Causes and consequences of RNA:protein cross-links – lessons from chemotherapy

Specific RNAs and proteins function together to impart function within cells. This ranges from binary interactions through to large macromolecular machines such as the ribosome. The emergence of the epitranscriptome over the past 20 years provides an excellent example of this relationship. The epitranscriptome is written on RNA molecules by protein-based enzymes, with these modifications required to diversify RNA function. The need for these functions in turn necessitates tight proximity between specific RNA transcripts and proteins. Here we describe an unwanted by-product of RNA:protein proximity - RNA:protein cross-links (RPCs). We describe how covalent bonds between RNAs and proteins form through one of two mechanisms. Throughout, we provide examples detailing clinical compounds that induce RPCs. The first mechanism of cross-linking is purely proximity-defined, occurring because of reactive third-party agents joining adjacent biomolecules. We discuss endogenous and exogenous agents that impart this activity and how the chemotherapeutic agent oxaliplatin induces cross-links by the same mechanism. The second class of RPCs forms between RNAs and specific RNA-modifying enzymes. These enzymes form transient covalent intermediates as part of their mechanisms of action, which we suggest can endure under certain conditions. We summarise evidence that the cancer drug 5-fluorouracil induces RPCs following its incorporation into RNA. Enzyme trapping occurs for specific modifier enzymes that target the non-canonical structure of the drug. Finally, we summarise recent work showing that cells contain specific molecular mechanisms to detect and resolve RPCs, placing this in the context of clinical cross-link induction.