Labeling of Long Noncoding RNAs to Study Virus-Induced Nuclear Aggregates

Nuclear RNA-protein condensates, including nuclear speckles and paraspeckles, are highly dynamic subnuclear compartments that influence RNA processing and transcriptional control. During viral infection, particularly by herpes simplex virus 1 (HSV-1), these structures undergo marked reorganization. The long noncoding RNA NEAT1 is a key determinant of paraspeckle assembly and activity under such conditions. This chapter reviews current insights into how viruses manipulate or disrupt nuclear condensates and presents a practical protocol for visualizing NEAT1-positive paraspeckles in HSV-1-infected HeLa cells by RNA fluorescence in situ hybridization (RNA FISH). The protocol provides stepwise guidance for cell preparation, viral infection, probe labeling, and fluorescence microscopy, supplemented with troubleshooting notes to support reproducibility. These approaches allow sensitive detection of virus-driven nuclear RNA assemblies and enable detailed investigation of host-virus interactions within the nucleus.