Genome-wide mapping of nucleosome position and histone code polymorphisms in yeast

Abstract

Nucleosomes are the building blocks of chromatin and control the physical access of regulatory proteins to DNA either directly or through epigenetic changes. Its positioning across the genome leaves a significant impact on the DNA dependent processes, particularly on gene regulation. Though they form structural repeating units of chromatin they differ from each other by DNA/histone covalent modifications establishing diversity in natural populations. Such differences include DNA methylation and histone post translational modifications occurring naturally or by the influence of environment. DNA methylation and histone post translational modifications interact with DNA resulting in gene expression level changes without altering the DNA sequences and show high degree of variation among individuals. Therefore, precise mapping of nucleosome positioning across the genome is essential to understand the genome regulation. Nucleosome positions and histone borne polymorphism are usually detected by MNase-Seq and ChIP-CHIP/ChIP-Seq techniques, respectively. Various computational software are put forth to analyze the data and create high resolution maps, which would offer precise knowledge about nucleosome positioning and genomic locations associated with histone tail modifications. This chapter describes genome level mapping of nucleosome positions and histone code polymorphisms in yeast Saccharomyces cerevisiae.