Talk abstracts
Talk on Friday 01:30-01:45pm submitted by Molly Evans
Maximizing quantitative structural information from high-throughput RNA structure probing
Molly E. Evans (Department of Chemical and Biological Engineering, Northwestern University), Angela M Yu (Tri-institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine), Petr Sulc (Biodesign Center for Molecular Design and Biomimetics, Arizona State University), Julius B. Lucks (Department of Chemical and Biological Engineering, Northwestern University)
Abstract:
RNAs enact numerous cellular functions through their formation of intricately folded structures. High-throughput RNA structure probing experiments that couple chemical probing of RNA structure to high-throughput sequencing can be used to determine signatures of these biologically relevant structures that can be used to construct models of functional RNA folds. While this experimental approach has so far yielded useful data, several major limitations have precluded our ability to obtain precise and quantitative RNA structural information, including a lack of standards for experimental and data processing steps that result in inconsistent generation and interpretation of the primary chemical probing ‘reactivity’ data that is generated by these experiments. This in turn has prevented rigorous comparison of experimental results within and between experiments.
Here, we have designed and begun to characterize a standard benchmark panel of RNAs of known structure that can be used as experimental calibration standards to allow comparison of reactivities within and between experiments. By implementing calibration standards, measurements of reactivity in RNA structure probing experiments will become more quantitative, allowing the maximal amount of structural information to be extracted from these experiments across laboratories. Additionally, in order to precisely define measured reactivity, we have leveraged our expertise in RNA design by creating a panel of RNAs that vary in sequence but are designed to fold into the same simple secondary structure. Our preliminary studies show that using improved experimental methods, chemical probing reactivities match to the predicted secondary structures of the first panel of RNAs. These RNAs will be used as a starting point to develop and validate an accurate and quantitative definition of chemical probe reactivity that is directly linked to RNA structure.
Keywords: high-throughput structure probing, standardization, SHAPE-Seq