Correlating SHAPE signatures with three-dimensional RNA structures
| Autor: | Yi Wang, Michaela Wendeler, Stuart F.J. Le Grice, Eckart Bindewald, Bruce A. Shapiro, Mark J. Pritt, Marion K. Bona, Michal Legiewicz |
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| Rok vydání: | 2011 |
| Předmět: |
Electrophoresis
Models Molecular Genetics Transcription Genetic Nucleotides Sequence Analysis RNA Base pair Acylation Amino Acid Motifs Stacking Probabilistic logic RNA Biology Article Primer extension Nucleic acid secondary structure Transcription (biology) Nucleic Acid Conformation heterocyclic compounds Nucleic acid structure Biological system Base Pairing Molecular Biology DNA Primers |
| Zdroj: | RNA. 17:1688-1696 |
| ISSN: | 1469-9001 1355-8382 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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