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

基因的调节可以发生在许多步骤中，其中一些是使用基因组方法一次常规地研究数千或数万个步骤。这些方法大多集中在mRNA上，因为完整的mRNA对基因功能至关重要。该项目将扩大PARE （RNA末端平行分析）的能力，PARE是一种新的基因组学方法，可以通过检查细胞丢弃的mRNA分子片段来研究基因调控。筛选这些细胞垃圾，一次筛选数百万个分子，将是识别以前错过的新类型调控的有力方法。PARE以前非常成功地检测了被称为miRNAs的调节因子破坏的mrna。这项工作将利用参考植物拟南芥开发PARE来检测更广泛的mRNA片段。当植物暴露于不利的环境条件时，不同组织中mRNA片段的产生模式也将被研究。这将导致鉴定出受干旱、高温等因素的mRNA破坏水平控制的基因。这项工作应该是一个重大的进步，因为以前很难研究mRNA破坏产生的细胞垃圾，而PARE的应用范围很广，如下所述。PARE作为下一代基因调控研究技术的发展将在许多方面产生深远的影响。利用PARE技术研究植物对环境胁迫的反应，可能为植物的抗逆性研究提供新的途径。它也将有助于解释其他方法的现有数据，这些方法不能将完整的mRNA从mRNA片段中分离出来。更重要的是，由于mRNA及其破坏在从细菌到人类的所有生物中都是至关重要的，因此该项目将使在所有这些系统中使用PARE来研究mRNA破坏在任何条件下是如何调节的成为可能。这些数据将在我们用户友好的网站上向全世界公开，并提供分析工具。一名博士后将在该项目下接受指导，它还应该导致新的合作，并让其他科学家和潜在的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.