A high-throughput approach to profile RNA structure

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• dc.contributor.author Delli Ponti, Riccardo, 1987-ca
• dc.contributor.author Marti, Stefanieca
• dc.contributor.author Armaos, Alexandros, 1989-ca
• dc.contributor.author Tartaglia, Gian Gaetanoca
• dc.date.accessioned 2018-06-26T08:13:16Z
• dc.date.available 2018-06-26T08:13:16Z
• dc.date.issued 2017
• dc.description.abstract Here we introduce the Computational Recognition of Secondary Structure (CROSS) method to calculate the structural profile of an RNA sequence (single- or double-stranded state) at single-nucleotide resolution and without sequence length restrictions. We trained CROSS using data from high-throughput experiments such as Selective 2΄-Hydroxyl Acylation analyzed by Primer Extension (SHAPE; Mouse and HIV transcriptomes) and Parallel Analysis of RNA Structure (PARS; Human and Yeast transcriptomes) as well as high-quality NMR/X-ray structures (PDB database). The algorithm uses primary structure information alone to predict experimental structural profiles with >80% accuracy, showing high performances on large RNAs such as Xist (17 900 nucleotides; Area Under the ROC Curve AUC of 0.75 on dimethyl sulfate (DMS) experiments). We integrated CROSS in thermodynamics-based methods to predict secondary structure and observed an increase in their predictive power by up to 30%.
• dc.description.sponsorship The research leading to these results has received funding from European Union Seventh Framework Programme [FP7/2007-2013]; European Research Council [RIBOMYLOME_309545 to GGT]; Spanish Ministry of Economy and Competitiveness [BFU2014-55054-P to GGT]; AGAUR [2014 SGR 00685 to GGT]; Spanish Ministry of Economy and Competitiveness, European Research Development Fund ERDF, 'Centro de Excelencia Severo Ochoa 2013-2017' [SEV-2012-0208]. Funding for open access charge: European Research Council [RIBOMYLOME_309545 to GGT]; Spanish Ministry of Economy and Competitiveness [BFU2014-55054-P to GGT]. The authors also thank the CRG fellowship to SM.
• dc.format.mimetype application/pdf
• dc.identifier.citation Delli Ponti R, Marti S, Armaos A, Tartaglia GG. A high-throughput approach to profile RNA structure. Nucleic Acids Res. 2017 Mar 17;45(5):e35. DOI: 10.1093/nar/gkw1094
• dc.identifier.doi http://dx.doi.org/10.1093/nar/gkw1094
• dc.identifier.issn 0305-1048
• dc.identifier.uri http://hdl.handle.net/10230/34970
• dc.language.iso eng
• dc.publisher Oxford University Pressca
• dc.relation.ispartof Nucleic Acids Research. 2017 Mar 17;45(5):e35
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/309545
• dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2014-55054-P
• dc.rights © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
• dc.subject.keyword Nucleic acid conformation
• dc.subject.keyword Saccharomyces cerevisiae
• dc.subject.keyword Polymorphism
• dc.title A high-throughput approach to profile RNA structureca
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion