Single-molecule RNA fluorescence in situ hybridization is a technique that holds great potential for the study of long noncoding RNA. It enables quantification and spatial resolution of single RNA molecules within cells via hybridization of multiple, labeled nucleic acid probes to a target RNA. It has recently become apparent that single-molecule RNA FISH probes targeting noncoding RNA are more prone to off-target binding yielding spurious results than when targeting mRNA. Here we present a protocol for the application of single-molecule RNA FISH to the study of noncoding RNA as well as an experimental procedure for validating legitimate signals.
Dunagin, M., Cabili, M. N., Rinn, J., & Raj, A. (2015). Nuclear Bodies and Noncoding RNAs. In Methods in Molecular Biology (Vol. 1262, pp. 3–19). Retrieved from http://link.springer.com/10.1007/978-1-4939-2253-6