Mechanisms of chromatin organization in genome dictated by DNA structural properties.

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Gene expression in eukaryotic cells involves the interaction of proteins with DNA packaged into nucleosomes. Nucleosomes are often located at distinct positions in promoter regions to regulate transcription. Thus, the factors that influence the nucleosome positioning are essential to elucidating the mechanism of gene expression. In this project, we have examined the role of DNA structures in chromatin organization and its effect on gene expression in vivo.1.Effect of DNA structures on nucleosome positioning in vivo.We have examined effect of simple repeating sequences that can form alternative DNA conformations on nucleosome positioning using yeast minichromosome system. The repeating sequences are categorized into 4 groups in terms of nucleosome-promoting and nucleosome-disrupting properties.2.Effect of chromatin alteration through DNA structures on repression in yeast genome.In Saccharomyces cerevisiae, nucleosomes are precisely positioned in the promoters of a cell-specific genes such as STE6 and BAR1. Here, we have demonstrated that chromatin alteration by intrinsic DNA structures disrupts repression of BAR1 in genome and of STE6-lacZ reporter plasmids in a cells. Therefore, proper nucleosome positioning is essential for regulation of cell type-specific transcription and cell type identity.3.Effect of triplet repeat sequences on chromatin organization.We have shown that triplet repeat sequences that cause human hereditary diseases affect nucleosome organization in yeast minichromosomes. Their effect on gene expression is associated with their features on chromatin structure. The sticky DNA formation at longer GAA repeats from Friedreich's ataxia was also investigated in yeast minichromosomes.In summary, intrinsic DNA structures play important roles in nucleosome organization in vivo. Our studies also emphasizes that chromatin alteration through DNA structures would make it possible to modulate gene expression artificially in eukaryotes.