Identification of immunomodulatory RNA-binding proteins in tumors

Abstract

By binding RNA in a sequence- and/or structure-dependent manner, RNA-binding proteins (RBPs) and their target RNA form a ribonucleoprotein complex involved in the RNA's fate. In this context, RBPs were shown to act as key players for post-transcriptional gene regulation by controlling RNA editing, splicing, polyadenylation, translocation, and stability. So far, over 1900 RBPs were identified and their deregulation has been associated with the development and progression of various disorders including cancer. Although a number of sophisticated approaches are available, our knowledge about direct RNA-RBP interactions is, however, quite limited. Here we present a protocol with restricted requirements for equipment and devices to identify RBPs. This approach is based on (i) the purification of biotinylated RNA, (ii) chromatographic separation of co-purified proteins, and (iii) their identification by mass spectrometry.

Keywords: Immune modulation; Mass spectrometry; Post-transcriptional regulation; Proteomics; RNA; RNA-binding proteins.