Sequence Requirements for Small RNA Targeting in Plants

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Intellectual Merit: Every cell in a given organism contains exactly the same DNA genome, yet the organism contains many cell types that are differentiated and highly specialized for certain functions. The functional differences between various cell types with the same genome are dictated by the subset of DNA-encoded genes that are activated (turned on) or silenced (turned off). The control of gene expression (on or off) thus plays a fundamental role in shaping cellular function in complex organisms. One type of gene expression control mechanism is directed by small regulatory RNAs. Small RNAs function to identify target RNAs in the cell by RNA-RNA complementarity. Essentially, if a given small RNA has a good match in sequence to a given target RNA, that target RNA will be prevented from being utilized further, and expression of the target gene will be turned off. Small RNA-based methods of gene expression control are prominent in plants, play important roles in normal plant growth and agricultural productivity, and can be exploited in biotechnological applications where control of gene expression is desirable. This project is seeking to understand the rules by which small RNAs recognize their targets in plants. The project specifically will examine the extent and configuration of matching RNA bases required to allow small RNAs to recognize and regulate their targets in plants. The outcome of this project will be a much more complete understanding of how the small RNA-mediated gene expression system is able to discriminate its handful of target RNAs from the thousands of non-target RNAs present in the cell. Broader Impacts: Small RNAs are known to control key aspects of plant growth development, many of them with agricultural significance in crop plants. Small RNAs also dictate the repression of vast portions of plant genomes comprised of parasitic, so-called junk DNA. Manipulation of small RNAs already plays a key role in many plant biotechnology applications, but without a thorough understanding of how small RNAs work, these applications are limited. The understanding of small RNA target identification provided by this project should enhance such applications. This project also involves training of scientists, a critical national goal, both at the Ph.D. level and undergraduate level. One of the project goals will be used as a springboard for developing a new laboratory course in RNA Biology at Pennsylvania State University, thus enhancing scientific literacy and education of these students.