Alternate Junctions and Microheterogeneity of Tlr1, a Developmentally Regulated DNA Rearrangement in Tetrahymena thermophila

A large number of developmentally regulated DNA rearrangements occur during the development of the macronucleus in Tetrahymena thermophila, Tlr1 is a deletion element which has large inverted repeats near the rearrangement junctions and deletes more than 13 kbp of internal DNA. Previous analysis of caryonidal lines revealed alternate left junctions for the Tlr1 rearrangement in B strain cells. We show here that C2 strain Tetrahymena also use alternate rearrangement junctions. We have mapped and sequenced two additional rearrangement variants and find that both the left and right can vary over a range of approximately 200 bp. We also demonstrate the presence of sequence microheterogeneity in the most commonly found Tlr1 rearrangement product.