RNase Sensitivity Screening for Nuclear Bodies with RNA Scaffolds in Mammalian Cells

The mammalian cell nucleus is highly organized and contains membraneless nuclear bodies (NBs) characterized by distinct resident factors. The NBs are thought to serve as sites for biogenesis and storage of certain RNA and protein factors as well as assembly of ribonucleoprotein complexes. Some NBs are formed with architectural RNAs (arcRNAs) as their structural scaffolds and additional NBs likely remain unidentified in mammalian cells. Here, we describe an experimental protocol to search for new NBs built on certain arcRNAs. RNase-sensitive NBs were identified by monitoring nuclear foci visualized by tagging thousands of human cDNA products.