On ribosomal gene compensation in Drosophila

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.

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.

Segregation of heterogeneous rDNA segments during demagnification of a Neurospora crassa strain possessing a double nucleolar organizer

We have produced a duplication strain of Neurospora crassa, DpAR33-PR-6, which contains two cytologically visible nucleoli (a DNO or double nucleolar organizer strain). When freshly generated, this strain has approximately twice the number of rRNA cistrons found in the parental (single nucleolar organizer) strains. After several serial propagations, there is a marked reduction in rRNA cistron number, approximating that of the SNO parental strains. This reduction in rRNA cistrons ("demagnification") was not achieved by breakdown of the VL→IVL translocation used to generate the duplication, as rDNA from the two parents can be distinguished by the size of the non-transcribed spacer region in the rDNA repeat unit of each strain. rDNA characteristic of both parents is present even after demagnification, in approximately equal amounts, suggesting the rRNA cistrons are lost randomly and non-preferentially from each homologous chromatid. In addition, the steady-state growth rate appears to be affected by rRNA cistron number, decreasing in freshly generated DNO strains relative to the parental strains, and returning to parental levels after demagnification.

Ribosomal DNA organization before and after magnification in Drosophila melanogaster

In all eukaryotes, the ribosomal RNA genes are stably inherited redundant elements. In Drosophila melanogaster, the presence of a Ybb(-) 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 molecular-variant 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.

Nucleolar dominance in polytene cells of Drosophila

Previous studies indicate that genes from only one of the cell's nucleolus organizers undergo multiple rounds of DNA replication in polytene cells of Drosophila. This report presents evidence that this effect is mediated by a function that is associated with the ribosomal genes of the dominant or replicating X chromosome. This function can act in trans to result in replication of the ribosomal genes on the recessive X chromosome in flies that are bobbed for the dominant X chromosome. In these cases, ribosomal genes from both chromosomes undergo polytenization. Heterochromatic regions that flank the nucleolus organizer have little or no effect on nucleolar dominance. In addition, deletion of the compensatory response (cr(+)) locus does not affect the dominance, suggesting that ribosomal gene compensation and nucleolar dominance in polytene cells of Drosophila are separate genetic phenomena.

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.

Regulation of rRNA gene number in Drosophila melanogaster: new aspects resulting from the use of free duplications

We have isolated a bobbed (bb) mutant on the free duplication Dp(1;f)122bb(+) and we have measured the rDNA content of the bb(+) and the bb loci in genetic combinations in which none of the phenomena involved in the change of the rDNA redundancy occurs. We have also measured the rDNA content of the two bb loci carried by the free duplications in two different genetic combinations: (1) XXNO(-)/Dp122bb(+) and XXNO(-)/Dp122bb females in which there are two attached X chromosomes completely deleted for the nucleolus organizer (NO) regions and therefore the only rDNA is contributed by the free duplication; (2) X/Dp122bb(+) and X/Dp122bb males, in which there are two bb loci, one on the X chromosome and the other on the X free duplication. The bb(+) and the bb duplications produced an overall increase of the rDNA content in the two genetic conditions tested. These results are not in favour of both a cis and trans effect of the regulator locus (cr(+) locus) hypothesised as being involved in the disproportionate replication of rRNA genes.

Localization of ribosomal DNA insertion elements in polytene chromosomes of Drosophila simulans, Drosophila mauritiana and their interspecific hybrids

The locations of the ribosomal DNA (rDNA) insertion elements type I and type II along the polytene chromosomes of three Drosophila species of the melanogaster subgroup--D. simulans, D. mauritiana and D. melanogaster--have been compared. In situ hybridization has shown that the intragenomic distribution of type I as well as of type II insertions is different for these related species. In particular, we have revealed rDNA-free autosomal sites, containing type II element sequences within the D. simulans and D. mauritiana chromosomes. This finding confirms the ability of this type of insertion to transpose, as was demonstrated earlier for Bombyx mori. The appearance of the rDNA not associated with the nucleolar organizers, evident by additional nucleoli, occurred with species-specific frequency. At the same time, for all three species the pattern of such changes (an attachment of the nucleoli to varying sites of the chromosomes and the presence of ectopic contacts between them, a composition of the rDNA repeats in the nucleolar material not integrated at the nucleolar organizer) was similar. The number of additional nucleoli in the hybrid polytene nuclei corresponded to the value of the parental species exhibiting nucleolar replicative dominance.

Nucleolar dominance and replicative dominance in Drosophila interspecific hybrids

The replication of the rDNA complement of only one nucleolus organizer region during polytene chromosome formation (replicative dominance) was initially observed in Drosophila melanogaster. Here we demonstrate replicative dominance in Drosophila simulans and D. melanogaster/D. simulans interspecific hybrids. A second nucleolar phenomenon, nucleolar dominance, is observed in the diploid tissue of interspecific hybrids. In this case only one of two nucleolus organizer regions forms a nucleolus. However, reorganizations of the X chromosome heterochromatin which eliminate nucleolar dominance have no apparent effect on the expression of replicative dominance. These observations lead us to conclude that nucleolar dominance and replicative dominance are operationally separable functions influencing the rDNAs, and may be determined by differing regulatory events.

One-step and stepwise magnification of a bobbed lethal chromosome in Drosophila melanogaster

Bobbed lethal (bbl) chromosomes carry too few ribosomal genes for homozygous flies to be viable. Reversion of bbl chromosomes to bb or nearly bb+ occurs under magnifying conditions at a low frequency in a single generation. These reversions occur too rapidly to be accounted for by single unequal sister chromatid exchanges and seem unlikely to be due to multiple sister strand exchanges within a given cell lineage. Analysis of several one-step revertants indicates that they are X-Y recombinant chromosomes which probably arise from X-Y recombination at bb. The addition of ribosomal genes from the Y chromosome to the bbl chromosome explains the more rapid reversion of the bbl chromosome than is permitted by single events of unequal sister chromatid exchange. Analysis of stepwise bbl magnified chromosomes, which were selected over a period of 4-9 magnifying generations, shows ribosomal gene patterns that are closely similar to each other. Similarity in rDNA pattern among stepwise magnified products of the same parental chromosome is consistent with reversion by a mechanism of unequal sister strand exchange.

The molecular through ecological genetics of abnormal abdomen. III. Tissue-specific differential replication of ribosomal genes modulates the abnormal abdomen phenotype in Drosophila mercatorum

The abnormal abdomen (aa) syndrome in Drosophila mercatorum is controlled by two major X-linked genetic elements. We have previously shown that the major X-linked element of aa is associated with the presence of large inserts in the 28S gene of the ribosomal RNA (rDNA) genes. We show that, in polytene tissue of wild-type D. mercatorum, the uninterrupted rDNA repeats are overreplicated relative to interrupted repeats. Uninterrupted rDNA repeats are also overreplicated in polytene tissue of hybrid larval offspring from wild-type and aa parents. This overreplication of uninterrupted repeats is not observed in diploid tissues of wild-type hybrids (of wild-type and aa parents) and homozygous aa larvae or in polytene tissue of aa larvae. Furthermore, molecular analysis of an aa line that has reverted to the wild type indicates that the reversion phenomenon is associated with the ability to overreplicate uninterrupted rDNA repeats in polytene tissues. The patterns of differential replication of rDNA genes in wild-type hybrids and aa larvae of D. mercatorum offer a possible mechanism for the tissue-specific control of the aa phenotype and suggest that the molecular basis for the second X-linked genetic element of aa is involved in the control of differential replication in polytene tissues.

Selection and biased gene conversion in a multigene family: consequences of interallelic bias and threshold selection

In a previous paper, I investigated the interactions in a gene family of additive selection and biased gene conversion in a finite population when conversion events are rare. Here I extend my "weak-conversion limit" model by allowing biased interallelic conversion (conversion between alleles at the same locus) of arbitrary frequency and various threshold selection schemes for rare interlocus conversion events. I suggest that it is not unreasonable for gene families to experience threshold fitness functions, and show that certain types of thresholds can greatly constrain the rate at which advantageous alleles are fixed as compared to other fitness schemes, such as additive selection. It is also shown that the double sampling process operating on a gene family in a finite population (sampling over the number of genes in the gene family and over the number of individuals in the population) can have interesting consequences. For selectively neutral alleles that experience interallelic bias, the probability of fixation at each single locus may be essentially neutral, but the cumulative effects on the entire gene family of small departures from neutrality can be significant, especially if the gene family is large. Thus, in some situations, gene families can respond to directional forces that are weak in comparison to drift at single loci.

Magnification of rRNA gene number in a Neurospora crassa strain with a partial deletion of the nucleolus organizer

Some progeny from crosses between the Neurospora crassa translocation strain T(IL----VL)OY321 and normal sequence N. crassa strains are duplication strains with a partial deletion of the nucleolus organizer. Despite the deletion, these progeny are viable and produce a functional nucleolus. Quantification of rRNA gene number in these deletion progeny demonstrated a significant loss of rRNA genes, down to 60% of the parental wild-type level. Initially, all of these reduced nucleolus organizer (RNO) strains demonstrated a reduction in the rate of mycelial elongation in growth tubes. After several vegetative growth cycles some progeny reverted to the normal growth phenotype, and also showed an increase in the number of rRNA genes to approximately that of the wild type.

A stochastic mechanism controls the relative replication of equally competent ribosomal RNA gene sets in individual dipteran polyploid nuclei

The endoreplication of the two nucleolar organizers (NOs) of the diploid genome has been examined in individual polyploid nuclei of the dipteran Calliphora erythrocephala. Crosses between two strains with diagnostic nontranscribed spacer polymorphisms in their rRNA genes were used to provide progeny with distinguishable NOs, and single nuclei of two highly polyploid cell types--salivary gland and nurse cells--were examined from individual F1 animals. Initially the representation of the two NOs in total polyploid tissue DNA was determined. This revealed that, although the NO regions present in one of the strains (Tom) were very similar in spacer composition, they displayed two types of behavior in the hybrids containing the single NO region typical of the second strain (Karla). In TW phenotype F1 progeny, very little replication of the Tom NO relative to the Karla NO occurred, whereas in TS phenotype progeny replication of the Tom and Karla NOs was approximately equivalent. When individual polyploid nuclei of the TS phenotype animals were examined, however, the relative replication of the Tom and Karla NOs was found not to be a fixed genetic property but to vary dramatically from cell to cell. This was true even for the nurse cell nuclei within a single ovarian follicle, which are the products of only four mitotic divisions of a single germ-line cell. These findings indicate that for NOs of similar replicative competence, a stochastic mechanism governs the relative usage of each NO for endoreplication and that the relative activity of the two NOs is not stably determined through the mitotic divisions preceding polyploidization. Stochastic selection after mitotic DNA replication could be a general phenomenon governing the relative usage (transcription) of different, but equally competent, alleles of any gene in individual cells, if the required factors are in short supply.

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.

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.

Amplification of rDNA and type I sequences in Drosophila males deficient in rDNA

rDNA magnification is a heritable change in rDNA content that occurs in D. melanogaster males when chromosomes deficient in rDNA are placed together for several generations. We have examined the restriction endonuclease cleavage pattern of the rDNA from an X chromosome undergoing magnification, and find no evidence for the selective amplification of either uninterrupted rDNA units or those containing insertion sequences. In addition, we observe an amplification of rDNA in the first generation of extremely bobbed male progeny to a level exceeding that of wild-type flies, but that reduces to the wild-type level in subsequent generations. The type I rDNA insertion elements also occur as tandem arrays, independently of rDNA. Southern hybridizations indicate that the majority of these sequences are located in the heterochromatin surrounding the nucleolus organizer on the X chromosome, and we find that they, too, amplify transiently in the first generation of magnifying males.

Sequence replication and banding organization in the polytene chromosomes of Drosophila melanogaster

The relative proportions of cloned DNA fragments from all known hierarchies of sequence organization in polytene and diploid chromosomes were compared. It was found that unique sequences of varying sizes and chromosomal locations are equally replicated in salivary gland chromosomes. Sequences of euchromatic polydisperse gene families are also replicated proportionately in polytene and diploid tissues. Perhaps the most significant finding is that the histone gene repeats, despite their normal banding organization, are under-replicated in the polytene chromosome of Drosophila melanogaster. However, the clustered and well-banded 5S genes are most likely equally replicated. It is therefore concluded that differential sequence replication plays no apparent role in either the assembly or morphology of a band; and likewise, the assembly of polytenic DNA into band units is not affected by either the local abundancy or arrangement of middle repetitive sequences. The likelihood that the clustered arrangement is an important factor in the selection of sequences for under-replication is discussed.

Pleiotropic effects associated with the deletion of heterochromatin surrounding rDNA on the X chromosome of Drosophila

In Drosophila melanogaster X chromosome heterochromatin (Xh) constitutes the proximal 40% of the X chromosome DNA and contains a number of genetic elements with homologous sites on the Y chromosome, one of which is well defined, namely, the bobbed locus, the repetitive structural locus for the 18S and 28S rRNAs. This report presents the localisation of specific repeated DNA sequences within Xh and the employment of this sequence map in constructing new chromosomes to analyse the nature of the heterochromatin surrounding the rDNA region. Repeated sequences were located relative to inversion breakpoints which differentiate Xh cytogenetically. When the rDNA region was manipulated to be in a position in the chromosome so that it was without the Xh which normally surrounds it, the following observations were made. (i) The rDNA region of Xh is intrinsically heterochromatic, remaining genetically active and yet possessing major heterochromatic properties even in the absence of the flanking heterochromatin regions. (ii) The size of the deletion removing the portion of Xh normally located distal to the rDNA region affected the dominance relationship between the X and Y nucleolar organizers (activity/endoreduplication assayed in male salivary glands). The X rDNA without any flanking heterochromatin was dominant over Y rDNA while the presence of some Xh allowed both the X and Y rDNA to be utilized. (iii) Enhancement of the position effect variegation on the white locus was demonstrated to occur as a result of the Xh deletions generated. EMS mutagenesis studies argue that the regions of Xh flanking the rDNA region contain no vital loci despite the fact that they strongly effect gene expression in some genotypes. This is consistent with early studies using X-ray mutagenesis (Lindsley et al., 1960). The pleiotropic effects of deleting specific regions of Xh is discussed in relation to the possible influence of heterochromatin on the organisation of the functional interphase nucleus.

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

The question of whether the Ybb- chromosome contains ribosomal genes has been examined by using Southern blot analysis and comparing rDNA hybridization patterns for X/X and X/Ybb- DNA. The results demonstrate that the Ybb- chromosome contains sequences that hybridize to an rDNA probe under stringent conditions. Differential hybridization of some of these sequences with DNAs corresponding to different regions of a complete ribosomal gene repeat provides evidence that some of the genes on the Ybb- chromosome are type 2 repeats. Because data obtained by other workers suggest that type 2 repeats are transcribed only to low levels, these repeats may be classed as "nonfunctional". A further finding is that the ribosomal genes on the Ybb- chromosome do not undergo multiple rounds of DNA replication during polytenization of X/Ybb- cells.

Differing levels of dispersed repetitive DNA among closely related species of Drosophila

The genomic concentrations of certain middle repetitive DNA sequences vary considerably among closely related species of Drosophila. In fact, the chromosomes of D. melanogaster appear to carry approximately 3 times as much middle repetitive DNA as those of the sibling species D. simulans. Although most of the middle repetitive DNA of D. melanogaster consists of segments of "nomadic" DNA that occupy different dispersed chromosomal locations in different strains of flies, repeated DNA sequences recovered from the D. simulans genome are most often restricted to single chromosomal positions. Apparent differences in the total concentrations of middle repetitive DNA in the two species are most easily attributed to an approximately sevenfold difference in their dispersed repetitive and nomadic DNA contents. These differences may affect the relative mutation rates of these species or contribute to their reproductive isolation or both.

Regulation of ribosomal RNA cistron number in a strain of Neurospora crassa with a duplication of the nucleolus organizer region

Some progeny from a cross of the translocation mutant T(VL leads to IVL)AR33 with wild-type Neurospora crassa are double nucleolus organizer (DNO) strains, usually displaying two distinct nucleolus organizer regions. The DNO strain is sterile but displays the same growth response as normal laboratory strains of Neurospora. We used DNA-DNA hybridization techniques to quantify the number of rRNA cistrons in the DNO mutant and its vegetative progeny. Comparisons of the rate of hybridization of genomic DNA from the parental AR33 strain and from the DNO strain showed that hybridization was more rapid for the DNO strain than for the parental strain. Successive vegetative progeny of the DNO strain displayed hybridization rates intermediate to those of the original DNO strain and the parental single nucleolus strain, indicating that the number of rRNA cistrons had decreased during vegetative propagation. Estimates of rRNA cistron number obtained from comparisons of the amount of single copy DNA and rDNA hybridized to genomic DNO and AR33 DNA at saturation indicate that the parental AR33 strain contains 225 copies of the rRNA repeat unit while the DNO strain has approx. 440 copies. The number of rRNA cistrons decreases gradually in the successive vegetative progeny, approximating the parental haploid value by the eleventh vegetative transfer.

RNA-DNA hybridization analyses of tRNA-Val-3b in Drosophila melanogaster

Transfer RNA was extracted from 50-300 mg of adult flies and specifically labeled in vitro. The level of individual isoacceptors was quantitated by efficient annealing to Drosophila tRNA genes carried on recombinant DNA plasmids immobilized on nitrocellulose filters. The level of tRNAVal3b in the tRNA isolated from flies deficient in the major tRNAVal3b loci has been examined. The results show that deletion of the major tRNAVal3b loci resulted in a reduction of approximately 50% in the level of tRNAVal3b but did not produce the Minute phenotype; furthermore the effects of deficiencies at two loci were approximately additive.

Rate of turnover of structural variants in the rDNA gene family of Drosophila melanogaster

A high degree of polymorphism for the length and copy number of rDNA spacers, in both the X and Y chromosome clusters, has been found in a wild population of Drosophila melanogaster. The genetic behaviour of rDNA structural variants in separate and mixed populations derived from isofemale lines suggest that they are not subject to strong selection and are stable for over 1,000 generations. The high structural variability suggests an evolutionary rapid process of turnover in the family which could partly explain widespread sequence homogeneity (concerted evolution) of rDNA within a species.

Selective replication of ribosomal DNA repeats after loss of the abnormal oocyte phenotype in Drosophila melanogaster

Drosophila melanogaster females homozygous for the abnormal oocyte mutation produce a large excess of female offspring when crossed with XY/0 males. After several generations in abo homozygous stock, this maternal effect is no longer observed. The disappearance of the abo phenotype is coupled with an increase in the amount of DNA coding for rRNA (rDNA). We have used restriction endonuclease analysis of total DNA extracted from adult females and from single female larval brains to investigate the molecular organization of rDNA before and after the loss of abo phenotype. The rDNA increase is associated with variations of the restriction pattern of the nontranscribed spacer, probably due to a selective increase of rDNA repeats.