title: SHAPE-Seq: High-Throughput RNA Structure Analysis.
abstract: Knowledge of RNA structure is critical to understanding both the important functional roles of RNA in biology and the engineering of RNA to control biological systems. This article contains a protocol for selective 2'-hydroxyl acylation analyzed by primer extension and sequencing (SHAPE-Seq) that, through a combination of structure-dependent chemical probing and next-generation sequencing technologies, achieves structural characterization of hundreds of RNAs in a single experiment. This protocol is applicable in a variety of conditions, and represents an important tool for understanding RNA biology. The protocol includes methods for the design and synthesis of RNA mixtures for study, and the construction and analysis of structure-dependent sequencing libraries that reveal structural information of the RNAs in the mixtures. The methods are generally applicable to studying RNA structure and interactions in vitro in a variety of conditions, and allows for the rapid characterization of RNA structures in a high-throughput manner. Curr. Protoc. Chem. Biol. 4:275-297 © 2012 by John Wiley & Sons, Inc.
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, California.
authors.forename: Stefanie A
authors.initials: SA
authors.lastname: Mortimer
authors.forename: Cole
authors.initials: C
authors.lastname: Trapnell
authors.forename: Sharon
authors.initials: S
authors.lastname: Aviran
authors.forename: Lior
authors.initials: L
authors.lastname: Pachter
authors.forename: Julius B
authors.initials: JB
authors.lastname: Lucks
keywords: RNA structure; chemical probing; high throughput; next‐generation sequencing