Post-transcriptional regulatory networks: The dynamic interplay of RNA-binding proteins

Post-transcriptional regulation of gene expression is orchestrated by RNA-binding proteins (RBPs), which regulate key aspects of the RNA life cycle including splicing, localization, translation, and decay. Although RBPs have been initially considered as isolated regulators, it is becoming clear that RNA molecules are commonly bound by several RBPs whose coordination directs their fate. These combinatorial interactions produce complex, context-dependent post-transcriptional regulatory networks (PTRNs) whose outcomes are difficult to predict. RBPs may also switch function depending on cell state, subcellular localization, or post-translational modification, adding further complexity to RNA regulation. This review focuses on recent technological advances expanding our ability to map and interpret PTRNs. Multiplexed methods allow profiling of the RNA-binding patterns of several RBPs in parallel, whereas deeper interaction proteomics studies reveal protein-protein connections and changes in distinct biological settings. Complementary RNA-targeting pulldown and single-molecule imaging strategies enable real-time and single-cell-resolution visualization of ribonucleoprotein assembly and dynamics, while functional high-throughput screens allow assignment of first order functions for these RBPs. Overall, these approaches set the stage for comprehensive decoding of the spatiotemporal structure of PTRNs and reveal how RBP interactions coordinate sets of RNAs to collectively regulate them in response to physiological demands. In addition to describing these systems-level approaches, we outline key future analytical and experimental innovations that could transform our understanding of RBP function. We believe that a systems-level understanding of RBPs as dynamic, integrated components of multiscale regulatory regimes is required to fully understand the complexity of gene expression control and its disruption in disease.