nucleosomal context of TFBSs influences TF binding and subsequent gene regulation remains to be elucidated. Using genome-wide nucleosome positioning and TF binding data in budding yeast, we found that binding affinities of TFs to DNA tend to decrease with increasing nucleosome occupancy of the associated binding sites. We further demonstrated that nucleosomal context of binding sites is correlated with gene regulation of the corresponding TF. Nucleosome-depleted TFBSs are linked to high gene activity and low expression noise, whereas nucleosome-covered TFBSs are associated with low gene activity and high expression noise. Moreover, nucleosome-covered TFBSs tend to disrupt coexpression of the corresponding TF target genes. We conclude that nucleosomal context of binding sites influences TF binding affinity, subsequently affecting the regulation of TFs on their target genes. This emphasizes the need to include nucleosomal context of TFBSs in modeling gene regulation.

关键词： gene regulation nucleosome transcription factor binding site

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Insights into DNA signals for nucleosome positioning

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Frontiers of Electrical and Electronic Engineering in China 2008年第4期3卷 388-393页

作者： zhiming dai xianhua dai jihua feng qian xiang Yangyang DENG Jiang WANG Department of Electronic Engineering Sun Yat-sen UniversityGuangzhou 510275China

The nucleosome is the fundamental unit of eukaryotic *** positioning in the promoter region plays a central role in regulating gene *** evidence suggests that the genomic DNA sequence is one important determinant of nucleosome *** approaches have been developed to predict nucleosome positions based on DNA sequence features,but the results indicate that there is room for *** paper presents a new computational approach to predict genome-wide nucleosome locations in promoter ***,the proposed approach outperforms existing approaches in *** anal-ysis demonstrates that DNA signals for nucleosome posi-tioning vary with species and composition of *** of individual genes reveals that the role of the underlying DNA sequence in nucleosome positioning var-ies with genes.

关键词： nucleosome DNA sequence preferences nucleosome positioning signals

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