Identification and characterization of DNA methylation variation within maize

Abstract

DNA methylation is a genetic modification known to repress the activity of transposable elements, repetitive sequences, and in some cases genes. Although DNA methylation is often found in common locations across different individuals, evidence has shown that DNA methylation can vary between individuals at certain loci and can therefore have the opportunity to create a unique regulatory environment for the surrounding sequence. Beyond this, the relationship between DNA methylation state and the genetic content of an individual is still unclear. DNA methylation may act as a downstream effect of certain genetic signals, or it may act independently of genetic state as an epigenetic modification. The goal of this thesis is to profile the DNA methylation landscape across maize (Zea mays) and identify the genomic regions that display differential DNA methylation patterns. These regions of differential methylation are then further studied to understand their stability across generations, their influences on gene expression, as well as their connection to the genetic context they are found. The chapters describe the identification of thousands of differentially methylated regions (DMRs) between maize lines. These DMRs are shown to occur throughout the genome and have high stability across generations. In contrast, few DMRs are found across different tissues within the same genotype. DMRs are shown to often be associated with the local genetic variation. This genetic relationship is highlighted, along with the discovery of a mechanism of genetic control by the spreading of DNA methylation from certain retrotransposable elements. These results indicate that DMRs are present in maize and are created through both epigenetic and genetic means.