Iowa State University is awarded a grant to study alternative splicing in plants genes across species and gene expression platforms. Until recently, the complexity with which genes are encoded and decoded to build proteins has been greatly underestimated. Specifically, Alternative Splicing (AS) is the process of decoding a single gene's DNA into different protein products by mixing and matching different sections of the gene into alternative transcripts. One theory is that intron retention AS allows plants to rapidly adapt to stress. This project will exploit the large amount of existing expression data in the form of micro, exon, and tiling array data sets and use it to integrate with the deluge of new short-read sequence datasets to find and confirm exon skipping alternative splicing. The alternative splicing gene results will be integrated into a plant systems biology framework of metabolic pathways which specify context and interactions between chemical species. The aims of the project include: 1) Integration and comparison of alternative splicing patterns across expression platforms; 2) Development of model-based methods of splicing based on signal processing methods; 3) Integrating the alternatively spliced gene information with regulatory network models and metabolic pathway information.
Key innovation in this work comes from the integration of the engineering discipline of signal processing which focuses on estimating signal parameters and separating signals from noise to the problem of estimating the key parameters of exon and intron expression in RNAseq data. The research will compare the highly-domesticated plant, maize (Zea mays), to grape (Vitis vinifera), a less domesticated plant that is highly reactive to environmental effects. Understanding the similarities and differences between plant AS may be very important in creating future crops that can cope with extremes of temperature, precipitation, and pathogens. All results will be made publicly available at the PLant and pathogen EXpression database website (PLEXdb.org) as part of the gene atlas tool that allows users to perform comparative analysis between plant species across different experimental factors.
The project website is: www.eng.iastate.edu/~julied/research/AlternativeSplicing.