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

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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.