Joint Colloquium Distinguished Lecture Series

Modeling and Analysis of High-Throughput RNA Structure Mapping Experiments

Sharon Aviran

Wednesday, April 10, 2013
306 Soda Hall (HP Auditorium)
4:00 - 5:00 pm
3:30 - Refreshments will be served

Sharon Aviran
Postdoctoral Fellow, Center for Computational Biology, Molecular and Cell Biology and Mathematics, UC Berkeley

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ABSTRACT:
New regulatory roles continue to emerge for both natural and engineered RNAs, many of which have specific structures essential to their function. This highlights a growing need to develop technologies that enable rapid and accurate characterization of RNA structure. Yet, available techniques that are reliable are also vastly limited, while the accuracy of popular computational methods is generally poor. These limitations pose a major barrier to determination of structure from sequence.

To address this need, we have developed a high-throughput structure characterization assay, called SHAPE-Seq, which simultaneously measures structural information at nucleotide-resolution for hundreds of distinct RNAs. SHAPE-Seq combines a novel chemistry with next-generation sequencing of its products. Following sequencing, we extract the structural information using a fully automated algorithmic pipeline that we developed. In this talk, I will focus on SHAPE-Seq's analysis methodology, which relies on a novel probabilistic model of a SHAPE-Seq experiment, adjoined by maximum-likelihood parameter estimation. I will demonstrate the accuracy, simplicity, and efficiency of our approach, and will then present an algorithm that uses such structure mapping data to inform computational RNA secondary structure prediction.

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