LTR, Ty3, and rDNA sequences do not all localize to the nucleolus. W303-1a cells were analyzed for the nuclear location of the genomic LTR and Ty3 sequences compared to rDNA. Probes containing rDNA sequences were biotinylated and detected by successive incubations in FITC-avidin, biotinylated antiavidin, and finally FITC-avidin (pseudocolored green). Probes containing control plasmid, LTR, or Ty3 sequences were labeled with digoxigenin. Hybridized digoxigenin probes were detected using antidigoxigenin and then anti-mouse IgG-Alexa-586 (pseudocolored red). DNA was stained with DAPI (pseudocolored blue). Each frame represents the indicated overlay.