Macronuclei and micronuclei of ciliates have related genomes, with macronuclei developing from zygotic micronuclei through programmed DNA rearrangements. While Paramecium tetraurelia wild-type strain 51 and mutant strain d48 have the same micronuclear genome, qualitative differences between their macronuclear genomes have been described, demonstrating that programmed DNA rearrangements could be epigenetically controlled in ciliates. Macronuclear chromosomes end downstream of gene A (A51 Mac ends) and at the 5 end of gene A (Ad48 Mac ends) in strains 51 and d48, respectively. To gain further insight into the process of chromosome end formation, we performed an extensive analysis of locus A rearrangement in strains d48 and 51, in strain d12, which harbors a gene A deletion, and in interstrain cross progeny. We show that (i) allele A d12 harbors a deletion of >16 kb, (ii) A51 Mac ends distribute over four rather than three DNA regions, (iii) strains d48 and 51 display only quantitative differences (rare Ad48 and A51 Mac ends do form in strains 51 and d48, respectively), (iv) the level of A51 Mac ends is severalfold enhanced in d12-and d48-derived progeny, and (v) this level inversely correlates with the level of Ad48 Mac ends in the d48 parent. Together, these data lead to a model in which the formation of Ad48 Mac ends is epigenetically controlled by a d48 factor(s). We propose that the d48 factor(s) may be derived from RNA molecules transcribed from the Ad48 Mac ends and encompassing the truncated A gene and telomeric repeats.Ciliate cells harbor two types of nuclei that ensure separate functions. Macronuclei that are transcriptionally active carry out the vegetative functions of these unicellular eukaryotes. Micronuclei that are transcriptionally silent during vegetative growth provide genetic continuity between sexual generations. In the course of conjugation, old maternal macronuclei do not replicate their DNA (they will be ultimately lost), while micronuclei enter meiosis. New macronuclei and micronuclei then develop from mitotic copies of zygotic nuclei. Macronuclear genomes result mainly from micronuclear genome fragmentation into short DNA molecules, at the ends of which telomeric repeats are added, excision of internal eliminated sequences (IESs) that are eventually eliminated, and massive DNA amplification that accounts for the large size (and the name) of macronuclei (20,21). Once developed (the whole process takes just a few hours), macronuclear genomes are clonally stable throughout the cellular life span. Although chromosome breakage occurs in a wide range of genomes, the frequency with which this takes place in ciliates is unique and provides an opportunity to study the underlying regulation and mechanisms.In the two species of Paramecium, P. primaurelia and P. tetraurelia, the micronuclear genome is organized into 60 to 90 chromosomes with an average size of 2 Mb, while macronuclear chromosomes range in size from 50 to 800 kb (note that although macronuclear DNA molecules are called chro-
