The ciliated protozoan Tetrahymena thermophila undergoes extensive programmed DNA rearrangements during the development of a somatic macronucleus from the germ line micronucleus in its sexual cycle. To investigate the relationship between programmed DNA rearrangements and transposable elements, we identified several members of a family of non-long terminal repeat (LTR) retrotransposons (retroposons) in T. thermophila, the first characterized in the ciliated protozoa. This multiple-copy retrotransposon family is restricted to the micronucleus of T. thermophila. The REP (Tetrahymena non-LTR retroposon) elements encode an ORF2 typical of non-LTR elements that contains apurinic/apyrimidinic endonuclease (APE) and reverse transcriptase (RT) domains. Phylogenetic analysis of the RT and APE domains indicates that the element forms a deep-branching clade within the non-LTR retrotransposon family. Northern analysis with a probe to the conserved RT domain indicates that transcripts from the element are small and heterogeneous in length during early macronuclear development. The presence of a repeated transposable element in the genome is consistent with the model that programmed DNA deletion in T. thermophila evolved as a method of eliminating deleterious transposons from the somatic macronucleus.Developmentally programmed DNA rearrangements occur in a wide variety of organisms (reviewed in reference 5). Functions such as altering gene dosage or directly regulating gene expression have been assigned to many but not all examples of programmed DNA rearrangements. A clinically important example of a programmed DNA rearrangement is V(D)J recombination (2). In addition, a variety of mammalian parasites use programmed DNA rearrangements to vary their surface antigens to avoid host immune response (4). The function of other programmed DNA rearrangements is not as clear. The extensive genome rearrangements that occur during nuclear development in the ciliated protozoa provide an example of programmed DNA rearrangements with poorly understood function.Like all ciliated protozoa, the oligohymenopheran Tetrahymena thermophila displays nuclear dimorphism with a mostly transcriptionally silent diploid germ line nucleus (micronucleus) and a polyploid and transcriptionally active somatic nucleus (macronucleus) within the same cell. The macronucleus develops from a mitotic product of the micronucleus during conjugation. When two cells of different mating types conjugate, the micronucleus in each divides meiotically and mitotically to generate a haploid gametic nucleus that is reciprocally exchanged and fuses with that of its partner to form a zygotic nucleus. This zygotic nucleus divides and from one of the products develops a new macronucleus, while the old macronucleus is concurrently degraded. In T. thermophila, macronuclear development involves extensive programmed DNA rearrangements, including chromosome fragmentation, DNA amplification, and site-specific interstitial DNA deletion (12). Interstitial DNA deletion is responsible for t...

We used a reverse genetic approach to identify three members of the SNF2 superfamily of chromatin remodeling genes in the ciliated protozoan Tetrahymena thermophila in order to investigate possible functions of ATP-dependent chromatin remodeling factors in growth and nuclear development. Comparative sequence analysis of the gene product of the Tetrahymena brahma-related gene (TtBRG1) indicates it is a member of the SNF2/BRM subgroup of the SNF2 superfamily. Northern analysis suggests that TtBRG1 has roles in growth and nuclear development in Tetrahymena. Indirect immunofluorescence analysis during nuclear development indicates that TtBrg1p localizes to both the parental and developing macronucleus of Tetrahymena during the time period corresponding to genome rearrangements. We generated germ line knockout heterokaryons for TtBRG1 and demonstrated that expression of the gene is required to complete nuclear development of Tetrahymena. In addition, the formation of distinct Pdd1p-containing structures is disturbed during the late stages of conjugation in TtBRG1 germ line knockout heterokaryons. We discuss these results in light of possible roles of SNF2-related proteins in growth and nuclear development of Tetrahymena.DNA transactions, such as recombination, replication, and transcription, occur within a chromatin medium. The basic modular unit of chromatin is the nucleosome, which is composed of 147 bp of DNA wrapped 1.7 times around a histone octamer (33). Histones contain a core globular domain and a flexible, amino-terminal tail that projects from the nucleosome. Chromatin remodeling is a general term used to refer to the fact that DNA must be completely or partially unraveled from the histone octamer for DNA transactions, such as transcription, recombination, and replication, to occur (1). There are three methods utilized to remodel chromatin. The first involves various covalent modifications of specific residues in the histone N-terminal tail, such as acetylation, methylation, phosphorylation, and ubiquitination (19). The second method occurs through the ATP-dependent physical disruption or the movement of the nucleosome (61), and the third involves the insertion of histone variants into chromatin (29). The latter two examples of chromatin remodeling appear to be performed by multisubunit protein complexes that are nucleated by a variety of DNA-dependent ATPases. These ATPase subunits are members of the SNF2 superfamily of nucleic acidstimulated ATPases (13). This superfamily has three major groups based upon the presence or absence of other conserved protein motifs flanking the core ATPase. The CHD class (chromodomain helicase DNA-binding domains) contains two copies of a chromodomain, the SNF2 class, a C-terminal bromodomain, and the ISWI class, neither.The ciliated protozoan Tetrahymena thermophila exhibits nuclear dimorphism with a mostly transcriptionally silent diploid germ line nucleus (micronucleus [MIC]) and a polyploid and transcriptionally active somatic nucleus (macronucleus [MAC]) contained withi...