Genetically engineered RNA inducers of proximity for protein regulation

Current genetic engineering technology that based on complementary base pairing for target recognition is a powerful tool to control protein expression at DNA or RNA levels. Nonetheless, limited research has utilized genetic strategies to directly manipulate proteins. To address this gap, we have developed a method of genetically engineered RNA inducers of proximity (GENRIP), one strategy that leverages RNA structure-dependent protein recognition to precisely regulate protein activity. GENRIP is a modular and bifunctional RNA comprising two kinds of motifs: a conserved RNA motif that recruits endogenous RNA-binding enzymes for protein modification, and a variable motif responsible for recognizing different proteins of interest (POIs). By inducing proximity between effector enzymes and POIs, GENRIP enables precise post-translational modification of POIs. Using the RNA-binding E3 ligase MEX3A and RNA-binding kinase CamK as model effectors, we have demonstrated its capability to achieve ubiquitination-mediated degradation and phosphorylation-induced activation of POI, respectively. Furthermore, GENRIP offers superior advantages in modularity, programmability, precise subcellular localization targeting, and cell-type selectivity. This approach represents a paradigm shift in genetic engineering, holding profound implications in the field of post-translational protein regulation. Current genetic engineering techniques enable protein modulation at the DNA/RNA levels. Here, the authors design an RNA platform to bring target protein and effector enzyme into proximity, realizing direct protein regulation.