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

Polymorphism of rRNA gene loci in the dog

We examined the number of ribosomal gene (rDNA) loci in the metaphase spreads of 54 dogs by FISH method. We found that in 16 dogs (30%) one or two loci were missing. The total number of rDNA loci was varied from 5 to 7 in males and from 4 to 6 in females. As the male dog consistently bears the rDNA on the Y chromosome, the polymorphism of the rDNA locus was ascribed to the absence of autosomal rDNA loci. Indeed, the frequency of polymorphism is almost equivalent in both sexes in the beagle. In one female beagle dog, remarkable intense fluorescence signals were observed at the four autosomal loci, indicating the in situ amplification of rDNA.

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.

Structure and organization of the rDNA intergenic spacer in lake trout (Salvelinus namaycush)

A total-genomic cosmid library was created to isolate complete copies of the rDNA cistron of lake trout (Salvelinus namaycush) in order to study the structure and organization of the intergenic spacer (IGS) in this species. A total of 60 rDNA-positive clones (average inserts > 25 kb) was recovered by screening the library with a rDNA-specific probe. Positive clones were assayed for the presence of the two internal rDNA spacers (ITS-1 and ITS-2) and the entire IGS fragment was successfully amplified from 42 clones by PCR. Length of the IGS fragments ranged from 9.4 to 17.8 kb. Comparative restriction mapping of the IGS-PCR products of several clones indicated two regions of extensive length variation surrounding a central region with sequence conservation. DNA sequence analysis was used to investigate the molecular basis of the IGS length variation and focused on identifying the region responsible for this variation. Over 9 kb of DNA sequence was obtained for one clone (A1) with a total IGS length of approximately 12.4 kb. Sequence of a conserved central region contained two open reading frames and a number of short direct repeats. Length variation in the IGS was determined by RFLP to result from differences in the number of copies of repetitive DNA sequences. These included an 89-bp tandem repeat (alpha repeats), an 82-bp element (beta repeats), a 168-177-bp element (chi repeats), and a 179-201-bp element (delta repeats). Overall nucleotide composition of the IGS was biased towards A and T (%GC = 47.4). Maintenance of discrete rDNA-length variants in lake trout suggests that the rate of gene conversion is insufficient to produce homogeneous copies across the genome.

Structure and organization of ribosomal DNA

Three trends are seen in the organization of ribosomal DNA genes during evolution: 1) gradual separation and separability of the regulation of transcription of 5S and larger subunit rRNAs; 2) retention of a transcription unit containing both large and small rRNAs; and 3) clustering of genes for both 5S and 18S-28S rDNAs, with the possible association of other 'non-rDNA' in the clusters of 18S-28S rDNA genes by the time mammals evolve.

Primary structure of the non-transcribed spacer region and flanking sequences of the ribosomal DNA of Neurospora crassa and comparison with other organisms

The non-transcribed spacer (NTS) region of the rDNA of Neurospora crassa contains the transcription regulatory sequences. We isolated a 3.4 kb EcoRI fragment from wild type N.crassa rDNA and cloned in the plasmid pBR325 at the EcoRI site. The insert contains the entire NTS region along with the flanking sequences. Nucleotide sequencing of 3592 nt shows many interesting features like: the NTS region is rich in G+C content (65% G+C); it contains the conserved rRNA processing site 6 (with the nucleotide sequence motif GGTGCGAGAACCCGG, from nt residue 226 to 240, a characteristic feature of most eukaryotic rDNA nontranscribed spacer region); and the NTS region also contains the transcription termination site with the representative Sal I box (from nt residue 1469 to 1477). The potential sequences of transcription termination site are located 288 nt downstream from the end of 26S rRNA gene, and another sequence motif CTTCCT (from nt residue 512 to 517) shows similarity with the human transcription termination site T-2 of its pre-rRNA. Nucleotide sequence homology matrix analysis suggests its relatedness to Saccharomyces cerevisiae and not to human, mouse, rat, Drosophila, Xenopus, wheat, rice and cucumber NTS region. The phylogenetic implication of the NTS region and exploitation of N.crassa NTS rDNA clone to correlate the otherwise indistinguishable species of Neurospora and the correlation with other organisms has been discussed. To the best of our knowledge this is the first report where the nucleotide sequence of the entire NTS region of a filamentous fungus has been determined.

Histo-blotting: hybridization in situ detection of specific RNAs on tissue sections transferred on nitrocellulose

A simple and rapid variant of in situ hybridization on tissue sections (histo-blotting) usable for detection of specific RNA distribution among tissues is proposed. Tissue sections prepared with a cryostatic microtome are placed on nitrocellulose and these "histo-blots" are hybridized with labelled DNA or RNA probes under conditions of Northern-blot hybridization without any particular pretreatment. Tissue specificity of the RNA distribution may be determined by comparison of autoradiograms with the histological structure of the stained section. Histological staining and light microscopy may be carried out after hybridization of histo-blots. Hybridization in situ may be easily combined with immunostaining under conditions of immunoblotting. Application of the proposed method is shown for alfa-fetoprotein (AFP) and endogenous provirus (ev-3) RNA detection in rat and chicken embryos, respectively. Histo-blotting results correlate with the distribution of given RNAs among tissues determined by independent methods. Sensitivity, specificity and resolution of histo-blotting have been evaluated and discussed.