nextPARS: parallel probing of RNA structures in Illumina

• DOI: 10.1261/rna.063073.117
• Publication Date: 2018-01-23T01:20:16Z
• Authors: Ester Saus; Jesse R. Willis; Leszek P. Pryszcz; Ahmed Hafez; Carlos Llorens; Heinz Himmelbauer; Toni Gabaldón
• Keywords: 0301 basic medicine; Sequence Analysis, RNA; 0206 medical engineering; Method; Computational Biology; High-Throughput Nucleotide Sequencing; 02 engineering and technology; RNA secondary structure; Multiplex sequencing; 03 medical and health sciences; Genome-wide enzymatic probing; Nucleic Acid Conformation; RNA, Messenger

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.