Protocol for the spatiotemporal profiling of RNA within nuclear compartments in human cell lines using SLAM-RT&Tag

Measuring RNA residence time within nuclear compartments provides insight into their roles as either storage sites or transient processing hubs. This protocol describes SLAM-RT&Tag, a genomic technique that integrates RNA metabolic labeling with RT&Tag, an RNA proximity labeling method. We detail steps for RNA labeling, library preparation, and computational quantification of T-to-C conversion events to infer RNA dynamics within nuclear compartments in human cell lines. For complete details on the use and execution of this protocol, please refer to Khyzha et al.1. Keywords: Bioinformatics; Cell Biology; Gene Expression; Genomics; Molecular Biology; Molecular/Chemical Probes; RNA-seq; Sequence analysis; Sequencing.