Arabidopsis 2010: Analysis of the Ribonucleases of Arabidopsis Thaliana

智力优点。 基因的功能和调节对于所有生物体的生长和发育至关重要。为了使基因发挥作用，其 DNA 必须被复制成 RNA，然后翻译成蛋白质以履行基因的作用，或者在某些情况下，RNA 直接发挥作用。 该过程可以通过控制 RNA 产生或降解的机制来调节。 该项目重点研究拟南芥中降解 RNA 的蛋白质，称为核糖核酸酶 (RNase)。 该项目之前的工作研究了一种名为 XRN4 的 RNase，它可以降解一端缺少保护帽的 RNA。 研究发现，XRN4 降解的一些 RNA 是被称为 miRNA 的小 RNA 切割的目标 RNA。 尽管表征 RNA 降解产物对于追踪 RNase 功能至关重要，但大多数 RNA 的降解产物可能难以捉摸，因为它们是异质的且存在量非常低。 该项目之前的工作克服了这些障碍，开发了一种名为 RNA 末端平行分析 (PARE) 的新基因组技术，这是一种用于检测部分降解的 RNA 分子的深度测序技术。 这项技术的一个令人兴奋的应用是在全基因组范围内表征切割的 miRNA 靶标。 该项目的假设是 PARE 将有助于检测 RNase 突变体中不正确降解且无法用不太敏感的方法检测到的 mRNA。这应该为一般的 RNA 降解，特别是 RNase 提供新的见解。 为了测试这些想法，PARE 将应用于选定的 RNase 突变体。 与正常植物中的 RNA 相比，降解发生改变的 RNA 将被鉴定出来。 这可以识别使 RNA 易受 RNase 影响的 RNA 特征，并表明 RNase 控制的新基因和生物过程。最终，这可能会提出农业改良的新策略或具有生物医学相关性。更广泛的影响。 该项目的数据将通过用户友好的网站在全球范围内提供，并提供分析工具，供所有学生、博士后和高级研究人员应用于自己的工作。这项 PARE RNase 工作应该广泛适用于其他植物、动物和微生物，并且可能会增强对无法将降解的 RNA 与完整 RNA 分开的其他基因调控实验的解释。该项目将为博士后助理/副科学家、本科生提供指导和培训，促成新的合作，并使其他科学家和潜在的公众接触到这项工作。

Intellectual Merit. The function and regulation of genes is of fundamental importance for growth and development in all organisms. For a gene to function, its DNA must be copied into an RNA that is then translated into protein to fulfill the gene's role, or in some cases, the RNA functions directly. The process can be regulated by mechanisms that control the production of the RNA or its degradation. This project focuses on the proteins that degrade RNA, which are called ribonucleases (RNases), in Arabidopsis. Prior work under this project studied an RNase called XRN4 that degrades RNAs that are missing a protective cap on one end. The research discovered that some of the RNAs that XRN4 degrades are RNAs targeted for cleavage by small RNAs called miRNAs. Although characterizing RNA degradation products is critical for tracking RNase function, the decay products of most RNAs can be elusive because they are heterogenous and present in very low amounts. Prior work under the project overcame these obstacles with the development of a new genomic technology called Parallel Analysis of RNA Ends (PARE), a deep sequencing technology for detecting partially degraded RNA molecules. An exciting application of this technology was to characterize cleaved miRNA targets genome-wide. The hypothesis underlying this project is that PARE will facilitate detection of mRNAs that are improperly degraded in RNase mutants and that cannot be detected with less sensitive approaches. This should provide new insights about RNA degradation in general and about RNases in particular. To test these ideas, PARE will be applied to selected RNase mutants. RNAs that have altered degradation compared with those in normal plants will be identified. This could identify features of the RNAs that make them susceptible to RNases, and indicate new genes and biological processes that RNases control. Ultimately, this may suggest new strategies for agricultural improvement or have biomedical relevance.Broader Impacts. The data from this project will be available world-wide on user-friendly websites with analysis tools for all students, postdocs and senior investigators to apply to their own work. This PARE RNase work should be broadly applicable to other plants, animals, and microbes, and may enhance interpretation of other experiments on gene regulation that cannot separate degraded from intact RNA. The project will provide mentoring and training to a postdoctoral associate/associate scientist, an undergraduate student, lead to new collaborations, and expose other scientists and potentially the general public to the work.