Mapping protein–RNA interactions

Robert Vaughan, William Running, Rongsu Qi, C Cheng KaoThe Biochemistry Interdisciplinary Program, Indiana University, Bloomington, IN, USAAbstract: There is a significant need to develop approaches for rapid and accurate mapping of protein–ribonucleic acid (RNA) interactions, especially to complement structure-based methods. Approaches using mass spectrometry to map regions in proteins that contact RNA have now been established. These include a reversible crosslinking affinity purification method, residue-specific modification interference assay, and photoactivatable crosslinking and mass spectrometry. Novel methods to identify nucleotides within RNA that contact proteins using photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation are also available. In combination, these methods should generate results that will lead to more specific hypotheses concerning the biological properties of protein–RNA interactions. This review summarizes some recent advances in select assays useful for mapping protein–RNA interactions.Keywords: hepatitis C virus, positive-strand RNA virus, reversible crosslinking, RNA binding, mass spectrometry