Investigation of protein–RNA interactions by mass spectrometry—Techniques and applications

Protein–RNA complexes play many important roles in diverse cellular functions. They are involved in a wide variety of different processes in growth and differentiation at the various stages of the cell cycle. As their function and catalytic activity are directly coupled to the structural arrangement of their components—proteins and ribonucleic acids—the investigation of protein–RNA interactions is of great functional and structural importance. Here we discuss the most prominent examples of protein–RNA complexes and describe some frequently used purification strategies. We present various techniques and applications of mass spectrometry to study protein–RNA complexes. We discuss the analysis of intact complexes as well as proteomics-based and crosslinking-based approaches in which proteins are cleaved into smaller peptides. This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry.

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► Direct protein–RNA interaction sites can be obtained by UV crosslinking.
► Proteome studies reveal interaction partners within protein–RNA complexes.
► Dynamic protein changes and kinetics can be monitored by quantitative proteomics.
► The interaction partners of distinct RNA motifs have been found by quantitative mass spectrometry.
► Protein stoichiometries, topology and subunit interactions can be achieved by native MS.