In all eukaryotes, the ribosomal RNA genes are stably inherited redundant elements. In Drosophila melanogaster, the presence of a Ybb 2 chromosome in males, or the maternal presence of the Ribosomal exchange (Rex) element, induces magnification: a heritable increase of rDNA copy number. To date, several alternative classes of mechanisms have been proposed for magnification: in situ replication or extra-chromosomal replication, either of which might act on short or extended strings of rDNA units, or unequal sister chromatid exchange. To eliminate some of these hypotheses, none of which has been clearly proven, we examined molecularvariant composition and compared genetic maps of the rDNA in the bb 2 mutant and in some magnified bb + alleles. The genetic markers used are molecular-length variants of IGS sequences and of R1 and R2 mobile elements present in many 28S sequences. Direct comparison of PCR products does not reveal any particularly intensified electrophoretic bands in magnified alleles compared to the nonmagnified bb 2 allele. Hence, the increase of rDNA copy number is diluted among multiple variants. We can therefore reject mechanisms of magnification based on multiple rounds of replication of short strings. Moreover, we find no changes of marker order when pre-and postmagnification maps are compared. Thus, we can further restrict the possible mechanisms to two: replication in situ of an extended string of rDNA units or unequal exchange between sister chromatids.
IN eukaryotes the 18S, 5.8/2S, and 28S rDNAs are contained in the same transcription unit, and many (hundreds to thousands) of rDNA transcription units are organized in clusters located in one or a few chromosomes. In Drosophila melanogaster each rDNA copy, Figure 1, is about 8 kb long and, in addition to the coding sequences, includes an external transcribed spacer (ETS) upstream of the 18S sequence and two internal transcribed spacers (ITS-1 and ITS-2) located between the 18S and 5.8/2S sequences and the 5.8/ 2S and 28S sequences, respectively (Wellauer and Dawid 1977;Tautz et al. 1988). Contiguous rDNA units are separated by intergenic spacers (IGS). The variable length of the IGS can reach 10-11 kb because it contains diverse numbers of 95-, 330-, and 240-bp-long subrepeats (Pellegrini et al. 1977;Long and Dawid 1980;Simeone et al. 1985;Tautz et al. 1987;Glover 1991).The genome of wild-type D. melanogaster has two similar rDNA clusters. A 2800-kb cluster is in the pericentromeric heterochromatin of the X chromosome long arm. The other, 2200 kb long, is located at the base of the short arm of the Y chromosome (Ritossa 1976;Polanco et al. 1998). Because of their heterochromatic locations, meiotic recombination in the rDNA arrays is rare. Both clusters consist of about 200-250 rDNA units (Tartof 1971;Tautz et al. 1988), in both head-totail (tandem) and head-to-head (reversed) orientations, with a variable number of orientation switches in different stocks (Robbins and Swanson 1988). Cytologically, the rDNA cluster corresponds to the n...