title: Transcriptome-wide measurement of plant RNA secondary structure.
abstract: RNAs fold into intricate and precise secondary structures. These structural patterns regulate multiple steps of the RNA lifecycle, while also conferring catalytic and scaffolding functions to certain transcripts. Therefore, a full understanding of RNA posttranscriptional regulation requires a comprehensive picture of secondary structure. Here, we review several high throughput sequencing-based methods to globally survey plant RNA secondary structure. These methods are more accurate than computational prediction, and more scalable than physical techniques such as crystallography. We note hurdles to reliably measuring secondary structure, including RNA-binding proteins, RNA base modifications, and intramolecular duplexes. Finally, we survey the functional knowledge that has been gleaned from each of these methods, and identify some unanswered questions that remain.
authors.affiliation: Department of Biology, University of Pennsylvania School of Arts and Sciences, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
authors.forename: Shawn W
authors.initials: SW
authors.lastname: Foley
authors.affiliation: Department of Biology, University of Pennsylvania School of Arts and Sciences, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
authors.forename: Lee E
authors.initials: LE
authors.lastname: Vandivier
authors.affiliation: Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
authors.forename: Pavel P
authors.initials: PP
authors.lastname: Kuksa
authors.affiliation: Department of Biology, University of Pennsylvania School of Arts and Sciences, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA. Electronic address: bdgregor@sas.upenn.edu.
authors.forename: Brian D
authors.initials: BD
authors.lastname: Gregory
mesh_terms: D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing; D017433:Protein Structure, Secondary; D018749:RNA, Plant / Q000737:chemistry / Q000235:genetics*; D059467:Transcriptome
chemical_list: D018749:RNA, Plant