Saus E, Willis JR, Pryszcz LP, Hafez A, Llorens C, Himmelbauer H, Gabaldón T. nextPARS: parallel probing of RNA structures in Illumina.
RNA 2018;
24:609-619. [PMID:
29358234 PMCID:
PMC5855959 DOI:
10.1261/rna.063073.117]
[Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 01/03/2018] [Indexed: 06/07/2023]
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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