Intellectual Merit. The product of gene expression (or transcription), RNA and the product of these RNAs (via translation), namely proteins, often interact to allow numerous post-transcriptional mechanisms to control mRNA expression and translation. In fact, from the initial synthesis of transcripts in the nucleus to their final translation and decay in the cytoplasm, mRNAs are involved in a multitude of complex interactions with hundreds of RNA binding proteins (RBPs), resulting in the formation of dynamic multi-component ribonucleoprotein complexes (RNPs). The importance of these RNPs to plant biology has been demonstrated by studies revealing that plant developmental, hormone, and stress responses require many RBPs with diverse functions and regulatory targets within the plant transcriptome. In fact, crop plants over- or under-expressing specific RBPs can be made more resistant to certain biotic and abiotic stresses. Thus, RNA-protein interactions are necessary for the functionality, processing, and regulation of many RNA molecules in plant cells. Unfortunately, there is still very little known about the global landscape of RNA-protein interactions in plants. To this end, this project will use a novel technology to uncover these RNA-protein interactions and their effect on the plant transcriptome and translatome during hormone and stress responses. This research will also begin to reveal the conservation of RNA-protein interaction sites within the plant kingdom. Overall, this project will provide unprecedented insights into the role of RNA-protein interactions in regulating eukaryotic gene expression, as well as provide important new findings and resources for future studies focused on crop improvement and plant-focused biofuel research.
Broader Impacts. This project will have a significant impact on biological research, and the classroom as well. Specifically, a key feature of this project is that it provides many research opportunities for graduate, undergraduate, and high school students. Furthermore, the data obtained from this research will provide a resource not only to other scientists, but also for use in an RNA Biology course to develop teaching modules focused on ribonucleoprotein complexes and for computational-based analyses of high-throughput sequencing data for use in Genome Sciences courses. These teaching modules will be made freely available, so that faculty and students at other institutions can make use of them. These freely available teaching resources will also be made appropriate for high school level learning. Overall, this project will have a broad impact on the training and development of future scientists, with a focus on computer-aided research methods.