Arabidopsis 2010: Analysis of the Ribonucleases of Arabidopsis Thaliana

University Of Delaware, Newark DE

Investigators

Abstract

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.