UCLA

High-throughput sequencing makes it possible to study epigenetic properties such as DNA methylation genome-wide with single base pair precision. Two research projects were done studying epigenetic properties in plants using high-throughput sequencing using DNA from the model organism Arabidopsis Thaliana. The first project looks at the conservation of DNA methylation on an evolutionary time scale to determine to what degree DNA methylation is conserved with respect to the underlying DNA sequence. This is done by comparing pairs of duplicated genes in Arabidopsis resulting from a genome duplication event 40-80 million years ago in addition to non-coding repeats in the genome. DNA methylation was found to be significantly conserved but methylated cytosines had a tendency to deaminate to thymine which was the most common type of mutation in the underlying DNA sequence. In the second project DNA methylation, nucleosome density and gene expression are compared between tissues in Arabidopsis. Using shoots (entire above ground section) and roots as two different tissues, significant epigenetic differences are found in certain genes, related in function, between the two tissue types. Methylation and nucleosome density are found to be periodic in nature and similar between shoot and root at a genome-wide scale. Positioning of methylation and nucleosomes across the gene body show significant change among genes that are differentially expressed between shoot and root.