EAGER: Development of the PARE approach for genome-wide profiling of mRNA decay in Arabidopsis

基因的调节可能发生在许多步骤中，其中一些步骤通常一次使用基因组方法进行数千或数万次的研究。这些方法中的许多都集中在mRNA上，因为完整的mRNA对基因功能是必不可少的。这个项目将扩展PARE(RNA末端平行分析)的能力，这是一种新的基因组学方法，它允许通过检查细胞丢弃的信使核糖核酸分子片段来研究基因调控。对这些细胞垃圾进行筛选，一次筛选数百万个分子，将是识别以前遗漏的新类型调控的有效方法。PARE以前非常成功地检测到mRNAs的破坏是由称为miRNAs的调节器引起的。这项工作将开发PARE，用于使用参考植物拟南芥检测范围更广的mRNA片段。还将研究不同组织中产生的信使核糖核酸片段的模式，以及植物暴露在不利环境条件下的模式。这应该会导致识别那些被干旱、高温等因素控制在mRNA破坏水平上的基因。这项工作应该是一个重大的进步，因为以前很难研究来自mRNA破坏的细胞垃圾，如下所述，PARE具有广泛的适用性。拟议研究的广泛影响。PARE作为研究基因调控的下一代技术的发展将在许多方面产生深远的影响。利用PARE来研究环境胁迫反应，可能会为植物抗逆性研究提供新的途径。它还将有助于解释来自其他方法的现有数据，这些方法无法将完整的mRNA从mRNA片段中分离出来。更重要的是，由于信使核糖核酸及其破坏在从细菌到人类的所有生物体中都是至关重要的，这个项目将使在所有这些系统中使用PARE来研究在任何条件下信使核糖核酸的破坏是如何调节的成为可能。这些数据将在我们方便用户的网站上向全世界公开，并提供分析工具。一名博士后助理将在该项目下得到指导，它还应该导致新的合作，并让其他科学家甚至可能是普通公众接触到这项工作。

The regulation of genes can occur at many steps, some of which are routinely investigated thousands or tens of thousands at a time using genomic approaches. Many of these methods focus on mRNA because intact mRNA is essential for gene function. This project will expand the capabilities of PARE (Parallel Analysis of RNA Ends), a new genomics method that allows gene regulation to be studied by examining pieces of mRNA molecules that cells are throwing away. Sifting through this cellular trash, millions of molecules at a time, will be a powerful way to identify new types of regulation that were missed previously. PARE was previously very successful for detecting mRNAs whose destruction was caused by regulators called miRNAs. This work will develop PARE for detection of a much broader range of mRNA pieces using the reference plant Arabidopsis. The patterns of mRNA pieces produced in different tissues and when plants are exposed to adverse environmental conditions will also be investigated. This should result in the identification of genes that are controlled at the level of mRNA destruction by drought, high temperature and more. The work should represent a major advance because the cellular trash from mRNA destruction has been very difficult to study previously and PARE is broadly applicable as discussed below.Broader impacts of the proposed researchThe development of PARE as a next-generation technology for the study of gene regulation will be far-reaching in many ways. The use of PARE to the study environmental stress responses, may suggest new ways to make plants stress-resistant. It will also help interpret existing data from other approaches that can not separate intact mRNAs from mRNA pieces. More importantly, because mRNA and its destruction are critical in all organisms from bacteria to man, this project will make it possible to use PARE in all of these systems to study how mRNA destruction is regulated under any condition. The data will be made publicly available worldwide on our user-friendly websites with tools for its analysis. A postdoctoral associate will be mentored under the project, and it should also lead to new collaborations and expose other scientists and potentially the general public to the work.