Intellectual merit: The genes that an organism inherits from its mother and father are usually expressed at similar levels. However, some genes exhibit the phenomenon of imprinted expression, in which the maternally and paternally inherited gene copies, or alleles, are not expressed equally. Imprinting is considered epigenetic because the expression level of maternally and paternally inherited alleles is not determined by the DNA sequence. Imprinting is critical for normal development in flowering plants and mammals. In plants, imprinting primarily occurs in endosperm, the embryo-nourishing tissue found within seeds. Differential expression of maternally and paternally inherited alleles of a gene in the endosperm is often correlated with differential cytosine DNA methylation, a chemical modification to the DNA that serves as a key epigenetic mark. The methylation differences frequently occur at sequences that resemble transposable elements, invasive pieces of DNA that can move throughout the genome and are usually methylated. These results have led to the hypothesis that imprinted gene expression arises as a byproduct of epigenetic control of transposable elements. Because the presence, genomic location, and epigenetic modification of transposable elements are variable within and between closely related species, this research will test the hypothesis that many instances of imprinting could be specific to alleles from certain genetic backgrounds. Using high-throughput genome-wide approaches to take advantage of natural genetic and epigenetic variation, imprinted expression and DNA methylation will be assessed in three plant species with distinct modes of reproduction and genome structure, Arabidopsis thaliana, Arabidopsis lyrata, and Zea mays, to test specific hypothesis about the mechanism, evolution, and function of imprinting in plants. There has been relatively little effort directed at understanding the degree of conservation or variability of imprinting within and between species. Examples of conserved imprinting between distantly related plant species like Arabidopsis and maize might reflect instances in which the process of imprinting has been repeatedly adopted at a particular gene to regulate endosperm development. This research is likely to have substantial outcomes in further determining the functional consequences of imprinting and in understanding how the control of transposable elements can lead to important developmental regulatory processes. In addition, the project will provide a better understanding of the differences in maternal and paternal contributions to offspring in plant species.
Broader Impacts: This project provides interdisciplinary education and training opportunities for high school students, undergraduates, a graduate student and a postdoctoral fellow. The research will require the integration of classical genetics, molecular biology, genomics, and bioinformatics. This provides a valuable opportunity for biologists to become skilled in bioinformatics analysis and computer scientists to become conversant in biology. These skills are increasingly necessary as new technologies drive biology to become more quantitative. Undergraduate students from primarily undergraduate minority-serving institutions who do not have access to top-notch research facilities will work on the project for three summers under the guidance of the postdoctoral fellow. This experience will provide critical research experience for the undergraduates and important training in mentoring for the postdoctoral fellow. Additionally, high school students will take advantage of tools created as part of this research to learn about the plant life cycle and mechanisms of inheritance.