Poster abstracts
Poster number 37 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), Julius B. Lucks (Department of Chemical and Biological Engineering, Northwestern University)
Abstract:
RNAs enact numerous cellular functions through the formation of intricately folded structures. High-throughput RNA structure probing experiments couple chemical probing of RNA structure with high-throughput sequencing. These experiments can be used to determine signatures of biologically relevant structures in order 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. These limitations include 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 collected from these experiments. This in turn has prevented rigorous comparison of experimental results within and between laboratories.
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. Our preliminary studies have shown the value of standards to correct for experimental variation, and we have additionally used these standard RNAs to compare and evaluate current experimental methods of high-throughput RNA structure probing. These RNAs serve as a strategy 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