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Open Access Publications from the University of California

Studying Nucleosome Positioning, DNA Methylation, and Other Epigenetic Factors Using Genomic Approaches

  • Author(s): Chodavarapu, Ramakrishna Kant
  • Advisor(s): Pellegrini, Matteo
  • et al.

Epigenomics is the genome-wide study of the factors that cause changes to gene expression, but are not directly related to the primary DNA sequence. Among these factors are DNA methylation, nucleosome positioning, and histone modifications. Two epigenomic projects are described here. The first describes a ten base periodicity of DNA methylation and an enrichment of DNA methylation over nucleosomal DNA. It also describes nucleosomes being enriched over exons and being placed preferentially at intron-exon boundaries. The other describes an integrative study of BS-seq, RNA-seq, and siRNA-seq data in rice hybrids. SNPs were found between two closely related subspeicies of rice at a rate of 1/253 bp and the frequency of DNA methylation differences between the ecotypes was much higher at nearly 8%. DNA methylation differences between the parents and the hybrids were much more muted, at nearly 1%. It also describes the impact of the DNA methylation differences on differential expression of genes between the parents and the hybrids and the two ecotypes. The dissertation includes a brief discussion on the main methods employed in these two studies as well.

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