A high-throughput approach to profile RNA structure
| Autor: | Stefanie Marti, Riccardo Delli Ponti, Gian Gaetano Tartaglia, Alexandros Armaos |
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| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Protein Data Bank (RCSB PDB) Nucleic acid conformation Animals Area Under Curve Humans Mice RNA RNA Long Noncoding ROC Curve Saccharomyces cerevisiae Software Thermodynamics Algorithms Nucleic Acid Conformation Polymorphism Single Nucleotide Genetics Computational biology Biology Primer extension 03 medical and health sciences Nucleic acid structure Polymorphism Throughput (business) Protein secondary structure Protein primary structure 030104 developmental biology Methods Online XIST |
| Zdroj: | Nucleic Acids Research Recercat. Dipósit de la Recerca de Catalunya instname |
| ISSN: | 1362-4962 0305-1048 |
| DOI: | 10.1093/nar/gkw1094 |
| Popis: | 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%. 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. |
| Databáze: | OpenAIRE |
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