A high-throughput approach to profile RNA structure
Identifieur interne : 001013 ( Main/Exploration ); précédent : 001012; suivant : 001014A high-throughput approach to profile RNA structure
Auteurs : Riccardo Delli Ponti [Espagne] ; Stefanie Marti [Espagne] ; Alexandros Armaos [Espagne] ; Gian Gaetano Tartaglia [Espagne]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2016.
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
Url:
DOI: 10.1093/nar/gkw1094
PubMed: 27899588
PubMed Central: 5389523
Affiliations:
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Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Universitat Pompeu Fabra (UPF), 08003 Barcelona</wicri:regionArea><placeName><region nuts="2" type="communauté">Catalogne</region><settlement type="city">Barcelone</settlement></placeName><orgName type="university">Université Pompeu Fabra</orgName></affiliation></author><author><name sortKey="Marti, Stefanie" sort="Marti, Stefanie" uniqKey="Marti S" first="Stefanie" last="Marti">Stefanie Marti</name><affiliation wicri:level="2"><nlm:aff id="AFF1">Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona</wicri:regionArea><placeName><region nuts="2" type="communauté">Catalogne</region></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="AFF2">Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Universitat Pompeu Fabra (UPF), 08003 Barcelona</wicri:regionArea><placeName><region nuts="2" type="communauté">Catalogne</region><settlement type="city">Barcelone</settlement></placeName><orgName type="university">Université Pompeu Fabra</orgName></affiliation></author><author><name sortKey="Armaos, Alexandros" sort="Armaos, Alexandros" uniqKey="Armaos A" first="Alexandros" last="Armaos">Alexandros Armaos</name><affiliation wicri:level="2"><nlm:aff id="AFF1">Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona</wicri:regionArea><placeName><region nuts="2" type="communauté">Catalogne</region></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="AFF2">Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Universitat Pompeu Fabra (UPF), 08003 Barcelona</wicri:regionArea><placeName><region nuts="2" type="communauté">Catalogne</region><settlement type="city">Barcelone</settlement></placeName><orgName type="university">Université Pompeu Fabra</orgName></affiliation></author><author><name sortKey="Tartaglia, Gian Gaetano" sort="Tartaglia, Gian Gaetano" uniqKey="Tartaglia G" first="Gian Gaetano" last="Tartaglia">Gian Gaetano Tartaglia</name><affiliation wicri:level="2"><nlm:aff id="AFF1">Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona</wicri:regionArea><placeName><region nuts="2" type="communauté">Catalogne</region></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="AFF2">Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Universitat Pompeu Fabra (UPF), 08003 Barcelona</wicri:regionArea><placeName><region nuts="2" type="communauté">Catalogne</region><settlement type="city">Barcelone</settlement></placeName><orgName type="university">Université Pompeu Fabra</orgName></affiliation><affiliation wicri:level="2"><nlm:aff id="AFF3">Institució Catalana de Recerca i Estudis Avançats (ICREA), 23 Passeig Lluıs Companys, 08010 Barcelona, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Institució Catalana de Recerca i Estudis Avançats (ICREA), 23 Passeig Lluıs Companys, 08010 Barcelona</wicri:regionArea><placeName><region nuts="2" type="communauté">Catalogne</region></placeName></affiliation></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Abstract</title><p>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 <italic>Xist</italic> (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%.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Mortimer, S A" uniqKey="Mortimer S">S.A. 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Tartaglia</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Espagne</li></country><region><li>Catalogne</li></region><settlement><li>Barcelone</li></settlement><orgName><li>Université Pompeu Fabra</li></orgName></list><tree><country name="Espagne"><region name="Catalogne"><name sortKey="Delli Ponti, Riccardo" sort="Delli Ponti, Riccardo" uniqKey="Delli Ponti R" first="Riccardo" last="Delli Ponti">Riccardo Delli Ponti</name></region><name sortKey="Armaos, Alexandros" sort="Armaos, Alexandros" uniqKey="Armaos A" first="Alexandros" last="Armaos">Alexandros Armaos</name><name sortKey="Armaos, Alexandros" sort="Armaos, Alexandros" uniqKey="Armaos A" first="Alexandros" last="Armaos">Alexandros Armaos</name><name sortKey="Delli Ponti, Riccardo" sort="Delli Ponti, Riccardo" uniqKey="Delli Ponti R" first="Riccardo" last="Delli Ponti">Riccardo Delli Ponti</name><name sortKey="Marti, Stefanie" sort="Marti, Stefanie" uniqKey="Marti S" first="Stefanie" last="Marti">Stefanie Marti</name><name sortKey="Marti, Stefanie" sort="Marti, Stefanie" uniqKey="Marti S" first="Stefanie" last="Marti">Stefanie Marti</name><name sortKey="Tartaglia, Gian Gaetano" sort="Tartaglia, Gian Gaetano" uniqKey="Tartaglia G" first="Gian Gaetano" last="Tartaglia">Gian Gaetano Tartaglia</name><name sortKey="Tartaglia, Gian Gaetano" sort="Tartaglia, Gian Gaetano" uniqKey="Tartaglia G" first="Gian Gaetano" last="Tartaglia">Gian Gaetano Tartaglia</name><name sortKey="Tartaglia, Gian Gaetano" sort="Tartaglia, Gian Gaetano" uniqKey="Tartaglia G" first="Gian Gaetano" last="Tartaglia">Gian Gaetano Tartaglia</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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