Epigenetic Programming of Developmental Genome Rearrangements in Ciliates

a radically different answer to the specificity problem. Epigenetic phenomena are widespread among widely The d48 Paradigm: A Maternally Inherited divergent eukaryotes. They have most often been reSomatic Mutation vealed by their effects on gene expression, and indicate The first evidence of an epigenetic regulation of rethat identical genomic sequences can be stably mainarrangement patterns came from the study of a mutant tained in alternative states within similar nuclear envistrain of Paramecium tetraurelia unable to express the A ronments. Inherited epigenetic modifications of genogene, a member of a multi-gene family encoding surface mic sequences, such as altered chromatin structure or antigens (Epstein and Forney, 1984). In the wild-type DNA methylation status, can, however, affect other asstrain, macronuclear telomeres are added in three alterpects of DNA metabolism. This review focusses on renative regions located downstream of the A gene. In the cent evidence for an epigenetic regulation of genome d48 strain, macronuclear chromosomes showa terminal rearrangements in ciliates. deletion of the A gene; telomeres are added in a single In these unicellular eukaryotes, sexual events are folregion located at the 59 end of the coding sequence lowed by a complex developmental program in which (Figure 1, Panels A and B). In each of these two strains, two kinds of nuclei, somatic macronuclei and germthe variant rearrangement is faithfully reproduced insexline micronuclei, differentiate from the diploid zygotic ual progeny during autogamy, a self-fertilization process nucleus within the same cytoplasm. During developoccurring after meiosis of the micronuclei in single cells. ment of the macronucleus, the germ-line genome is amSurprisingly, in crosses between the two strains, the plified to a high ploidy level and extensively rearranged alternative rearrangements do not show Mendelian in(for a general review, see Prescott, 1994). Germ-line heritance, but are maternally (cytoplasmically) transmitchromosomes are fragmented into shorter, acentroted to progeny. The genetic analysis, later confirmed meric macronuclear chromosomes which are healed by by reciprocal transplantation of vegetative micronuclei, the addition of new telomeres. Substantial genome reshowed that the d48 germ-line genome is entirely wildduction (up to 90% in some species) results both from type. In both conjugation and autogamy, the developDNA elimination between macronuclear chromosomes, ment of the zygotic macronucleus simply reproduces and from the excision of a large number of internal sethe particular rearrangement pattern observed in the quence elements, including multi-copy transposons and maternal macronucleus, still present in the cytoplasm single-copy IESs (Internal Eliminated Sequences). Reat that time. Transfer of cytoplasm between cells at arrangements are generally highly reproducible, though specific developmental stages provided evidence that not always precise at the nucleotide level. In some spea cytoplasmic factor transiently produced by the A genecies, for example, addition of macronuclear telomeres containing maternal macronucleus is able to restore amoccurs at random sites within specific regions. plification of the A gene in the developing macronucleus It is generally assumed that the rearrangement proof the d48 strain (Koizumi and Kobayashi, 1989). gram is entirely encoded in the germ-line genome, i.e., Homology-Dependent Rescue that the observed reproducibility is solely determined of Macronuclear Deletions by cis-acting sequence elements. Some cis-acting deSome insight into the molecular nature of the cytoterminants have indeed been identified, such as the Cbs plasmic factor involved in this puzzling trans-nuclear (Chromosome breakage sequence) in Tetrahymena, a effect could be obtained by transformation of the vege15 base pair sequence which was shown to direct chrotative macronucleus, which leads to autonomous replimosome breakage and telomere addition in its vicinity. cation of any DNA molecule as linear monomers and However, no conserved sequence element has been multimers. Transformation of the d48macronucleus with identified in the loosely defined but reproducible teloan A-gene plasmid was shown to cause a permanent mere addition regions of Paramecium. It is also unclear reversion of d48 to wild type: although the plasmid itself how some tens of thousands of single-copy IESs are is eventually lost with the maternal macronucleus after specifically recognized in the germ-line genomes of Euautogamy of the transformed cell line, the germ-line A plotes and Paramecium. Indeed these non-coding elegene is amplified in the developing macronucleus, and ments, which can be as short as 28 base pairs, contain maintained in the following sexual generations (Figure no conserved sequence other than the 59-TA-39 direct 1C). Thus, the trans-acting factor required for amplificarepeats marking their boundaries, one copy of which is tion of the A gene appears to be produced by the A left after precise excision. Statistical analyses of IES gene itself. However, even a fragment of the coding ends have revealed a short, poorly conserved consensequence is enough to rescue the d48 mutation, indicat-