title: Correlating SHAPE signatures with three-dimensional RNA structures.
abstract: Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) is a facile technique for quantitative analysis of RNA secondary structure. In general, low SHAPE signal values indicate Watson-Crick base-pairing, and high values indicate positions that are single-stranded within the RNA structure. However, the relationship of SHAPE signals to structural properties such as non-Watson-Crick base-pairing or stacking has thus far not been thoroughly investigated. Here, we present results of SHAPE experiments performed on several RNAs with published three-dimensional structures. This strategy allows us to analyze the results in terms of correlations between chemical reactivities and structural properties of the respective nucleotide, such as different types of base-pairing, stacking, and phosphate-backbone interactions. We find that the RNA SHAPE signal is strongly correlated with cis-Watson-Crick/Watson-Crick base-pairing and is to a remarkable degree not dependent on other structural properties with the exception of stacking. We subsequently generated probabilistic models that estimate the likelihood that a residue with a given SHAPE score participates in base-pairing. We show that several models that take SHAPE scores of adjacent residues into account perform better in predicting base-pairing compared with individual SHAPE scores. This underscores the context sensitivity of SHAPE and provides a framework for an improved interpretation of the response of RNA to chemical modification.
authors.affiliation: Basic Science Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA.
authors.forename: Eckart
authors.initials: E
authors.lastname: Bindewald
authors.forename: Michaela
authors.initials: M
authors.lastname: Wendeler
authors.forename: Michal
authors.initials: M
authors.lastname: Legiewicz
authors.forename: Marion K
authors.initials: MK
authors.lastname: Bona
authors.forename: Yi
authors.initials: Y
authors.lastname: Wang
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Pritt
authors.forename: Stuart F J
authors.initials: SF
authors.lastname: Le Grice
authors.forename: Bruce A
authors.initials: BA
authors.lastname: Shapiro
mesh_terms: D000215:Acylation; D020816:Amino Acid Motifs; D020029:Base Pairing; D017931:DNA Primers; D004586:Electrophoresis; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000235:genetics; D012313:RNA / Q000737:chemistry* / Q000235:genetics*; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic
chemical_list: D017931:DNA Primers; D009711:Nucleotides; D012313:RNA