Delli Ponti, Riccardo, 1987-Marti, StefanieArmaos, Alexandros, 1989-Tartaglia, Gian Gaetano2018-06-262018-06-262017Delli 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/gkw10940305-1048http://hdl.handle.net/10230/34970Here 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%.application/pdfeng© 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.cominfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1093/nar/gkw1094Nucleic acid conformationSaccharomyces cerevisiaePolymorphisminfo:eu-repo/semantics/openAccess