Protocol to distinguish pre-mRNA from mRNA in RNA-protein interaction studies

Transcriptome-wide studies on interactions between RNA-binding proteins (RBPs) and protein-coding RNAs in general preclude interpretations regarding RBP preference for binding to the more abundant mRNA over the less abundant pre-mRNA. Here, we present a protocol to determine the binding preference of the RBP tristetraprolin (TTP, Zfp36) for pre-mRNA versus mRNA. We describe steps for the identification and quantitation of intronic and exonic fragments in RNA bound to TTP. This protocol can potentially be applied to any RBP. For complete details on the use and execution of this protocol, please refer to Bestehorn et al.1. Keywords: Bioinformatics; Gene Expression; Genomics; Molecular Biology; RNA-seq; Sequence analysis; Sequencing.