The role of regulated degradation in controlling cytoplasmic mRNA levels

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This project will provide novel insights into how messenger RNA (mRNA) molecules are degraded. In cells, mRNA levels reflect a balance between synthesis and degradation. Whereas, many studies have focused on mRNA synthesis, not many yet have centered on degradation. This research seeks to fill this gap as a way to obtain a more complete picture of how gene expression levels are controlled. The experimental approaches will include analysis of large genomics data sets using statistical and mathematical modeling methods carried out in collaboration between biologists and mathematicians. Therefore the project will offer opportunities for both biology and math students to receive training in areas that are important for the workforce of tomorrow. The project will include individuals at many career stages, including postdoctoral scholars, graduate students, undergraduates, and a small team of high school students. The high school students will work to develop apps that will allow the project data to be easily accessed by scientists, thus enhancing learning of high school students and making the obtained data easily accessible to the broader scientific community. Laboratory personnel will also contribute to the REFUGES program at the University of Utah, which provides training to middle school students from the diverse refugee communities that live in Salt Lake City, Utah. The research addresses mechanisms, specificity, and regulatory roles of cytoplasmic mRNA degradation (also known as decay). Using the plant Arabidopsis thaliana as a model eukaryote, preliminary genome-wide studies revealed two intriguing findings that form the foundation of this project. First, a study of mRNA decay rates, showed that mRNAs have half-lives ranging from less than four minutes to more than 24 hours. The mRNAs with the shortest half-lives tend to encode regulatory proteins, like transcription factors, and proteins that function in signaling, like protein kinases. Moreover, the half-lives of these mRNAs are longer than normal in mutants that lack functional components of the RNA decay machinery. These results led to the hypothesis that mRNAs with high turnover rates might be regulated by a selective stabilization mechanism, perhaps modulated by phosphorylation of proteins involved in the decay machinery. Experiments will address this hypothesis by analyzing decay rates under different environmental conditions that induce rapid changes in phosphorylation, and testing whether phosphorylation of proteins known to participate in mRNA decay affects decay rates or association with other decay-associated protein subunits. The second preliminary observation to be pursued in this project is that the presence of specific codons in mRNAs affects the mRNA decay rates. This suggested that mRNA decay might occur in association with the process of protein synthesis, or translation. This idea will be tested by analyzing the effect of altered tRNA levels and by testing decay rates of mRNAs with altered codon use. In addition, a direct search for mutants impaired in this process will be conducted to identify components of this translation-coupled decay pathway. Together, the results of the research are expected to reveal novel insights into the process of mRNA decay and thereby provide a more comprehensive view of the factors that help balance mRNA levels in the cellular cytoplasm.