title: Characterizing RNA structures in vitro and in vivo with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).
abstract: RNA molecules adopt a wide variety of structures that perform many cellular functions, including, among others, catalysis, small molecule sensing, and cellular defense. Our ability to characterize, predict, and design RNA structures are key factors for understanding and controlling the biological roles of RNAs. Fortunately, there has been rapid progress in this area, especially with respect to experimental methods that can characterize RNA structures in a high throughput fashion using chemical probing and next-generation sequencing. Here, we describe one such method, selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq), which measures nucleotide resolution flexibility information for RNAs in vitro and in vivo. We outline the process of designing and performing a SHAPE-Seq experiment and describe methods for using experimental SHAPE-Seq data to restrain computational folding algorithms to generate more accurate predictions of RNA secondary structure. We also provide a number of examples of SHAPE-Seq reactivity spectra obtained in vitro and in vivo and discuss important considerations for performing SHAPE-Seq experiments, both in terms of collecting and analyzing data. Finally, we discuss improvements and extensions of these experimental and computational techniques that promise to deepen our knowledge of RNA folding and function.
authors.affiliation: School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, United States.
authors.forename: Kyle E
authors.initials: KE
authors.lastname: Watters
authors.affiliation: School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, United States; Tri-Institutional Program in Computational Biology and Medicine, Cornell University, Ithaca, New York, Weill Cornell Medical College, New York, New York, Memorial Sloan-Kettering Cancer Center, New York, New York, United States; Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, United States.
authors.forename: Angela M
authors.initials: AM
authors.lastname: Yu
authors.affiliation: School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, United States.
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Strobel
authors.affiliation: School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, United States.
authors.forename: Alex H
authors.initials: AH
authors.lastname: Settle
authors.affiliation: School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, United States. Electronic address: jblucks@cornell.edu.
authors.forename: Julius B
authors.initials: JB
authors.lastname: Lucks
mesh_terms: D000215:Acylation; D001483:Base Sequence; D002478:Cells, Cultured; D003198:Computer Simulation; D017931:DNA Primers / Q000737:chemistry; D017665:Hydroxyl Radical; D055029:Inverted Repeat Sequences; D008958:Models, Molecular; D012313:RNA / Q000737:chemistry* / Q000648:ultrastructure; D059370:RNA Folding; D017423:Sequence Analysis, RNA
chemical_list: D017931:DNA Primers; D017665:Hydroxyl Radical; D012313:RNA
keywords: In vivo RNA structure; RNA; RNA structure prediction; RNA structure probing; RNA-ligand interactions; SHAPE; SHAPE-Seq