Inheritance of rDNA spacer length variants in man

Human rDNA copy number is unstable in metastatic breast cancers

Chromatin-mediated silencing, including the formation of heterochromatin, silent chromosome territories, and repressed gene promoters, acts to stabilize patterns of gene regulation and the physical structure of the genome. Reduction of chromatin-mediated silencing can result in genome rearrangements, particularly at intrinsically unstable regions of the genome such as transposons, satellite repeats, and repetitive gene clusters including the rRNA gene clusters (rDNA). It is thus expected that mutational or environmental conditions that compromise heterochromatin function might cause genome instability, and diseases associated with decreased epigenetic stability might exhibit genome changes as part of their aetiology. We find the support of this hypothesis in invasive ductal breast carcinoma, in which reduced epigenetic silencing has been previously described, by using a facile method to quantify rDNA copy number in biopsied breast tumours and pair-matched healthy tissue. We found that rDNA and satellite DNA sequences had significant copy number variation - both losses and gains of copies - compared to healthy tissue, arguing that these genome rearrangements are common in developing breast cancer. Thus, any proposed aetiology onset or progression of breast cancer should consider alterations to the epigenome, but must also accommodate concomitant changes to genome sequence at heterochromatic loci.

POPULATION STRUCTURE AND KINSHIP IN POLISTES (HYMENOPTERA, VESPIDAE): AN ANALYSIS USING RIBOSOMAL DNA AND PROTEIN ELECTROPHORESIS

Six variable protein loci and one variable ribosomal DNA restriction site were used for an analysis of population structure in five species of Polistes from Texas. A sample-reuse algorithm was developed that estimated F_ST , F_IS , and ø (the coefficient of kinship) from probabilities of identity. Of the four species analyzed in detail only one, Polistes exclamans, had statistically significant values of F_ST . These values may reflect natural constraints on successful nesting for migrants of this species. Three of the four species had significant values of F_IS and three of the four species had significant values of ø. In many cases ø also differed from the expected value under haplodiploidy and random mating. Values of ø did not differ from expectations under haplodiploidy and local inbreeding. These results emphasize that theories of social behavior and evolution based on coefficients of kinship should include some explicit consideration of population structure.

The boundary of macaque rDNA is constituted by low-copy sequences conserved during evolution

In Macaca mulatta, the single rDNA array is flanked by a patchwork of sequences including subregions of human Yp11.2, 4q35.2, and 10p15.3. This composite DNA region is characterized by unique or low-copy sequences, resembling a potentially transcribed region. The analysis of Cercopithecus aethiops, Presbytis cristata, and Hylobates lar suggests that this complex sequence organization could be shared by Old World monkey and lesser ape species. After the lesser apes/great apes divergence, the unique or nonduplicated DNA region underwent amplification and spreading, preferentially marking the p arm of acrocentric chromosomes bearing the rDNA. The molecular analysis of human acrocentric chromosomes revealed some extent of remodeling of the rDNA boundary: near the human NOR, a large 4q35.2 duplication partially resembles that found in MMU; conversely, infrequently represented Yp11.2 sequences totally differed from those of the macaque, and 10p15.3 sequences were lacking. Thus, although evolutionary events modified the sequence organization of the MMU rDNA boundary, its overall sequence feature and the preferential location in vicinity to the NOR have been conserved.

Human rDNA: Evolutionary Patterns within the Genes and Tandem Arrays Derived from Multiple Chromosomes

Human rDNA forms arrays on five chromosome pairs and is homogenized by concerted evolution through recombination and gene conversion (loci RNR1, RNR2, RNR3, RNR4, RNR5, OMIM: 180450). Homogenization is not perfect, however, so that it becomes possible to study its efficiency within genes, within arrays, and between arrays by measuring and comparing DNA sequence variation. Previous studies with randomly cloned genomic DNA fragments showed that different parts of the gene evolve at different rates but did not allow comparison of rDNA sequences derived from specific chromosomes. We have now cloned and sequenced rDNA fragments from specific acrocentric chromosomes to (1) study homogenization along the rDNA and (2) compare homogenization within chromosomes and between homologous and nonhomologous chromosomes. Our results show high homogeneity among regulatory and coding regions of rDNA on all chromosomes, a surprising homogeneity among adjacent distal non-rDNA sequences, and the existence of one to three very divergent intergenic spacer classes within each array.

Position effects of ribosomal RNA multigene loci on meiotic recombination in wheat

Homeologous wheat chromosome arms that differ by the presence or absence of a Nor locus or greatly differ in the numbers of copies of rRNA genes per Nor locus show conspicuous differences in the distribution of recombination. To assess directly the position effects of Nor loci on recombination across chromosome arms, a Triticum monococcum Nor9 haplotype was substituted for Triticum aestivum Nor9 haplotypes on two T. aestivum 1A chromosomes in the isogenic background of cv Chinese Spring. The numbers of rRNA genes in the 1A Nor9 haplotypes are greatly reduced relative to the T. monococcum haplotype. The substitution resulted in reduced recombination rate in the vicinity of the Nor9 locus. An intra-arm compensatory increase was observed in the proximal region of the arm so that the genetic length of the chromosome arm was unchanged. These findings suggest that Nor loci suppress recombination in their vicinity and change recombination patterns in Nor-bearing chromosome arms.

Restriction site and length polymorphism of the rDNA unit in the cultivated basidiomycetePleurotus cornucopiae

In the ribosomal DNA unit ofPleurotus cornucopiae, the rDNA coding regions are in the order 5', 5S-18S-5.8S-25S, 3', with the 5' location of the 5S gene differing from its 3' location found in other basidiomycetes. The most discriminating probe used to study the rDNA polymorphism consisted of a fragment that included the 5S, 18S and part of the 5.8S and 25S genes flanking three intergenic sequences. A high degree of rDNA polymorphism was observed in the sevenP. cornucopiae dikaryons studied. For the first time within a basidiomycete species, the restrictions maps distinguished two types of rDNA units (I and II). In each rDNA type, length variations in the external intergenic sequence IGS 1 located between the 25S and 5S genes allowed characterization of two different rDNA units in type I and four rDNA units in type II. This suggested that theP. cornucopiae rDNA units were derived from two kinds of ancestors (type I and II) by insertion or deletion events (100-700 bp) in the IGS 1. In four dikaryotic strains, two rDNA units of the same type (I or II) differing only by the IGS 1 length, were found in a similar number of copies, and presented a meiotic segregation in homokaryotic progeny. In one progeny, some homokaryotic strains possessed two different rDNA units: one with a high copy number and another with a lower one, showing that two different rDNA units could coexist in a single nucleus.

The gene for a novel human lamin maps at a highly transcribed locus of chromosome 19 which replicates at the onset of S-phase

A previously described human DNA fragment which is replicated early in S-phase of HL-60 cell DNA (C. Tribioli, G. Biamonti, M. Giacca, M. Colonna, S. Riva, and A. Falaschi, Nucleic Acids Res. 15:10211-10232, 1987) was used to screen a genomic library in lambda Ch28. A clone which contained a 13.7-kb insert (L30E) found to code for several transcripts was isolated. The transcription of L30E DNA exhibited a complex pattern and a tissue-specific and proliferation-dependent type of regulation. The data were consistent with two tandemly arranged transcription units, the 3' end of one separated from the 5' end of the other by a sequence of about 600 bp containing an active promoter. The isolation and sequencing of L30E-specific cDNAs permitted identification of two genes, one of which encoded a B-type human lamin (analogous to mouse lamin B2). L30E DNA was mapped by in situ hybridization at the G-negative subtelomeric band p13.3 of chromosome 19. Interestingly, in synchronized HL-60 cells, L30E DNA is replicated in the first minute of S-phase. Replication of the lamin gene early in S-phase may reflect a coupling between early replication and transcription of genes for S-phase-specific proteins such as lamins.

The gene for a novel human lamin maps at a highly transcribed locus of chromosome 19 which replicates at the onset of S-phase

A previously described human DNA fragment which is replicated early in S-phase of HL-60 cell DNA (C. Tribioli, G. Biamonti, M. Giacca, M. Colonna, S. Riva, and A. Falaschi, Nucleic Acids Res. 15:10211-10232, 1987) was used to screen a genomic library in lambda Ch28. A clone which contained a 13.7-kb insert (L30E) found to code for several transcripts was isolated. The transcription of L30E DNA exhibited a complex pattern and a tissue-specific and proliferation-dependent type of regulation. The data were consistent with two tandemly arranged transcription units, the 3' end of one separated from the 5' end of the other by a sequence of about 600 bp containing an active promoter. The isolation and sequencing of L30E-specific cDNAs permitted identification of two genes, one of which encoded a B-type human lamin (analogous to mouse lamin B2). L30E DNA was mapped by in situ hybridization at the G-negative subtelomeric band p13.3 of chromosome 19. Interestingly, in synchronized HL-60 cells, L30E DNA is replicated in the first minute of S-phase. Replication of the lamin gene early in S-phase may reflect a coupling between early replication and transcription of genes for S-phase-specific proteins such as lamins.

Detection of variation in the ribosomal RNA gene clusters by a modified fluorescence in situ hybridization method

Physical mapping of genes by fluorescence in situ hybridization (FISH) has become routine using fluorescein isothiocyanate (FITC) for probe detection and propidium iodide (PI) for chromosome staining. We have modified this conventional FISH method in a way that utilizes Texas red (TR) for signal detection and quinacrine mustard (QM) for chromosome banding. Using this Texas red and quinacrine (TRQ) method, we were able to identify individual acrocentric chromosomes with varying degrees of ribosomal RNA gene clusters. Two acrocentric chromosomes were found to carry extremely small number of rRNA gene copies as compared to the other eight counterparts in human diploid lymphoblastoid cell line GM00130B. Thus, the TRQ method allows one to probe for a specific sequence while identifying individual chromosomes and will be powerful for the chromosomal localization of various genes.

Variation in the ribosomal DNA intergenic spacer of a maize population mass-selected for high grain yield

Variation in the intergenic spacer of ribosomal DNA (rDNA) was detected among individual plants of the open-pollinated maize variety 'Hays Golden' and populations derived from this variety. rDNA intergenic spacer-length variants were detected at approximately 200 bp intervals, consistent with the number of 200 bp subrepeats as the basis for this variation. Inheritance data revealed that more than one spacer-length class may be present on an individual chromosome. Fourteen different predominant rDNA intergenic spacer hybridization fragment patterns were detected. C-29, a population developed by 29 cycles of mass-selecting Hay Golden for high grain yield, exhibited a significant change in rDNA intergenic spacer hybridization fragment pattern composition in comparison to Hays Golden. This change included a reduction in frequency of the shortest predominant space-length variant (3.4 kb) and an increase in a 5.2 -kb hybridization fragment. I-31, a population developed through thermal neutron irradiation of Hays Golden and 31 generations of mass selection for high grain yield, did not exhibit a significant change in overall rDNA intergenic spacer composition. I-31 did exhibit an increase in frequency of the 5.2-kb hybridization fragment and a significant change in two specific hybridization fragment patterns that had also changed in C-29. These data, particularly for the C-29 population, suggest that rDNA intergenic spacer-length variants and/or associated loci were influenced by selection.

Linkage in human heterochromatin between highly divergent Sau3A repeats and a new family of repeated DNA sequences (HaeIII family)

The hybridization of human DNA with three non-cross-hybridizing monomers (68 bp in length) of the heterochromatic Sau3A family of DNA repeats, indicates the coexistence within a Sau3A-positive genomic block of divergent Sau3A units as well as of unrelated sequences. To gain some insight into the structure of these human heterochromatic DNA regions, three previously cloned Sau3A-positive genomic fragments (with a total length of approximately 1900 base-pairs (bp] were sequenced. The analysis of the sequences showed the presence of clustered Sau3A units with different degrees of divergence and of two DNA regions of approximately 100 bp and 291 bp in length, unrelated to the family of repeats. A consensus sequence derived from the 24 identified Sau3A monomers presents, among highly variable regions, two less variant regions of 8 bp and 10 bp in length, respectively. The Sau3A-unrelated DNA fragment 291 bp in length, used as a probe on genomic DNA digested with a series of restriction enzymes, defines a "new" family of DNA repeats possessing periodicities for HaeIII (HaeIII family). Sau3A and HaeIII repeats display a high degree of linkage in a collection of Sau3A-positive genomic recombinant phages.

Variability of human rRNA genes: inheritance and nonrandom chromosomal distribution of structural variants of nontranscribed spacer sequences

Human rRNA genes contain variable regions, one of which is located in nontranscribed spacers (NTSs) closely downstream from the 3'-end of the transcribed region. This polymorphism may be detected by means of blot hybridization analysis as a set of distinct restriction fragments corresponding to this part of the rRNA genes. We have analyzed DNA of 51 individuals and found eight structural NTS variants of this region; two of these were common to all individuals analyzed, and six others were found in different combinations and with different frequencies. The copy number of each variant also differed but was not less than 10-20 copies per cell. The analysis of DNA isolated from leukocytes of the members of 11 families indicated that some of the structural variants (of the NTS region) are inherited as a single Mendelian locus. We propose that rRNA genes that belong to one particular structural variant form clusters on separate chromosomes. To test this proposition, we developed a combined method, including AgNO3-staining of chromosomes, in situ hybridization, and DNA analysis with methylation-sensitive restrictases, and used it for study of persons who had methylated rRNA genes located on AgNO3-negative nucleolar organizers. It was found that in three of four cases methylated genes really belonged to one structural variant. This approach may be used for detailed localization of separate classes of NTS structural variants of human rRNA genes.

Ribosomal DNA inheritance and recombination in Neurospora crassa

The genetic segregation of ribosomal DNA (rDNA) in Neurospora crassa was analyzed by exploiting restriction fragment length polymorphisms in the nontranscribed spacer (NTS) sequences of nine laboratory wild-type strains and wild-collected strains. In an analysis of random spore progeny from seven crosses, and of ordered tetrads from two of those crosses the rDNA was shown to be inherited in a simple, stable Mendelian fashion, exhibiting an approximately 1:1 ratio of the two parental rDNA types. No meiotic recombinants were detected among the progeny, indicating that non-sister-chromatid crossing over is highly suppressed in the rDNA region. The basis for this suppression of meiotic recombination is not known.

Variation in the ribosomal RNA genes among individuals of Vicia faba

Length heterogeneity in the ribosomal repeat of Vicia faba is due to the presence of variable numbers of a 325 bp subrepetitive element within the nontranscribed spacer region. The distribution of size classes among 88 individuals within a population was investigated by blot-hybridization. We find that individual plants can exhibit more than 20 size classes and that hybridization patterns are highly diverse from individual to individual, more so than for any species so far investigated. In contrast, no such differences are observed in patterns for different tissues from a single plant or from parental to F1 generation. Some changes were observed in the F2 generation. We conclude that unequal recombination can give rise to the diversity that we observe for the V. faba rDNA repeats.

Transcribed human ribosomal RNA genes are attached to the nuclear matrix

Nuclear matrices were prepared from HeLa nuclei in high or low-salt buffers. After digestion with restriction enzymes, the DNA associated with the nuclear matrix was analysed for its content of ribosomal DNA sequences (rDNA). In both salt conditions, the entire rDNA repeat unit was found to be enriched in the matrix DNA. No enrichment, however, was detected in the absence of rRNA transcription either due to treatment with actinomycin D or when cells arrested in the G0 stage were used to prepare matrices. rDNA was found to be linked to chromosomal scaffolding structures when similar experiments were performed on chromosomes. Moreover, a gradient of enrichment along the rDNA repeat unit was observed, in which the promoter-containing portion was the most highly enriched. I conclude from these experiments that the tandem repeats of rDNA are not randomly associated with matrix or scaffold structure but are probably attached at transcription complexes.