Simultaneous observation of Pol II and potato spindle tuber viroid RNA in the nucleus by combining immunofluorescence and RNA in situ hybridization

RNA comprises a versatile group of biomolecules that play diverse roles in a wide range of biological processes. From synthesis to degradation, RNAs interact with cognate proteins that assist in processes such as transcription, splicing, modification, trafficking, and the execution of their functions. While numerous valuable techniques exist to study RNA-protein interactions, observing RNAs and their associated proteins simultaneously within cells remains a challenge, despite its potential to provide deeper insights into RNA-protein interactions. In this study, we adapted a modified immunofluorescence (IF) assay combined with RNA fluorescence in situ hybridization (FISH) to successfully visualize the colocalization of potato spindle tuber viroid with RNA polymerase II in the nucleus. This new method that combines IF and FISH will facilitate future studies on RNA and protein colocalization in various plant systems.