Mapping protein–RNA interactions

Abstract

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 combina- tion, 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