The role of regulated degradation in controlling cytoplasmic mRNA levels

该项目将为信使RNA(信使RNA)分子如何降解提供新的见解。在细胞中，信使核糖核酸水平反映了合成和降解之间的平衡。然而，许多研究都集中在信使核糖核酸的合成上，还没有太多的研究集中在降解上。这项研究试图填补这一空白，以此来更全面地了解基因表达水平是如何控制的。实验方法将包括使用生物学家和数学家合作进行的统计和数学建模方法对大型基因组数据集进行分析。因此，该项目将为生物和数学专业的学生提供机会，让他们在对未来劳动力至关重要的领域接受培训。该项目将包括许多职业阶段的个人，包括博士后学者、研究生、本科生和一小群高中生。高中生将致力于开发应用程序，使科学家能够轻松访问项目数据，从而促进高中生的学习，并使获得的数据更容易被更广泛的科学界访问。实验室人员还将为犹他大学的避难所项目做出贡献，该项目为居住在犹他州盐湖城的不同难民社区的中学生提供培训。这项研究解决了细胞质mRNA降解(也称为衰变)的机制、特异性和调节作用。利用植物拟南芥作为真核生物的模型，初步的全基因组研究揭示了两个有趣的发现，构成了这个项目的基础。首先，一项对信使核糖核酸衰减率的研究表明，信使核糖核酸的半衰期从不到4分钟到超过24小时不等。半衰期最短的mRNAs倾向于编码调节蛋白，如转录因子，以及起信号作用的蛋白质，如蛋白激酶。此外，在缺乏RNA衰退机制功能组件的突变体中，这些mRNAs的半衰期比正常情况下要长。这些结果导致了一种假设，即高周转率的mRNAs可能受到选择性稳定机制的调节，可能是由参与衰退机制的蛋白质的磷酸化来调节的。实验将通过分析不同环境条件下的衰减率来解决这一假说，这些环境条件会导致磷酸化的快速变化，并测试已知的参与mRNA衰变的蛋白质的磷酸化是否会影响衰减率或与其他衰变相关的蛋白质亚基的联系。本项目要进行的第二个初步观察是，mRNAs中特定密码子的存在会影响mRNAs的mRNAs衰减率。这表明，mRNA的衰退可能与蛋白质合成或翻译过程有关。这一想法将通过分析tRNA水平变化的影响和测试密码子使用变化的mRNAs衰减率来检验。此外，还将对在这一过程中受损的突变体进行直接搜索，以确定这一翻译耦合衰变途径的成分。总而言之，这项研究的结果有望揭示对mRNA衰退过程的新见解，从而提供有助于平衡细胞质中mRNA水平的因素的更全面的视角。

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.