The ribosomal DNA of Drosophila melanogaster is organized differently from that of Drosophila hydei

rDNA magnification is a unique feature of germline stem cells

Ribosomal DNA (rDNA) encodes ribosomal RNA and exists as tandem repeats of hundreds of copies in the eukaryotic genome to meet the high demand of ribosome biogenesis. Tandemly repeated DNA elements are inherently unstable; thus, mechanisms must exist to maintain rDNA copy number (CN), in particular in the germline that continues through generations. A phenomenon called rDNA magnification was discovered over 50 y ago in Drosophila as a process that recovers the rDNA CN on chromosomes that harbor minimal CN. Our recent studies indicated that rDNA magnification is the mechanism to maintain rDNA CN under physiological conditions to counteract spontaneous CN loss that occurs during aging. Our previous studies that explored the mechanism of rDNA magnification implied that asymmetric division of germline stem cells (GSCs) may be particularly suited to achieve rDNA magnification. However, it remains elusive whether GSCs are the unique cell type that undergoes rDNA magnification or differentiating germ cells are also capable of magnification. In this study, we provide empirical evidence that suggests that rDNA magnification operates uniquely in GSCs, but not in differentiating germ cells. We further provide computer simulation that suggests that rDNA magnification is only achievable through asymmetric GSC divisions. We propose that despite known plasticity and transcriptomic similarity between GSCs and differentiating germ cells, GSCs' unique ability to divide asymmetrically serves a critical role of maintaining rDNA CN through generations, supporting germline immortality.

Clustering of rDNA containing type 1 insertion sequence in the distal nucleolus organiser ofDrosophila melanogaster: implications for the evolution of X and Y rDNA arrays

The ribosomal RNAs produced by the multigene families on theXandYchromosomes ofDrosophila melanogasterare very similar despite the apparent evolutionary isolation of theXandYchromosomal rDNA.X–Yexchange through the rDNA is one mechanism that may promote co-evolution of the two gene clusters by transferringYrDNA copies to theXchromosome. This hypothesis predicts that the proximal rDNA ofXchromosomes will beY-like. Consequently, rDNA variants found only on theXchromosome (such as those interrupted by type 1 insertions) should be significantly clustered in the distalXnucleolus organizer. Proximal and distal portions of theXchromosome nucleolus organizer were separated by recombination between the inverted chromosomesIn(1)scv2(breakpoint in the centre of the rDNA) andIn(1)sc4Lsc8R(no rDNA). Molecular analyses of the resulting stocks demonstrated that rRNA genes containing type 1 insertions were predominantly located on the chromosome carrying the distal portion of theXrDNA, thus confirming a prediction of theX–Yexchange hypothesis for the co-evolution ofXandYchromosomal rDNA. Distal clustering is not predicted by the alternative hypotheses of selection or gene conversion.

Reduction of wild-typeXchromosomes with theYbb−chromosome ofDrosophila melanogaster

TheYbb−chromosome has been previously shown to induce reduction ofXchromosome ribosomal genes inXbb/Ybb−orXbb+/Ybb−flies. These reduction events are presumed to arise as one of the two products of unequal sister chromatid exchanges, which result in both magnified and reduced products. Bobbed reduced chromosomes may also arise as products of other recombinative events such as intrachromatid deletions. In this report we use theYbb−chromosome to reduce the number of ribosomal genes present onXchromosomes from two wild-type stocks under ‘non-magnifying’ conditions. We then show that the bobbed reducedXchromosomes show no detectable difference in their Southern blot rDNA patterns when compared with the parental wild-typeXchromosome. This indicates that reduction events do not preferentially delete certain repeat classes, and supports previous observations that the repeat types present in theD. melanogaster Xchromosome nucleolus organizer are not significantly clustered.

The distribution and spreading of rare variants in the histone multigene family of Drosophila melanogaster

We surveyed the distribution of rare variant restriction sites within and among histone gene arrays of Drosophila melanogaster using restriction fragment length polymorphism (RFLP) analysis. Seventy-three naturally occurring arrays were digested with restriction enzymes that had no recognition sites in the published histone sequence. Of the arrays surveyed, 68.5% had at least two nonconsensus restriction sites present as indicated by the presence of a small band or bands on the autoradiographs. These bands were almost always the length of a single repeat in the histone multigene family or a multiple of this length. In arrays with more than one band, intensity of the bands almost always decreased with increasing size. This shows that within these arrays variant restriction sites were predominantly located on adjacent repeats. If these bands are caused by spreading of variant sites, as is most likely, then variants spread along the array as an inverse function of distance. Overall, if a sequence spread it had a 92% probability of ending up in its nearest neighbor. This pattern may result from the noncontiguous nature of the histone family.

Molecular genetic analysis of Drosophila rDNA arrays

Large repeated DNA arrays are a major component of the eukaryotic genome, but we know little about their internal organization. Understanding their architecture, however, is critical for describing genome structure and for inferring the mechanisms that shape it. One repeated family that is yielding a picture of how structure, function and recombination mechanisms come together is the ribosomal DNA (rDNA) of Drosophila melanogaster.

Superstructure of the Drosophila ribosomal gene family

Determining the spatial organization of middle repetitive DNA has proven difficult for several reasons. Repeated arrays are often so large that molecular methods alone cannot resolve their organization, and the lack of phenotypic markers within arrays limits the value of classical genetic analysis. We have characterized the superstructure of one repeated gene family, the ribosomal gene family of Drosophila melanogaster, by a combination of recombinational and molecular analyses of spacer-length variants. The resulting genetic maps demonstrate that some spacer variants are widely dispersed, while others are limited in their distribution. Moreover, exchange among ribosomal DNA (DNA encoding rRNA) arrays was often unequal, leading to a prediction of little or no relationship between physical location in an array and relatedness of gene family members. Extensions of our procedure may be generally useful for mapping the superstructure of repetitive DNA.

Differential elimination of rDNA genes in bobbed mutants of Drosophila melanogaster

In Drosophila melanogaster, the multiply repeated genes encoding 18S and 28S rRNA are located on the X and Y chromosomes. A large percentage of these repeats are interrupted in the 28S region by insertions of two types. We compared the restriction patterns from a subcloned wild-type Oregon R strain to those of spontaneous and ethyl methanesulfonate-induced bobbed mutants. Bobbed mutations were found to be deficiencies that modified the organization of the rDNA locus. Genes without insertions were deleted about twice as often as genes with type I insertions. Type II insertion genes were not decreased in number, except in the mutant having the most bobbed phenotype. Reversion to wild type was associated with an increase in gene copy number, affecting exclusively genes without insertions. One hypothesis which explains these results is the partial clustering of genes by type. The initial deletion could then be due either to an unequal crossover or to loss of material without exchange. Some of our findings indicated that deletion may be associated with an amplification phenomenon, the magnitude of which would be dependent on the amount of clustering of specific gene types at the locus.

Differential elimination of rDNA genes in bobbed mutants of Drosophila melanogaster

In Drosophila melanogaster, the multiply repeated genes encoding 18S and 28S rRNA are located on the X and Y chromosomes. A large percentage of these repeats are interrupted in the 28S region by insertions of two types. We compared the restriction patterns from a subcloned wild-type Oregon R strain to those of spontaneous and ethyl methanesulfonate-induced bobbed mutants. Bobbed mutations were found to be deficiencies that modified the organization of the rDNA locus. Genes without insertions were deleted about twice as often as genes with type I insertions. Type II insertion genes were not decreased in number, except in the mutant having the most bobbed phenotype. Reversion to wild type was associated with an increase in gene copy number, affecting exclusively genes without insertions. One hypothesis which explains these results is the partial clustering of genes by type. The initial deletion could then be due either to an unequal crossover or to loss of material without exchange. Some of our findings indicated that deletion may be associated with an amplification phenomenon, the magnitude of which would be dependent on the amount of clustering of specific gene types at the locus.

Expression and amplification of the genes for ribosomal RNA in bobbed mutants of Drosophila melanogaster

We have employed stocks bearing clonally derivedXchromosomes to investigate several features of the bobbed mutant syndrome, and the amplification of rDNA genes inD. melanogaster. We report that posterior macroscutellar bristle length correlates well with the rDNA content (i.e. dose ofivs–, or uninterrupted genes) in clonedXderivative strains.X/Omales andX/Xfemales with statistically indistinguishable rDNA contents have virtually identical bristle lengths. This indicates that (with respect to this phenotypic character) the rDNAs in these two genotypes are expressed equally, without apparent sexual dimorphism or dosage compensation. However, the severity of bobbed phenotype in terms of bristle morphology, turgite etching, and delayed eclosion is greater in theXbb/XNO−female than in theXbb/Omale genotype for the alleles examined. We estimate the minimum dose of functioning rRNA genes required for viability at 26 δC to be 70 genes per diploid genome. We have examined the capacity of severalXchromosomes which bear bobbed mutant alleles to compensate inX/Omales, and find that disproportionate replication of these rDNAs does not take place. In contrast, at least one of the non-compensating bobbed alleles does appear to undergo rDNA magnification.

Non-random loss of uninterrupted ribosomal DNA repeating units upon induction of a bobbed mutation

To investigate the physical organization of ribosomal RNA genes of two bobbed (bb) loci carried by the Dp(1;f)122 free duplication, a wild type and a deleted one derived from it, genomic DNAs from XXNO-/Dp122bb+ and XXNO-/Dp122bb adult females were analyzed by restriction enzyme digestions. We found that in the bb mutant there was a loss of uninterrupted genes, while genes interrupted by type I and type II insertions remained apparently unchanged. This is an indication that at least in this wild type bb+ locus, carried by the 122 free duplication, the different repeating units are not distributed randomly. In fact, after digestion of the rDNA carried by the bb+ duplication with the enzyme BamHI that cuts only in type I insertions, we have obtained long uncleaved fragments of DNA containing uninterrupted genes.

Chromosomal arrangement of the two main rDNA size classes of Ascaris lumbricoides

The two main rDNA size classes of 8.8 kb and 8.4 kb length from Ascaris lumbricoides, which comprise more than 95% of the total nuclear rDNA, are arranged as internally homogeneous clusters and are not intermingled with each other. The rRNA genes are present on a single autosomal locus as could be demonstrated by in situ hybridization of fluorochrome-labelled 18S and 26S rRNA to metaphase chromosomes of spermatocytes I. The quantitative ratio of the two rDNA size classes varies largely between individuals being on the average roughly 10:1 in the investigated wild population of A. lumbricoides. However, there are no differences in the hybridization pattern of the two rDNAs in the DNA eliminating nematode A. lumbricoides between germ line and somatic cells in any of the individuals that have been analyzed.

Determination of the region of rDNA involved in polytenization in salivary glands of Drosophila hydei

During the formation of polytene chromosomes in salivary glands of Drosophila hydei, the genes for ribosomal RNA (rDNA) are underreplicated relative to the rest of the genome. We have measured the number of rRNA genes with and without intervening sequences (ivs+ and ivs- genes) in polytene chromosomes of different genotypes. In the group of genotypes having a large number of ivs- rRNA genes polytenization only occurs within the cluster of ivs- genes. In each of these genotypes rDNA polytenization reaches a constant level of 150 ivs- genes per two chromatid sets (2C); X/X constitutions having two nucleolus organizers (NOs) in the diploid set polytenize the same amount of rDNA as X/O constitutions. In the group of genotypes with small ivs- gene numbers, the rDNA region involved in polytenization is longer and has an average length of 1,700 kb per NO, which is constant in these genotypes. Polytenization of rDNA is extended into the cluster of ivs+ genes, in spite of the fact that these genes appear to be nonfunctional. The smaller the number of ivs- genes, the greater the number of ivs+ genes that are polytenized in the NO. In these genotypes, X/X females replicate twice as much rDNA as X/O males, suggesting that both NOs of the diploid set are polytenized. A comparison of the pattern of spacer length heterogeneity in hybrids between different stocks also demonstrates that both NOs are replicated during polytenization.