title: A high-throughput approach to profile RNA structure.
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%.
authors.affiliation: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain.|Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
authors.forename: Riccardo
authors.initials: R
authors.lastname: Delli Ponti
authors.affiliation: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain.|Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
authors.forename: Stefanie
authors.initials: S
authors.lastname: Marti
authors.affiliation: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain.|Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
authors.forename: Alexandros
authors.initials: A
authors.lastname: Armaos
authors.affiliation: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain.|Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.|Institució Catalana de Recerca i Estudis Avançats (ICREA), 23 Passeig Lluıs Companys, 08010 Barcelona, Spain.
authors.forename: Gian Gaetano
authors.initials: GG
authors.lastname: Tartaglia
mesh_terms: D000465:Algorithms; D000818:Animals; D019540:Area Under Curve; D006801:Humans; D051379:Mice; D009690:Nucleic Acid Conformation; D020641:Polymorphism, Single Nucleotide; D012313:RNA / Q000737:chemistry*; D062085:RNA, Long Noncoding / Q000235:genetics / Q000378:metabolism; D012372:ROC Curve; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D012984:Software; D013816:Thermodynamics
chemical_list: D062085:RNA, Long Noncoding; C077885:XIST non-coding RNA; D012313:RNA