Tandemly repeated C-C-C-C-A-A hexanucleotide of Tetrahymena rDNA is present elsewhere in the genome and may be related to the alteration of the somatic genome.

The ribosomal RNA genes of the Tetrahymena macronucleus exist as extrachromosomal, linear molecules. The termini of these molecules have been shown to contain the tandemly repeated hexanucleotide (C-C-C-C-A-A)n. In this study the same or related sequences were found in other locations of the genome. Using the depurination method, we showed that macronuclear DNA contained this sequence even after rDNA had been removed. The sequence was found mainly in the repetitive fraction of the DNA. The presence of this sequence in both the macronucleus and the micronucleus was also shown by Southern hybridization using C-C-C-C-A-A repeat as a probe. Comparison between the hybridization patterns of macronuclei and micronuclei reveals interesting differences. Whereas the two nuclei share the same genetic origin, the majority of the restriction enzyme digestion sites flanking the C-C-C-C-A-A repeat appear to be different. Such a difference was found to be specific for this sequence, because it was not detected when other sequences were used for hybridization. These results suggest that some kind of alteration has occurred in the genome during the formation of the macronucleus, and that the C-C-C-C-A-A repeat may be related to this process.