Molecular characterization of ribosomal genes on the Ybb- chromosome of Drosophila melanogaster

The peculiar genetics of the ribosomal DNA blurs the boundaries of transgenerational epigenetic inheritance

Our goal is to draw a line-hypothetical in its totality but experimentally supported at each individual step-connecting the ribosomal DNA and the phenomenon of transgenerational epigenetic inheritance of induced phenotypes. The reasonableness of this hypothesis is offset by its implication, that many (or most) (or all) of the cases of induced-and-inherited phenotypes that are seen to persist for generations are instead unmapped induced polymorphisms in the ribosomal DNA, and thus are the consequence of the peculiar and enduringly fascinating genetics of the highly transcribed repeat DNA structure at that locus.

Transgenerational dynamics of rDNA copy number in Drosophila male germline stem cells

rDNA loci, composed of hundreds of tandemly duplicated arrays of rRNA genes, are known to be among the most unstable genetic elements due to their repetitive nature. rDNA instability underlies aging (replicative senescence) in yeast cells, however, its contribution to the aging of multicellular organisms is poorly understood. In this study, we investigate the dynamics of rDNA loci during aging in the Drosophila male germline stem cell (GSC) lineage, and show that rDNA copy number decreases during aging. Our study further reveals that this age-dependent decrease in rDNA copy number is heritable from generation to generation, yet GSCs in young animals that inherited reduced rDNA copy number are capable of recovering normal rDNA copy number. Based on these findings, we propose that rDNA loci are dynamic genetic elements, where rDNA copy number changes dynamically yet is maintained through a recovery mechanism in the germline.

Transgenerational inheritance of diet-induced genome rearrangements in Drosophila

Ribosomal RNA gene (rDNA) copy number variation modulates heterochromatin formation and influences the expression of a large fraction of the Drosophila genome. This discovery, along with the link between rDNA, aging, and disease, high-lights the importance of understanding how natural rDNA copy number variation arises. Pursuing the relationship between rDNA expression and stability, we have discovered that increased dietary yeast concentration, emulating periods of dietary excess during life, results in somatic rDNA instability and copy number reduction. Modulation of Insulin/TOR signaling produces similar results, indicating a role for known nutrient sensing signaling pathways in this process. Furthermore, adults fed elevated dietary yeast concentrations produce offspring with fewer rDNA copies demonstrating that these effects also occur in the germline, and are transgenerationally heritable. This finding explains one source of natural rDNA copy number variation revealing a clear long-term consequence of diet.

Reduced rDNA copy number does not affect "competitive" chromosome pairing in XYY males of Drosophila melanogaster

The ribosomal DNA (rDNA) arrays are causal agents in X-Y chromosome pairing in meiosis I of Drosophila males. Despite broad variation in X-linked and Y-linked rDNA copy number, polymorphisms in regulatory/spacer sequences between rRNA genes, and variance in copy number of interrupting R1 and R2 retrotransposable elements, there is little evidence that different rDNA arrays affect pairing efficacy. I investigated whether induced rDNA copy number polymorphisms affect chromosome pairing in a "competitive" situation in which complex pairing configurations were possible using males with XYY constitution. Using a common normal X chromosome, one of two different full-length Y chromosomes, and a third chromosome from a series of otherwise-isogenic rDNA deletions, I detected no differences in X-Y or Y-Y pairing or chromosome segregation frequencies that could not be attributed to random variation alone. This work was performed in the context of an undergraduate teaching program at Texas A&M University, and I discuss the pedagogical utility of this and other such experiments.

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 centric region of the X chromosome rDNA functions in male meiotic pairing in Drosophila melanogaster

In Drosophila melanogaster males, sex chromosome pairing at meiosis is ensured by so-called pairing site(s) located discretely in the centric heterochromatin. The property of the pairing sites is not well understood. Recently, an hypothesis has been proposed that 240 bp repeats in the nontranscribed spacer region of rDNA function as the pairing sites in male meiosis. However, considerable cytogenetic evidence exists that is contrary to this hypothesis. Hence, the question is whether the chromosomal rDNA clusters, in which a high copy number of 240 bp repeats exists, are involved in the pairing. In order to resolve the problem we X-rayed Drosophila carrying the X chromosome inversion In(1)scV2L sc8R and generated free, mini-X chromosomes carrying a substantial amount of rDNA. We defined cytogenetically the size of the mini-chromosomes and studied their meiotic behavior. Our results demonstrate that the heterochromatin at the distal end of the inversion, whose length is approximately 0.4 times that of the fourth chromosome, includes a meiotic pairing site in the male. We discuss the cytological location of the pairing site and the possible role of rDNA in meiotic pairing.

Constitutive magnification by the Ybb- chromosome of Drosophila melanogaster

Ybb- is an rDNA-deficient chromosome of Drosophila that has often been used in magnification experiments to induce high-frequency reversion of bobbed (bb) chromosomes. We observed previously that Ybb- causes ring chromosome loss even when the rings are bb+, suggesting that Ybb- induces magnifying sister chromatid exchanges in bb+ rings. Here we show that the Ybb- chromosome causes low levels of bb magnification in bb+ flies. We refer to the ability of Ybb- to bypass the rDNA deficiency requirement for magnification as 'constitutive' magnification. We have magnified the ribosomal genes on the Ybb- chromosome and analysed the revertant chromosomes using genetic and molecular methods. We find that magnified Ybb- chromosomes also exhibit constitutive magnifier activity. Molecular analysis shows that both type 1 and type 2 intron+ ribosomal gene repeats are associated with magnified Ybb- chromosomes. Type 2 introns have been described previously in the rDNA of both X and Y chromosomes. However, type 1 intervening sequences are thought to be present only in X, but not Y, ribosomal genes. Some of the Ybb- type 1 insertions differ from those present in the rDNA of X chromosomes in that they contain an EcoRI site, and some may be present in tandem arrays. The constitutive magnifier activity of Ybb- may reside either in the structurally unusual ribosomal gene intervening sequences associated with the chromosome, or in the locus on YL that is required for magnification to occur.

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.