Poster abstracts

Poster number 93 submitted by Jian Wu

High-throughput RNA 3D motif structure prediction and validation

Jian Wu, Cuiji Zhou, Ying Wang, James Li, Dana Driver (Dept. of Molecular Genetics, Center for Applied Plant Sciences, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210), Neocles Leontis (Dept. of Chemistry, Bowling Green State University, Bowling Green, OH 43403), Craig Zirbel (Dept. of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403), David M. Bisaro (Dept. of Molecular Genetics, Center for Applied Plant Sciences, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210), Biao Ding (Dept. of Molecular Genetics, Center for Applied Plant Sciences, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210)

Abstract:
The genomic RNA and its derivatives of an RNA virus or subviral agent (a viroid, satellite RNA or satellite RNA virus) specifies all biological functions required to establish infection. These functions are accomplished through the encoded protein products or through the regulatory structural elements of the RNA itself. Because RNA-RNA or RNA-protein interactions critical for function are often mediated by local 3D motifs, a key to understand viral evolution and function is genome-wide knowledge of these motifs. X-ray crystallography and NMR have played a major role in deciphering the 3D structures of some viral RNA motifs, but the technical challenges render genome-wide determination of viral RNA local 3D motifs a daunting task. We use Potato spindle tuber viroid (PSTVd) as a model to develop a high-throughput platform for local 3D motif structure analysis, by combining homology-based structural prediction using existing structural information from the database, deep-sequenced viroid population information, and mutagenesis-based functional determination. With this approach we have predicted and validated the 3D structures of many PSTVd loops. We will present our data and discuss the broad implications of our approach.

Keywords: RNA, 3D sturucture, PSTVd