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Updated: Sep 14, 2025
An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA
Published on: February 17, 2023
Protocol to distinguish pre-mRNA from mRNA in RNA-protein interaction studies
Christina Zeiler1, Annika Bestehorn2, Pavel Kovarik2
1Max Perutz Labs, Vienna BioCenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria; University of Vienna, Max Perutz Labs, Department of Microbiology, Immunobiology and Genetics, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria; Vienna BioCenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria.
Abstract:
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.
