Function of Arabidopsis Small RNA-ARGONAUTE Complexes

Oregon State University, Corvallis OR

Investigators

Abstract

Intellectual Merit: The genomes of plants and animals have evolved to control the function of genes required for development, response to environmental change, and invasive pathogens. Many of the genes within these organisms are controlled by tiny RNA molecules, called microRNA (miRNA) and short-interfering RNA (siRNA), through a process called gene silencing. The small RNA delivers proteins in the ARGONAUTE (AGO) family to target RNA molecules by functioning as sequence-specific guides. The AGO protein can then cause degradation, mislocalization, or repression of the target RNA, thereby achieving gene regulation. The model plant Arabidopsis contains up to 10 functional AGO proteins, roughly one-half of which have been assigned at least some function or shown to interact with a set of specific small RNA. Extensive analyses have revealed highly abundant, complex landscape of multiple small RNAs (generally 21-24 nucleotides) corresponding to sequences across the plant genome. However, small RNA activity, rather than simply accumulation, is key to understanding small RNA-based silencing on a genome-wide scale. Once small RNA are formed, how and to what extent are AGO-small RNA complexes formed? Once these complexes form, which are active to target other RNA molecules? For the major AGO proteins (AGO1 and AGO10), how are target RNA pools affected at the stabilization and translational repression levels? This project addresses each of these three questions by focusing on how silencing information is processed and managed. Understanding how gene silencing works at the molecular and genome-wide levels will shed light on how plants use and control a large amount of genetic information. Broader Impacts: The project will have significant broader impact beyond the actual scientific results. The project involves front-line participation of undergraduate students in research. Two student researchers will be supported for the duration of the project. The project also provides a clear mentoring plan for two postdoctoral scientists, and involves participation in an outreach collaboration with the Scientists and Teachers Education Partnerships (STEPS, www.steps.org), an Oregon State University-based program that provides training to K-12 teachers and exposure of students to experimental science. The P.I.s work with the STEPS Program Coordinator for Grades 6-12, Dr. Kari Van Zee, to develop summer workshops in the Advances in Biotechnology series. This provides teachers with professional development workshops, lectures, and hands-on training for school-appropriate laboratory experiments. The Arabidopsis Small RNA Project Database, the primary portal for information and data generated by the previous NSF-funded project, will continue to operate in the public domain for anyone seeking genome-wide small RNA data. Programs developed to process and analyze high-throughput sequencing data, such as CASHX and TargetFinder, will continue to be made available through the ASRP website. Finally, this project is leading to better ways to use the inherent genetic potential of plants for our food, fiber, and energy needs.