Toward Mapping Spatiotemporally Resolved Transcriptomes and RNA-Protein Interactions

RNAs navigate highly regulated life cycles that include synthesis, processing, ribonucleoprotein complex formation, localization, and degradation. However, most transcriptome-wide methods capture static, cell-wide averages that obscure the spatiotemporal aspects-where and when-of RNA life. Here we review recent advances that bring spatial and temporal resolution to transcriptome and RNA-protein interaction analyses by labeling RNA either in defined subcellular locales (RNA proximity labeling) or during defined transcriptional time windows to capture the kinetics of RNA synthesis, degradation, and processing (RNA metabolic labeling). We further discuss how RNA labeling approaches can be integrated with RNA-protein interaction mapping, opening new possibilities for studying ribonucleoprotein dynamics in space and time. Finally, we highlight emerging developments and outline future directions for spatiotemporal analysis of the RNA life cycle.