X chromosome nucleolus organizer mutants which alter major type I repeat multiplicity in Drosophila melanogaster

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.

Increase in the resistance to the Bacillus thuringiensis supernatant effect in a Drosophila melanogaster wild type Oregon R line

We report here the genetical and X chromosome rDNA molecular study of two Drosophila melanogaster Oregon R lines. These lines differ extensively in the degree of resistance of the females both to the lethal effect of an increased temperature and to that of Bacillus thuringiensis beta-exotoxin, which is an inhibitor of the nucleolar RNA polymerase. The 3B line, whose females are resistant, came from an Oregon R population subjected over several generations to increased temperature, 28 degrees C or over, while the other line is derived from the initial stock. Twofold variation was observed in the total number of ribosomal genes between the two lines. This variation applied to most ribosomal units, including the active ones. Variations among X chromosome rDNA content in a wild type population have thus been revealed using tests of resistance to the Bacillus thuringiensis beta-exotoxin. Additive variations in specific unit types between the two lines indicate that modifications to the rDNA content are not rare events.

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.

Nucleolus organizer-suppressed position-effect variegation in Drosophila melanogaster

The white locus is inactivated in a cell-by-cell variegated pattern when juxtaposed with the proximal or distal parts of the nucleolus organizer region (NO) by X chromosome inversion. Recombinants for two such inversions, wm51b and wm4, were obtained and randomized for genetic background. White locus activity was much higher in the wm4 recombinant duplicated for most of the NO and much lower in the wm51b recombinant deficient for it. Although there may be other molecular differences between the heterochromatic regions of the recombinants, the most obvious is the dosage of NO. Suppression of a NO region-evoked variegated phenotype by additional NO doses is discussed in relation to four different classes of models for position-effect variegation (PEV): chromatin structure, nuclear geometry, incomplete transposition of mobile elements, and heterochromatin promoter-driven transcription. A corollary of the structural model is functional subdivision of heterochromatin, which would enable the use of PEV as a tool for its study.

The occurrence of long ribosomal transcripts homologous to type I insertions in bobbed mutants of Drosophila melanogaster

In Drosophila melanogaster up to two thirds of the rDNA genes contain insertion sequences of two types in the 28S coding region. Comparison of the ribosomal insertion transcripts in the wild type and in two bobbed mutants reared at two temperatures showed that the level of type I transcripts is dependent on both the number of genes with type I insertions in the bobbed loci and the intensity of bobbed phenotype. Importantly, a long transcript of 8.7 kb hybridized to the ribosomal probe, the INS I probe and also to the restriction fragment of the rDNA downstream of the point of insertion was found in one bobbed mutant. This result and also those from sandwich hybridization indicate that some interrupted ribosomal genes are functional.

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.

Preferential homogenization between adjacent and alternate subrepeats in wheat rDNA

DNA from the "non-transcribed spacer" (NTS) of two wheat ribosomal RNA gene (rDNA) clones was sequenced. The regions flanking the internal subrepeat arrays are highly conserved between the two clones; the nucleotide sequence differ by less than one-half percent. In contrast, the consensus sequences of the subrepeats in the two arrays differ by three percent. Mutations unique to each array, yet found in more than one subrepeat of the array, are preferentially found in adjacent and alternate subrepeats. The similarity of the DNA sequences of the flanking regions is consistent with a model of homogenization among rDNA gene units by intergenic conversion. We propose that a different mechanism, preferential conversion between neighboring subrepeats, is largely responsible for the homogenization of subrepeats within an array.

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.

Preferential DNase I sensitivity of insert-free ribosomal RNA repeats of Drosophila melanogaster

The five predominant types of rDNA repeats in D. melanogaster were analyzed with respect to their DNase I sensitivity. Only the insert-free repeats showed a generalized DNase I sensitivity pattern whereas the major type I, both minor type I and type II repeats were not as extensively degraded by the nuclease. For XX and XY embryonic nuclei, where there is rapid cell division, the majority of the In- repeats were DNase I sensitive. This indicated that these In- repeats have the potential to be transcribed during this developmental stage. When compared to the In- repeats, the chromatin configuration of the In+ repeats is indicative of a higher order of chromatin folding. The paucity of In+ primary gene transcripts observed in vivo could result from In+ repeats being packaged into a more condensed form of chromatin.

Suppression of ribosomal RNA genes in Drosophila melanogaster

The rDNA of fiveYchromosome mutants was examined with respect to their insert free (In−) repeat type multiplicity. The In− repeat number of each mutant was correlated with its hemizygousbobbedphenotype and additivity with anXNObobbed(bb) mutant. Four of these mutants showed a direct relationship between their In− frequency, hemizygousbbphenotype and additivity tests. A fifth mutant,bb1–4, had a sufficient number of In− repeats to ensure viability to the late pupal stage and show additivity; however, the In− repeats genetically behaved as a complete rDNA deletion. Possible mechanisms resulting in the suppression of thebb1–4In− repeats are discussed.

Different chromatin states of the intron- and type 1 intron+ rRNA genes of Calliphora erythrocephala

In most species of dipteran fly examined, a fraction of the rDNA cistrons are interrupted by introns. These dipteran intron+ rRNA genes are unique in that they are transcriptionally inactive. Previous studies have investigated the mechanism underlying this transcriptional repression for rRNA genes carrying the best characterized sequence family of such introns, the so-called type 1 introns first identified in Drosophila melanogaster. These studies have established that cloned examples of both intron-free and type 1 intron+ rRNA genes will support transcription in a cell-free system and suggest therefore that a difference in the chromatin state of the two gene types must underlie their very different potential for in vivo transcription. We have examined this possibility for the type 1 intron+ rDNA cistrons of Calliphora erythrocephala by in situ hybridization studies using the polytene chromosome complement of the pupal bristle-forming (trichogen) cells. These studies show that the chromatin configuration of the two gene types is strikingly different. The intron-free genes are preferentially localized in the actively transcribed fibrillar center of the nucleolus. The intron+ genes are preferentially condensed in the blocks of heterochromatin attached to the nucleolus.

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.

Nonselective amplification of ribosomal DNA repeat units in compensating genotypes of Drosophila melanogaster

Compensation is a mechanism by which the X-chromosome nucleolus organizer region of Drosophila melanogaster can increase its ribosomal DNA content up to twofold. It occurs in somatic cells under specific genetic conditions and is mediated by a defined genetic site, the compensatory response locus. The In- and various type I ribosomal DNA repeat units were separated by restriction endonuclease digestion. Comparison of the percentages of these repeat unit types between compensating and noncompensating genotypes showed the same distribution. Therefore no selective amplification of these repeat unit types occurs during ribosomal DNA compensation. These results demonstrate that two processes of rDNA amplification in somatic cells, compensation and independent rDNA polytenization, are exclusive events.