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In this study we have used the transcription assay with 5′-fluorouridine incorporation into nascent RNA to analyze the nuclear organization and dynamics of transcription sites in rat trigeminal ganglia neurons. The 5′-FU administrated by i.p. injection was successfully incorporated into nuclear domains containing actively transcribing genes of trigeminal neurons. 5′-Fluorouridine RNA-labeling was detected with immunocytochemistry at light and electron microscopy levels. The 5′-fluorouridine incorporation sites were detected in the nucleolus, particularly on the dense fibrillar component, and in numerous transcription foci spread throughout the euchromatin regions, without preferential positioning at the nuclear periphery or in the nuclear interior. Double labeling experiments to combine 5′-fluorouridine incorporation with molecular markers of nuclear compartments showed the absence of transcription sites in …