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RNA binding proteins (RBP) regulate the editing, localization, stabilization, translation, and degradation of ribonucleic acids (RNA) through their interactions with specific cis-acting elements within target RNAs. Post-transcriptional regulatory mechanisms are directly involved in the control of the immune response and stress response and their alterations play a crucial role in cancer related processes. In this review, we discuss mRNAs and RNA binding proteins relevant to tumorigenesis, current methodologies for detecting RNA interactions, and last, we describe a novel method to detect such interactions, which combines peptide modified, RNA imaging probes (FMTRIPs) with proximity ligation (PLA) and rolling circle amplification (RCA). This assay detects native RNA in a sequence specific and single RNA sensitive manner, and PLA allows for the quantification and localization of protein-mRNA interactions with single-interaction sensitivity in situ.

Can we observe changes in mRNA “state”? Overview of methods to study mRNA interactions with regulatory proteins relevant in cancer related processes