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Direct identification of base-paired RNA nucleotides by correlated chemical probing

Many RNA molecules fold into complex secondary and tertiary structures that play critical roles in biological function. Among the best-established methods for examining RNA structure are chemical probing experiments, which can report on local nucleotide structure in a concise and extensible manner....

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Autores principales: Krokhotin, Andrey, Mustoe, Anthony M., Weeks, Kevin M., Dokholyan, Nikolay V.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5159650/
https://www.ncbi.nlm.nih.gov/pubmed/27803152
http://dx.doi.org/10.1261/rna.058586.116
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author Krokhotin, Andrey
Mustoe, Anthony M.
Weeks, Kevin M.
Dokholyan, Nikolay V.
author_facet Krokhotin, Andrey
Mustoe, Anthony M.
Weeks, Kevin M.
Dokholyan, Nikolay V.
author_sort Krokhotin, Andrey
collection PubMed
description Many RNA molecules fold into complex secondary and tertiary structures that play critical roles in biological function. Among the best-established methods for examining RNA structure are chemical probing experiments, which can report on local nucleotide structure in a concise and extensible manner. While probing data are highly useful for inferring overall RNA secondary structure, these data do not directly measure through-space base-pairing interactions. We recently introduced an approach for single-molecule correlated chemical probing with dimethyl sulfate (DMS) that measures RNA interaction groups by mutational profiling (RING-MaP). RING-MaP experiments reveal diverse through-space interactions corresponding to both secondary and tertiary structure. Here we develop a framework for using RING-MaP data to directly and robustly identify canonical base pairs in RNA. When applied to three representative RNAs, this framework identified 20%–50% of accepted base pairs with a <10% false discovery rate, allowing detection of 88% of duplexes containing four or more base pairs, including pseudoknotted pairs. We further show that base pairs determined from RING-MaP analysis significantly improve secondary structure modeling. RING-MaP-based correlated chemical probing represents a direct, experimentally concise, and accurate approach for detection of individual base pairs and helices and should greatly facilitate structure modeling for complex RNAs.
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spelling pubmed-51596502018-01-01 Direct identification of base-paired RNA nucleotides by correlated chemical probing Krokhotin, Andrey Mustoe, Anthony M. Weeks, Kevin M. Dokholyan, Nikolay V. RNA Bioinformatics Many RNA molecules fold into complex secondary and tertiary structures that play critical roles in biological function. Among the best-established methods for examining RNA structure are chemical probing experiments, which can report on local nucleotide structure in a concise and extensible manner. While probing data are highly useful for inferring overall RNA secondary structure, these data do not directly measure through-space base-pairing interactions. We recently introduced an approach for single-molecule correlated chemical probing with dimethyl sulfate (DMS) that measures RNA interaction groups by mutational profiling (RING-MaP). RING-MaP experiments reveal diverse through-space interactions corresponding to both secondary and tertiary structure. Here we develop a framework for using RING-MaP data to directly and robustly identify canonical base pairs in RNA. When applied to three representative RNAs, this framework identified 20%–50% of accepted base pairs with a <10% false discovery rate, allowing detection of 88% of duplexes containing four or more base pairs, including pseudoknotted pairs. We further show that base pairs determined from RING-MaP analysis significantly improve secondary structure modeling. RING-MaP-based correlated chemical probing represents a direct, experimentally concise, and accurate approach for detection of individual base pairs and helices and should greatly facilitate structure modeling for complex RNAs. Cold Spring Harbor Laboratory Press 2017-01 /pmc/articles/PMC5159650/ /pubmed/27803152 http://dx.doi.org/10.1261/rna.058586.116 Text en © 2016 Krokhotin et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
spellingShingle Bioinformatics
Krokhotin, Andrey
Mustoe, Anthony M.
Weeks, Kevin M.
Dokholyan, Nikolay V.
Direct identification of base-paired RNA nucleotides by correlated chemical probing
title Direct identification of base-paired RNA nucleotides by correlated chemical probing
title_full Direct identification of base-paired RNA nucleotides by correlated chemical probing
title_fullStr Direct identification of base-paired RNA nucleotides by correlated chemical probing
title_full_unstemmed Direct identification of base-paired RNA nucleotides by correlated chemical probing
title_short Direct identification of base-paired RNA nucleotides by correlated chemical probing
title_sort direct identification of base-paired rna nucleotides by correlated chemical probing
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5159650/
https://www.ncbi.nlm.nih.gov/pubmed/27803152
http://dx.doi.org/10.1261/rna.058586.116
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