Highly localized tracks of specific transcripts within interphase nuclei visualized by in situ hybridization

Use of in situ hybridization optimized for fluorescent detection of nuclear RNA has revealed a striking localization of specific viral RNAs within nuclei of cells latently infected with EBV. Several hundred kb of specific transcripts is sharply restricted to a small region of the nucleus, frequently in a curvilinear "track". Detection of nuclear RNA was evidenced by hybridization without denaturation, sensitivity to RNAase, inhibition by actinomycin D, and specificity of transcribed sequences. Results indicate that RNA "tracks" extend from an internal genome into the nuclear periphery, and that RNA transport may be coupled to transcription. Localized nRNA is apparent for other viral sequences, different lymphoblastoid cell lines, nuclei prepared by two different methods, and an abundant, nonviral transfected sequence. Implications for understanding nuclear organization and the investigation of gene expression are discussed.