Genome-Wide Mapping of Nucleosome Position and Histone Code Polymorphisms in Yeast
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, par
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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 ChIPCHIP/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. Keywords Acetylation • ChIP • Epigenomics • Histone • Nucleosome • Yeast
M. Nagarajan () • V.R. Prabhu Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasargod 671314, Kerala, India e-mail: [email protected] © Springer International Publishing Switzerland 2016 K.-C. Wong (ed.), Big Data Analytics in Genomics, DOI 10.1007/978-3-319-41279-5_8
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M. Nagarajan and V.R. Prabhu
1 Introduction The size of the eukaryotic DNA is very large and therefore, it must undergo higher levels of compaction to fit well inside the tiny nucleus and concurrently must be able to perform its duty. To solve this issue, negatively charged DNA wraps around positively charged histone proteins and by neutralizing the charge they assemble as a DNA–protein complex known as chromatin. Nucleosomes are the basic repeating structural elements of chromatin which function in a paradoxical way by safeguarding and stabilizing the genetic material by compaction on one hand and on the other hand allowing the DNA to be accessible for various cellular processes. The positions of nucleosomes along a DNA sequence impact gene regulation and various other DNA dependent processes to a great extent. Nucleosome positions are non-random and conserved among similar cell types. Studies have succeeded in identifying factors like chromatin remodeling complexes and the underlying DNA sequences that provide substantial importance in nucleosome studies. But the dynamic and complex nature of these factors hampers the prediction of nucleosome positions in a genome leaving the task more challenging ones. Be
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