The Project
Major paradigm shifts in understanding gene regulation at the transcriptional and posttranscriptional levels have occurred in recent years through discoveries of RNA-based silencing systems. In plants, these systems form distinct classes of small RNAs (microRNAs, trans-acting siRNA, heterochromatin-associated siRNAs, and others) that associate with effector complexes containing ARGONAUTE proteins to suppress or regulate mRNAs, genetic loci or invasive elements. This 2010 Project proposal takes advantage of new technology to examine small RNA pathways at a genome-wide level using Arabidopsis thaliana as a central model. The Major Objectives of the proposal include:
- Analysis of functions, regulation and evolution of several RNA silencing pathways at a genome-wide level. New enabling technology and computation will be used for sequencing-based profiling of A. thaliana small RNAs in a series of silencing-defective mutants, developmental stages, and treatments, as well as in closely related species. This will provide key data to assess the impact, redundancy and evolution of small RNA pathways in plants.
- Identification of small RNAs and small RNA classes that associate with some of the silencing effector proteins in the ARGONAUTE (AGO) family. Associating small RNAs with effectors will provide a genome-wide benchmark to identify AGO specificities and functional redundancies.
This project will have broad impacts beyond our laboratory. The Arabidopsis Small RNA Database will be continued and expanded as a major public resource for Arabidopsis research. The project will engage undergraduates in a front-line research experience. Additionally, we will develop an exciting high school outreach module in collaboration with Science Education Partnerships (SEPS). This module will be integrated with broader SEPS activities to train teachers and students in new concepts relating to genome-enabled science and gene silencing, using interesting materials generated by this project.
Co-P.I.s -
James C. Carrington and Kristin D. Kasschau
Project Support -
The Arabidopsis Small RNA Project is supported generously by a 2010 Project grant
from the National Science Foundation (MCB-0618433). The project uses facilities and
resources provided by the Department of Botany and Plant Pathology, the Center for
Genome Research and Biocomputing, Oregon State University.
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