Protein Interaction Profile Sequencing (PIP‐seq) in Plants

: RNA secondary structure and RNA-protein interactions are necessary for maintaining biological functionality and regulatory mechanisms within eukaryotic transcriptomes. Determining the structural characteristics and protein-bound sites of RNA molecules has therefore become a major research objective and requires the development of global methods for probing intra- and intermolecular RNA interaction sites. Sequencing RNAs treated with single-strand- and double-strand-specific ribonucleases in the absence of proteins allows the inference of RNA secondary structure. These samples can be compared to samples treated with nucleases in the presence of interacting proteins to identify protein-bound sequences. Thus, these four libraries reveal a comprehensive, transcriptome-wide view of RNA secondary structure and RNA protein interaction sites in a single experiment for any plant species of interest. © 2016 by John Wiley & Sons, Inc.