3′ untranslated regions (3′ UTRs) of messenger RNAs (mRNAs) are best known to regulate mRNA-based processes, such as mRNA localization, mRNA stability, and translation. In addition, 3′ UTRs can establish 3′ UTR-mediated protein–protein interactions (PPIs), and thus can transmit genetic information encoded in 3′ UTRs to proteins. This function has been shown to regulate diverse protein features, including protein complex formation or posttranslational modifications, but is also expected to alter protein conformations. Therefore, 3′ UTR-mediated information transfer can regulate protein features that are not encoded in the amino acid sequence. This review summarizes both 3′ UTR functions—the regulation of mRNA and protein-based processes—and highlights how each 3′ UTR function was discovered with a focus on experimental approaches used and the concepts that were learned. This review also discusses novel approaches to study 3′ UTR functions in the future by taking advantage of recent advances in technology.