A molecular cartographer's toolkit for mapping RNA's uncharted realms

Deciphering RNA molecules' function and regulation requires an in-depth understanding of the myriad interactions these RNAs form within their cellular environment. In this review, we present a comprehensive overview of recent technological advances that collectively form a molecular toolkit for mapping the molecular environment of RNA. We discuss innovative RNA-centric methods designed to overcome long-standing challenges in capturing direct RNA-protein interactions in living cells. Additionally, we explore transformative proximity-labeling techniques that leverage engineered enzymes and chemical catalysts to spatially resolve the composition of RNA-associated microenvironments. By critically evaluating the strengths and limitations of these emerging methodologies, we highlight how they are reshaping our understanding of RNA function, from local binding events to the dynamic organization of RNA-scaffolded compartments. These advancements not only promise to elucidate the molecular grammar underlying RNA regulatory networks in unprecedented details but also pave the way for an integrative, system-level understanding of complex RNA-mediated cellular processes.