nextPARS: parallel probing of RNA structures in Illumina
- Ester Saus1,2,7,
- Jesse R. Willis1,2,7,
- Leszek P. Pryszcz1,2,3,
- Ahmed Hafez4,
- Carlos Llorens4,
- Heinz Himmelbauer1,2,5 and
- Toni Gabaldón1,2,6
- 1Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- 3International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
- 4Biotechvana, 46980 Paterna (Valencia), Spain
- 5Department of Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria
- 6Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
- Corresponding author: tgabaldon{at}crg.es
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↵7 These authors contributed equally to this work.
Abstract
RNA molecules play important roles in virtually every cellular process. These functions are often mediated through the adoption of specific structures that enable RNAs to interact with other molecules. Thus, determining the secondary structures of RNAs is central to understanding their function and evolution. In recent years several sequencing-based approaches have been developed that allow probing structural features of thousands of RNA molecules present in a sample. Here, we describe nextPARS, a novel Illumina-based implementation of in vitro parallel probing of RNA structures. Our approach achieves comparable accuracy to previous implementations, while enabling higher throughput and sample multiplexing.
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Footnotes
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Article is online at http://www.rnajournal.org/cgi/doi/10.1261/rna.063073.117.
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Freely available online through the RNA Open Access option.
- Received July 20, 2017.
- Accepted January 3, 2018.
This article, published in RNA, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
