The role of regulated degradation in controlling cytoplasmic mRNA levels

调控降解在控制细胞质 mRNA 水平中的作用

• 批准号: 1616779
• 负责人: Leslie Sieburth
• 金额: $ 88万
• 依托单位: University of Utah
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-09-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1616779&HistoricalAwards=false
• 关键词: role; regulated; degradation; controlling; cytoplasmic

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.

该项目将为信使RNA（mRNA）分子如何降解提供新的见解。在细胞中，mRNA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mRNA的合成，还没有很多集中在降解。这项研究试图填补这一空白，以获得基因表达水平如何控制的更完整的图片。 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，该项目将为生物学和数学学生提供机会，接受对未来劳动力重要的领域的培训。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，本科生和一个小型的高中生团队。 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，从而提高高中生的学习能力，并使更广泛的科学界能够轻松访问所获得的数据。 实验室人员还将为犹他州大学的难民项目做出贡献，该项目为来自犹他州湖城不同难民社区的中学生提供培训。该研究涉及细胞质mRNA降解（也称为衰变）的机制，特异性和调节作用。利用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，形成了这个项目的基础。 首先，一项关于mRNA衰变率的研究表明，mRNA的半衰期从不到4分钟到超过24小时不等。具有最短半衰期的mRNA倾向于编码调节蛋白，如转录因子，以及在信号传导中起作用的蛋白质，如蛋白激酶。 此外，这些mRNA的半衰期比缺乏RNA衰变机制的功能组分的突变体中的正常值长。这些结果导致了这样的假设，即具有高周转率的mRNA可能受到选择性稳定机制的调节，可能受到参与衰变机制的蛋白质磷酸化的调节。实验将通过分析不同环境条件下诱导磷酸化快速变化的衰变率来解决这一假设，并测试已知参与mRNA衰变的蛋白质的磷酸化是否影响衰变率或与其他衰变相关蛋白质亚基的关联。第二个初步观察是mRNA中特定密码子的存在会影响mRNA的衰变率。这表明mRNA的降解可能与蛋白质合成或翻译过程有关。这个想法将通过分析改变的tRNA水平的影响和通过测试改变密码子使用的mRNA的衰变率来测试。 此外，将进行直接搜索在此过程中受损的突变体，以确定此衰减耦合衰变途径的组成部分。 总之，研究结果有望揭示mRNA衰变过程的新见解，从而提供更全面的观点，帮助平衡细胞质中mRNA水平的因素。