Nuclear compartments are non-membrane-bound regions enriched in functionally related molecules that coordinate biochemical reactions in space and time. Many compartments have important roles in RNA maturation, positioning them as crucial regulators of gene expression. However, the study of nuclear compartments has been limited by technical challenges: they are difficult to isolate using conventional biochemical methods, and imaging approaches, though powerful, are often low-throughput and require prior knowledge of specific targets. These limitations underscore the need for high-throughput, proximity-based methods to study the dynamics of the transcriptome within these compartments.

A key strength of SLAM-RT&Tag is its antibody-guided specificity, which enables the comparison of RNA half-lives globally (via IgG) and within defined nuclear compartments. The half-life of a transcript in a compartment encompasses both its overall stability and how quickly it leaves that compartment. Thus, comparing compartment-specific and global half-lives reveals whether RNAs are transient visitors or stably localized. These insights illuminate compartment function — for example, whether they serve as storage sites or as transient processing hubs. Perturbation experiments further expand the utility of SLAM-RT&Tag by revealing how RNA kinetics shift in response to disruptions in compartment composition or biochemical activity. In addition to providing a compartment-level view, SLAM-RT&Tag sheds light on the roles of individual RNAs. Some RNAs may act as scaffolds that nucleate or maintain compartment architecture, whereas others function as clients that transiently localize to a compartment for processing. SLAM-RT&Tag is uniquely suited to disentangle these roles by capturing both localization and dynamics simultaneously.