The function and properties of RNA Polymerase IV in seed development

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This research investigates the mechanisms that control successful plant seed development. Plant seeds are fundamental to of all agriculture. Seeds are complex structures, consisting of a protective seed coat, an embryo, and a nutritive endosperm. Endosperm is one of the most important tissues in the biosphere – it provides two-thirds of the calories consumed by humans. Although endosperm does not pass on any genetic material to the next generation, proper endosperm development is essential for the formation of viable seeds and the completion of the flowering plant life cycle. This project focuses on the contribution of a plant-specific RNA polymerase, RNA Pol IV, to endosperm development and function. The research will increase fundamental understanding of endosperm biology and may facilitate the development of plant hybrids. This project also provides interdisciplinary, cutting-edge training for undergraduates from groups under-represented in science, graduate students, and postdocs in genomics, plant biology, epigenetics, biophysics, and bioinformatics. Teachers will also participate in aspects of the proposed research, facilitating transfer of the excitement of scientific discovery and scientific reasoning to their students. Endosperm has an unusual genetic constitution – it is typically triploid, with two maternally-inherited and one paternally-inherited genomes. RNA Pol IV regulates transcriptional programs and the balance of expression between maternal and paternal gene copies in endosperm. It is known that RNA Pol IV is required for the biogenesis of 24 nucleotide small RNAs. Typically, these small RNAs arise from transposable elements and other repetitive sequences and direct DNA methylation to matching genomic regions in a process termed RNA-directed DNA methylation. DNA methylation is an epigenetic mark that can influence transcription. However, in endosperm the relationship between Pol IV activity, small RNAs, DNA methylation, and gene expression profiles is not predictable based on current understanding of this pathway. The goal of the proposed research is to determine how, when, and where RNA Pol IV acts to influence gene transcription and to regulate expression from maternally- and patternally-derived genomes in Arabidopsis thaliana endosperm. Current thought suggests that RNA Pol IV mediates conflict between maternal and paternal genomes in the endosperm. The specific objectives of the research are to determine how RNA Pol IV activity in endosperm regulates gene expression and to determine the genetic and molecular basis of antagonistic RNA Pol IV maternal and paternal effects. Diverse genetic, genomic, biophysical, and developmental biology approaches will be employed to address these aims. The research activities will provide substantial new understanding of the epigenetic processes that act before and after fertilization to mediate parental genetic conflicts and promote seed viability.This project is co-funded by the Genetic Mechanisms Program in the Division of Molecular and Cellular Biosciences and by the Plant Genome Research Program in the Division of Integrative Organismal Systems, both in the Directorate for Biological Sciences.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.