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

Area of Science:

• Molecular Biology
• Genomics
• Cell Biology

Background:

• Understanding RNA dynamics within nuclear compartments is crucial for elucidating their functions.
• Nuclear compartments can act as RNA storage sites or transient processing hubs, but their precise roles are often unclear.

Purpose of the Study:

• To present a novel genomic protocol, SLAM-RT&Tag, for measuring RNA residence time within nuclear compartments.
• To provide a detailed methodology for researchers to study RNA dynamics in human cell lines.

Main Methods:

• SLAM-RT&Tag integrates RNA metabolic labeling with proximity labeling (RT&Tag).
• The protocol involves RNA labeling, library preparation, and computational analysis of T-to-C conversion events.
• This method allows inference of RNA dynamics within specific nuclear compartments.

Main Results:

• The study details the steps required for the successful execution of the SLAM-RT&Tag protocol.
• The described computational quantification enables the analysis of RNA dynamics.

Conclusions:

• SLAM-RT&Tag offers a powerful tool for investigating the spatiotemporal dynamics of RNA within the nucleus.
• This technique can provide critical insights into the functional roles of nuclear compartments in RNA metabolism and regulation.