EAGER:The Evolutionary Impact of Methylation on Grass Genomes and Gene Expression

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To meet the food needs of future generations in a sustainable manner, an understanding of crop plant growth and development is essential. Information about growth and development is encoded in a plant's DNA, which has four fundamental chemical components, often referred to as A, C, G and T. However, the C can also be modified by a process called methylation, which allows it to function as a 5th information component in DNA. While it is apparent that methylated Cs play an important role in plant growth and development, their role has yet to be fully understood. In this proposal, the number and pattern of methylated Cs among different crop plants will be compared, including barley, einkorn wheat and sorghum. These comparisons will be used to investigate the influence of methylated Cs on the function of genes. The overall goal is to better understand the contribution of methylated Cs to plant growth and development, so that eventually this information can be used for crop improvement.DNA methylation is one of several epigenetic modifications that are crucial to plant genome function. Recent work has also shown that methylation has broad consequences for genome evolution, including the composition of intergenic DNA, as a fundamental evolutionary property of specific genes, and as a driver of compositional biases among genomic regions. Given the importance of epigenetic mechanisms, a thorough understanding of the evolution and function of plant genomes requires characterization of epigenetic variation among plant species. Yet, such a characterization is presently lacking. This project will generate and analyze whole genome bisulfite sequencing (BSseq) and transcript (RNAseq) data for an array of grass species. The data will be released to the Short Read Archive and Gene Expression Omnibus databases prior to publication. The goal is to use the data to better understand the relationship among DNA methylation, gene evolution and gene function, as measured by gene expression. To achieve this end, a series of unique evolutionary analyses will be developed that will address three specific hypotheses: 1) that gene-body methylation is a conserved feature of functionally important genes and maintained over evolutionary time by natural selection; 2) that evolutionary shifts in gene body methylation (and/or the methylation of flanking regions) drive shifts in gene expression between species; and 3) that DNA methylation variation among tissues - specifically in genes and flanking regions - contributes to tissue-specific gene expression.