title: Genome-Wide Analysis of RNA Secondary Structure.
abstract: Single-stranded RNA molecules fold into extraordinarily complicated secondary and tertiary structures as a result of intramolecular base pairing. In vivo, these RNA structures are not static. Instead, they are remodeled in response to changes in the prevailing physicochemical environment of the cell and as a result of intermolecular base pairing and interactions with RNA-binding proteins. Remarkable technical advances now allow us to probe RNA secondary structure at single-nucleotide resolution and genome-wide, both in vitro and in vivo. These data sets provide new glimpses into the RNA universe. Analyses of RNA structuromes in HIV, yeast, Arabidopsis, and mammalian cells and tissues have revealed regulatory effects of RNA structure on messenger RNA (mRNA) polyadenylation, splicing, translation, and turnover. Application of new methods for genome-wide identification of mRNA modifications, particularly methylation and pseudouridylation, has shown that the RNA "epitranscriptome" both influences and is influenced by RNA structure. In this review, we describe newly developed genome-wide RNA structure-probing methods and synthesize the information emerging from their application.
authors.affiliation: Department of Chemistry.|Department of Biochemistry and Molecular Biology.|Center for RNA Molecular Biology.
authors.forename: Philip C
authors.initials: PC
authors.lastname: Bevilacqua
authors.affiliation: Department of Chemistry.|Center for RNA Molecular Biology.
authors.forename: Laura E
authors.initials: LE
authors.lastname: Ritchey
authors.affiliation: Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802; email: sma3@psu.edu.
authors.forename: Zhao
authors.initials: Z
authors.lastname: Su
authors.affiliation: Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802; email: sma3@psu.edu.
authors.forename: Sarah M
authors.initials: SM
authors.lastname: Assmann
mesh_terms: D001671:Biochemistry / Q000379:methods; D016678:Genome; D023281:Genomics / Q000379:methods*; D009690:Nucleic Acid Conformation; D026723:Polyadenylation; D014176:Protein Biosynthesis; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D012323:RNA Processing, Post-Transcriptional; D012326:RNA Splicing; D020871:RNA Stability; D017381:Spliceosomes / Q000235:genetics / Q000378:metabolism
chemical_list: D012313:RNA
keywords: DMS-seq; RNA structurome; SHAPE; Structure-seq; genome-wide; in vivo RNA folding