Showing papers on "Ribosomal DNA published in 1980"

Unequal crossing over in the ribosomal DNA of Saccharomyces cerevisiae

Abstract: Unequal sister chromatid exchanges occur at the ribosomal DNA locus of yeast during mitotic growth. The frequency of unequal crossing over, as measured by the deletion or duplication of an inserted genetic marker (LEU2), is sufficient to maintain the sequence homogeneity of the rDNA repeat units.

Molecular and chromosomal organization of DNA sequences coding for the ribosomal RNAs in cereals

Abstract: The chromosomal locations of ribosomal DNA in wheat, rye and barley have been determined by in situ hybridization using high specific activity 125I-rRNA. The 18S-5.8S-26S rRNA gene repeat units in hexaploid wheat (cv. Chinese Spring) are on chromosomes 1B, 6B and 5D. In rye (cv. Imperial) the repeat units occur at a single site on chromosome 1R(E), while in barley (cv. Clipper) they are on both the chromosomes (6 and 7) which show secondary constrictions. In wheat and rye the major 5S RNA gene sites are close to the cytological secondary constrictions where the 18S-5.8S-26S repeating units are found, but in barley the site is on a chromosome not carrying the other rDNA sequences. — Restriction enzyme and R-loop analyses showed the 18S-5.8S-26S repeating units to be approximately 9.5 kb long in wheat, 9.0 kb in rye and barley to have two repeat lengths of 9.5 kb and 10 kb. Electron microscopic and restriction enzyme data suggest that the two barley forms may not be interpersed. Digestion with EcoR1 gave similar patterns in the three species, with a single site in the 26S gene. Bam H1 digestion detected heterogeneity in the spacer regions of the two different repeats in barley, while in rye and wheat heterogeneity was shown within the 26S coding sequence by an absence of an effective Bam H1 site in some repeat units. EcoR1 and Bam H1 restriction sites have been mapped in each species. — The repeat unit of the 5S RNA genes was approximately 0.5 kb in wheat and rye and heterogeneity was evident. The analysis of the 5S RNA genes emphasizes the homoeology between chromosomes 1B of wheat and 1R of rye since both have these genes in the same position relative to the secondary constriction. In barley we did not find a dominant monomer repeat unit for the 5S genes.

The primary structure of 16S rDNA from Zea mays chloroplast is homologous to E. coli 16S rRNA.

Abstract: The nucleotide sequence of ribosomal DNA coding for 16S rRNA from Zea mays chloroplast has been determined. A comparison with the 16S rRNA sequence from Escherichia coli reveals strong homology and thereby demonstrates the prokaryotic nature of chloroplast ribosomes from a higher plant.

Variable patterns of total DNA and rDNA methylation in animals

Abstract: Restriction endonucleases were used to determine the degree of methylation at the sequences CCGG and GCGC in a wide range of animal DNAs. Both total DNA methylation and ribosomal DNA methylation were studied. Whole DNA methylation was indetectable in arthropods, fractional in other invertebrate phyla, and high in the vertebrates. Ribosomal DNA was predominantly unmethylated in all animals except fish and amphibia, where it was heavily methylated. We discuss the evolutionary and functional implications of these results, and suggest that the large differences between genome types are the result of evolutionary changes in the relative size of heavily methylated and unmethylated compartments.

More ribosomal spacer sequences from Xenopus laevis

Abstract: The base sequence analysis of a Xenopus laevis ribosomal DNA repeat (7) has been extended to cover almost the entire non-transcribed and external transcribed spacer. A compilation of these sequences is presented. All the repetitive and non-repetitive sequence elements of the spacer are identified and their evolution discussed. Comparison of the X.laevis and S.cerevisiae (25,26) ribosomal DNAs shows about 80% sequence conservation in the 18S gene but no sequence conservation, from the available data, in the external transcribed spacer. The sequence coding for the 3' terminus of the X.laevis 40S ribosomal precursor RNA is presented and its structural features analyzed.

DNase I sensitivity of ribosomal genes in isolated nucleosome core particles

Abstract: The level of chromatin structure at which DNase I recognizes conformational differences between inert and activated genes has been investigated. Bulk and ribosomal DNA's of Tetrahymena pyriformis were differentially labeled in vivo with [14C]- and [3H]-thymidine, respectively, utilizing a defined starvation-refeeding protocol. The 3H-labeled ribosomal genes were shown to be preferentially digested by DNase I in isolated nuclei. Staphylococcal nuclease digested the ribosomal genes more slowly than bulk DNA, probably owing to the higher GC content of rDNA. DNase I and staphylococcal nuclease digestions of purified nucleosomes and of nucleosome core particles isolated from dual-labeled, starved-refed nuclei were indistinguishable from those of intact nuclei. We conclude from these studies that DNase I recognizes an alteration in the internal nucleosome core structure of activated ribosomal genes.

The organization of the ribosomal RNA genes in the fungus Mucor racemosus.

Abstract: The rDNA of Mucor racemosus is contained on a 6.4 megadalton repeat unit. Two Bam H-1 restriction fragments that encompass the entire rDNA repeat, as well as two Hind III restriction fragments that lie within the region, have been cloned and analyzed. The rDNA unit has been defined with respect to eight restriction endonucleases and the position of the sequences encoding the 25S, 18S, and 5.8S rRNA species have been localized. In addition, the 55 RNA encoding sequence was found to reside within the basic repeat unit. The results indicate the organization of the rDNA of Mucor more closely resembles the arrangement observed in yeast than that observed in other eukaryotic organisms.

The transcription termination site of the ribosomal RNA operon in yeast

Abstract: The site at which transcription of the ribosomal RNA operon in yeast is terminated was precisely localized. First, the exact position of the 3' end of the 26S rRNA gene was mapped on the rDNA on the basis of RNA- and DNA sequence data. Next, the 3' terminus of the primary transcript, 37S precursor rRNA, was established by hybridization experiments and sequence analysis. 37S pre-rRNA appears to be just 7 nucleotides longer at its 3' end than 26S rRNA. The non-coding strand around the termination site is extremely T-rich: 15 out of 18 nucleotides are T-residues. An extensive dyad symmetry is present in the sequence downstream from the termination site; a possible role of this structure in the regulation of transcription termination is discussed. The 3'-terminal 110 nucleotides of yeast 26S rRNA have approx. 50% and 60% homology with the corresponding regions of E. coli 23S rRNA and Xenopus laevis 28S rRNA, respectively.

The nucleotide sequence of the putative transcription initiation site of a cloned ribosomal RNA gene of the mouse.

Abstract: Approximately one kilobase pairs surrounding and upstream the transcription initiation site of a cloned ribosomal DNA (rDNA) of the mouse were sequenced. The putative transcription initiation site was determined by two independent methods: one nuclease S1 protection and the other reverse transcriptase elongation mapping using isolated 45S ribosomal RNA precursor (45S RNA) and appropriate restriction fragments of rDNA. Both methods gave an identical result; 45S RNA had a structure starting from ACTCTTAG---. Characteristically, mouse rDNA had many T clusters (greater than or equal to 5) upstream the initiation site, the longest being 21 consecutive T's. A pentadecanucleotide, TGCCTCCCGAGTGCA, appeared twice within 260 nucleotides upstream the putative initiation site. No such characteristic sequences were found downstream this site. Little similarity was found in the upstream of the transcription initiation site between the mouse, Xenopus laevis and Saccharomyces cerevisiae rDNA.

Characterization of cloned ribosomal DNA from Drosophila hydei

Abstract: The structure of ribosomal genes from the fly Drosophila hydei has been analyzed. EcoRI fragments, cloned in a plasmid vector, were mapped by restriction enzyme analysis. The lengths of the regions coding for 18S and 28S rRNA were defined by R-loop formation. From these data a physical map of the rRNA genes was constructed. There are two major types of rDNA units in D. hydei, one having a size of 11 kb and the other a size of 17 kb. The 17 kb unit results from an intervening sequence (ivs) of 6.0 kb, interrupting the beta-28S rRNA coding region. Some homology between th D. hydei ivs and D. melanogaster type 1 ivs has been described previously (1). However, the restriction sites within these ivs show considerable divergence. Whereas D. hydei rDNA D. melanogaster rDNA, the nontranscribed spacer has little, if any, sequence homology. Despite difference in sequence, D. hydei and D. melanogaster spacers show structural similarities in that both contain repeated sequence elements of similar size and location.

Nucleolus organiser variation in wheat and rye revealed by in situ hybridisation

Abstract: The technique of in situ hybridisation has been used to demonstrate that some wheat varieties have very different numbers of ribosomal RNA genes clustered in homologous nucleolus organisers. In these experiments the labelled probe was RNA synthesized in vitro using wheat ribosomal DNA cloned in a bacterial plasmid as template. Homologous nucleolus organisers were identified by the use of intervarietal chromosome substitution lines. A variety of rye has been shown to be heterozygous for the number of rRNA genes clustered in its major pair of nucleolus organisers. The in situ hybridisation technique has also been used to demonstrate an anomalous deletion of rDNA in an aneuploid derivative of Chinese Spring wheat.

Multiple ribosomal gene sites revealed by in situ hybridization of Xenopus rDNA to Tritums lampbrush chromosomes

Abstract: A variety of 3H-labelled ribosomal gene probes were hybridized in situ to the nascent transcripts of lampbrush chromosomes from the crested newt, Tritums cristatus carnifex. The probes were from Xenopus laevis and included rDNA isolated by CsCl gradient centrifugation, recombinant plasmids and purified restriction fragments of rDNA. All the probes gave essentially the same result. About 10–15 loop pairs were distinctly labelled in each preparation, almost all of them located on the heteromorphic arms (HTAs) of chromosome 1. Ribosomal gene probes were also hybridized in situ to the DNA of denatured mitotic chromosomes from some of the individuals used to provide lampbrush preparations. Minor, scattered sites of hybridization were found in the HTAs, but the main clusters of ribosomal genes were found on chromosomes 6 and/or 9, in agreement with previous determinations of nucleolus organizer position in this species. However, the nucleolus organizers were not sites of labelled loops in lampbrush transcript hybridizations. — We have incubated isolated lampbrush-stage nuclei in media containing α-amanitin and labelled RNA precursors. Although extrachromosomal nucleolar genes incorporated label, supposedly due to transcription by RNA polymerase I, no lampbrush loops were labelled. — It appears that in T. c. carnifex there are ribosomal gene sequences at the main nucleolus organizers and at a number of sites scattered along the HTAs. The ribosomal genes at the nucleolus organizers are not extended in the form of actively transcribing loops unlike the ribosomal sequences on the HTAs, which are heavily labelled in transcript hybridization. The ribosomal sequences on the HTAs appear not to be transcribed by the same RNA polymerase that transcribes the ribosomal genes of extrachromosomal nucleoli.

The 10kb Drosophila virus 28S rDNA intervening sequence is flanked by a disect repeat of 14 base pairs of coding sequence

Abstract: Most repeat units of rDNA in Drosophila virilis are interrupted in the 28S rRNA coding region by an intervening sequence about 10 kb in length; uninterrupted repeats have a length of about 11 kb. We have sequenced the coding/intervening sequence junctions and flanking regions in two independent clones of interrupted rDNA, and the corresponding 28S rRNA coding region in a clone of uninterrupted rDNA. The intervening sequence is terminated at both ends by a direct repeat of a fourteen nucleotide sequence that is present once in the corresponding region of an intact gene. This is a phenomenon associated with transposable elements in other eukaryotes and in prokaryotes, and the Drosophila rDNA intervening sequence is discussed in this context. We have compared more than 200 nucleotides of the D. virilis 28S rRNA gene with sequences of homologous regions of rDNA in Tetrahymena pigmentosa (Wild and Sommer, 1980) and Xenopus laevis (Gourse and Gerbi, 1980): There is 93% sequence homology among the diverse species, so that the rDNA region in question (about two-thirds of the way into the 28S rRNA coding sequence) has been very highly conserved in eukaryote evolution. The intervening sequence in T. pigmentosa is at a site 79 nucleotides upstream from the insertion site of the Drosophila intervening sequence.

Coding and spacer sequences in the 5.8S-2S region of Sciara coprophila ribosomal DNA

Abstract: The sequence of 436 nucleotides around the region coding for 5.8S RNA in the Sciara coprophila rDNA transcription unit (1) has been determined. Regions coding for 5.8S and 2S RNAs have been identified; they are 80 - 90% homologous to the corresponding Drosophila sequences and are separated by a 22 nucleotide long spacer. This sequence as well as the two before the 5.8 and after the 2S coding region are very different from the corresponding Drosophila sequences. The main features reported in the Drosophila study (2) are however also found, i.e. all three spacers are very rich in A-T; the sequence of the internal spacer allows base pairing; 5.8S and 2S RNAs can pair through their 3' and 5' terminal regions respectively. The features previously proposed as processing sites in the Drosophila case are thus all found in Sciara in spite of very different spacer sequences.

Organization of the nuclear ribosomal DNA of Chlamydomonas reinhardii

Abstract: Hybridization of cytoplasmic ribosomal RNA (rRNA) to restriction endonuclease digests of nuclear DNA of Chlamydomonas reinhardii reveals two BamHI ribosomal fragments of 2.95 and 2.35 x 10(6) d and two SalI ribosomal fragments of 3.8 and 1.5 x 10(6) d. The ribosomal DNA (rDNA) units 5.3 x 10(6) d in size, appear to be homogeneous since no hybridization of rDNA to other nuclear DNA fragments can be detected. The two BamHI and SalI ribosomal fragments have been cloned and a restriction map of the ribosomal unit has been established. The location of the 25S, 18S and 5.8S rRNA genes has been determined by hybridizing the rRNAs to digests of the ribosomal fragments and by observing RNA/DNA duplexes in the electron microscope. The data also indicate that the rDNA units are arranged in tandem arrays. The 5S rRNA genes are not closely located to the 25S and 18S rRNA genes since they are not contained within the nuclear rDNA unit. In addition no sequence homology is detectable between the nuclear and chloroplast rDNA units of C. reinhardii.

Replication and meiotic transmission of yeast ribosomal RNA genes

Abstract: The yeast Saccharomyces cerevisiae has approximately 120 genes for the ribosomal RNAs (rDNA) which are organized in tandem within chromosomal DNA. These multiple-copy genes are homogeneous in sequence but can undergo changes in copy number and topology. To determine if these changes reflect unusual features of rDNA metabolism, we have examined both the replication of rDNA in the mitotic cell cycle and the inheritance of rDNA during meiosis. The results indicate that rDNA behaves identically to chromosomal DNA: each rDNA unit is replicated once during the S phase of each cell cycle and each unit is conserved through meiosis. Therefore, the flexibility in copy number and topology of rDNA does not arise from the selective replication of units in each S phase nor by the selective inheritance of units in meiosis.

The nucleolus organizers of diploid wheats revealed by in situ hybridization.

Abstract: Labelled RNA, transcribed in vitro from wheat ribosomal DNA cloned in a bacterial plasmid, has been hybridised to metaphase chromosomes of five diploid wheats. Autoradiography of the chromosomes has provided unequivocal evidence that these genotypes possess two pairs of nucleolus organizer chromosomes. The diploid wheat accessions used possess widely differing numbers of ribosomal RNA genes.

Characterization of the cloned ribosomal DNA of tobacco chloroplasts

Abstract: A physical map of the cloned ribosomal DNA of tobacco chloroplasts was constructed by cleavage with several restriction endonucleases and hybridization of the restriction fragments with labeled 16S and 23S rRNAs. The location of the 16S and 23S rRNA genes was determined by electron microscopic analysis of the R-loop containing molecules. No intervening sequences were detected in these genes. The 16S and 23S rRNA genes are separated by a 1.3×106 daltons spacer and coded for by the same DNA strand. The direction of transcription is from gene 16S to gene 23S.

Isolation and mapping of the rRNA genes in the macronucleus of Oxytricha fallax.

Abstract: The DNA in the macronucleus of the protozoan Oxytricha, unlike like that of typical eukaryotes, exists as short, gene-sized molecules. Within the macronucleus the rRNA genes are contained in molecules 7,380 nucleotide pairs in length. This rDNA has been substanially purified by selective denaturation of non-ribosomal DNA followed by Sl nuclease digestion. Results from restriction nuclease digestion and rRNA:DNA hybridization show that the rDNA is a linear, non-palindromic molecule which contains one gene each for the 19s and 25s rRNAs. A total of less than 600 base pairs of DNA lies between the 19s and 25s genes or at the 3′ end of the 25s gene. The non-coding portion of the ribosomal DNA is almost entirely limited to an approximately 1,400 base pair region at the 5′ end of the molecule.

Fine structure of ribosomal RNA. IV. Extraordinary evolutionary conservation in sequences that flank introns in rDNA.

Abstract: By hybridization and DNA sequencing, we have defined a specific region in Xenopus rDNA that is extremely conserved between Tetrahymena, a protozoan, and Xenopus, a vertebrate. This highly conserved region is found at the site where an intron has been shown to interrupt Tetrahymena rDNA [1,2], although we have not detected introns in genomic or cloned Xenopus rDNA. We have noted that the sequences corresponding to nuclear rDNA interon-flanking regions show an intriguing complementarity to tRNAiMet. This suggests possible models for tRNA-rRNA interactions in protein synthesis and/or rRNA splicing.