Extensive DNA rearrangement occurs during the development of the somatic macronucleus from the germ line micronucleus in ciliated protozoans. The micronuclear junctions and the macronuclear product of a developmentally regulated DNA rearrangement in Tetrahymena thermophila, Tlrl, have been cloned. The intrachromosomal rearrangement joins sequences that are separated by more than 13 kb in the micronucleus with the elimination of moderately repeated micronucleus-specific DNA sequences. There is a long, 825-bp, inverted repeat near the micronuclear junctions. The inverted repeat contains two diferent 19-bp tandem repeats. The 19-bp repeats are associated with each other and with DNA rearrangements at seven locations in the micronuclear genome. Southern blot analysis is consistent with the occurrence of the 19-bp repeats within pairs of larger repeated sequences. Another family member was isolated. The 19-mers in that clone are also in close proximity to a rearrangement junction. We propose that the 19-mers define a small family of developmentally regulated DNA rearrangements having elements with long inverted repeats near the junction sites. We discuss the possibility that transposable elements evolve by capture of molecular machinery required for essential cellular functions.Ciliated protozoa have two different kinds of nuclei: diploid, germ line micronuclei and transcriptionally active macronuclei. During sexual reproduction (conjugation), the old macronucleus is degraded and a new macronucleus develops from a mitotic product of the zygotic micronucleus.The developing macronucleus undergoes radical changes in genome organization. In the holotrichous ciliate Tetrahymena thermophila, there is a period of DNA replication which brings the DNA content of the macronucleus to 45 times the haploid DNA content of the micronucleus. When the developing nucleus is between 4C and 8C, about 15% of the germ line DNA sequences are eliminated from the somatic macronucleus (11,36,58). Since DNA sequence elimination is site specific, highly regular, and developmentally controlled, it is expected that DNA rearrangement involves the interaction of specific cis-acting sequences with the rearrangement machinery.Developmentally regulated DNA rearrangements in T. thermophila fall into two classes with respect to the fate of the macronucleus-destined sequences which flank the eliminated DNA (reviewed in reference 56