title: The Conservation and Function of RNA Secondary Structure in Plants.
abstract: RNA transcripts fold into secondary structures via intricate patterns of base pairing. These secondary structures impart catalytic, ligand binding, and scaffolding functions to a wide array of RNAs, forming a critical node of biological regulation. Among their many functions, RNA structural elements modulate epigenetic marks, alter mRNA stability and translation, regulate alternative splicing, transduce signals, and scaffold large macromolecular complexes. Thus, the study of RNA secondary structure is critical to understanding the function and regulation of RNA transcripts. Here, we review the origins, form, and function of RNA secondary structure, focusing on plants. We then provide an overview of methods for probing secondary structure, from physical methods such as X-ray crystallography and nuclear magnetic resonance (NMR) imaging to chemical and nuclease probing methods. Combining these latter methods with high-throughput sequencing has enabled them to scale across whole transcriptomes, yielding tremendous new insights into the form and function of RNA secondary structure.
authors: Department of Biology, School of Arts and Sciences, and.|Cell and Molecular Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104; email: bdgregor@sas.upenn.edu.
authors: Lee E
authors: LE
authors: Vandivier
authors: Department of Biology, School of Arts and Sciences, and.
authors: Stephen J
authors: SJ
authors: Anderson
authors: Department of Biology, School of Arts and Sciences, and.|Cell and Molecular Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104; email: bdgregor@sas.upenn.edu.
authors: Shawn W
authors: SW
authors: Foley
authors: Department of Biology, School of Arts and Sciences, and.|Cell and Molecular Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104; email: bdgregor@sas.upenn.edu.
authors: Brian D
authors: BD
authors: Gregory
mesh_terms: D018506:Gene Expression Regulation, Plant; D009690:Nucleic Acid Conformation; D010944:Plants / Q000235:genetics*; D012333:RNA, Messenger / Q000737:chemistry / Q000502:physiology; D018749:RNA, Plant / Q000737:chemistry / Q000502:physiology; D059467:Transcriptome
chemical_list: D012333:RNA, Messenger; D018749:RNA, Plant
keywords: RNA secondary structure; RNA-binding proteins; high-throughput sequencing; microRNAs; posttranscriptional regulation; small interfering RNAs