Probing RNA–protein networks: biochemistry meets genomics

•New methods probe RNA–protein interactions among whole proteomes and transcriptomes.•The RNA specificities of single proteins and protein complexes are now accessible.•The approaches yield a biochemical foundation for understanding RNA control networks.•Proteins and ligands of known specificity can be created to target specific RNAs.

RNA–protein interactions are pervasive. The specificity of these interactions dictates which RNAs are controlled by what protein. Here we describe a class of revolutionary new methods that enable global views of RNA-binding specificity in vitro, for both single proteins and multiprotein complexes. These methods provide insight into central issues in RNA regulation in living cells, including understanding the balance between free and bound components, the basis for exclusion of binding sites, detection of binding events in the absence of discernible regulatory elements, and new approaches to targeting endogenous transcripts by design. Comparisons of in vitro and in vivo binding provide a foundation for comprehensive understanding of the biochemistry of protein-mediated RNA regulatory networks.