title: RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP).
abstract: Many biological processes are RNA-mediated, but higher-order structures for most RNAs are unknown, which makes it difficult to understand how RNA structure governs function. Here we describe selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) that makes possible de novo and large-scale identification of RNA functional motifs. Sites of 2'-hydroxyl acylation by SHAPE are encoded as noncomplementary nucleotides during cDNA synthesis, as measured by massively parallel sequencing. SHAPE-MaP-guided modeling identified greater than 90% of accepted base pairs in complex RNAs of known structure, and we used it to define a new model for the HIV-1 RNA genome. The HIV-1 model contains all known structured motifs and previously unknown elements, including experimentally validated pseudoknots. SHAPE-MaP yields accurate and high-resolution secondary-structure models, enables analysis of low-abundance RNAs, disentangles sequence polymorphisms in single experiments and will ultimately democratize RNA-structure analysis.
authors.affiliation: 1] Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, USA. [2].
authors.forename: Nathan A
authors.initials: NA
authors.lastname: Siegfried
authors.affiliation: 1] Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, USA. [2].
authors.forename: Steven
authors.initials: S
authors.lastname: Busan
authors.affiliation: 1] Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, USA. [2].
authors.forename: Greggory M
authors.initials: GM
authors.lastname: Rice
authors.affiliation: Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA.
authors.forename: Julie A E
authors.initials: JA
authors.lastname: Nelson
authors.affiliation: Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, USA.
authors.forename: Kevin M
authors.initials: KM
authors.lastname: Weeks
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D004252:DNA Mutational Analysis / Q000379:methods*; D015497:HIV-1 / Q000235:genetics*; D008969:Molecular Sequence Data; D059372:Nucleotide Motifs; D012367:RNA, Viral / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D012367:RNA, Viral