Showing papers on "Ribosomal DNA published in 1981"
TL;DR: The boundaries between the 18S r DNA, internal transcribed spacer, 28s rDNA, and external nontranscribed spacer were determined by R-loop analysis, further defining the organization of the ribosomal RNA precursor.
211 citations
TL;DR: In this paper, short base-paired RNA fragments, and fragments containing intra-RNA cross-links, were isolated from E. coli 23S rRNA or 50S ribosomal subunits by two-dimensional gel electrophoresis.
Abstract: Short base-paired RNA fragments, and fragments containing intra-RNA cross-links, were isolated from E. coli 23S rRNA or 50S ribosomal subunits by two-dimensional gel electrophoresis. The interactions thus found were used as a first basis for constructing a secondary structure model of the 23S rRNA. Sequence comparison with the 23S rDNA from Z. mays chloroplasts, as well as with the 16S (large subunit) rDNA from human and mouse mitochondria, enabled the experimental model to be improved and extrapolated to give complete secondary structures of all four species. The structures are organized in well-defined domains, with over 450 compensating base changes between the two 23S species. Some ribosomal structural "'switches" were found, one involving 5S rRNA.
158 citations
TL;DR: The nucleotide sequence of 23S rDNA from Zea mays chloroplasts has been determined and reveals three small insertion sequences of 25, 65 and 78 base pairs, whereas maize 16S r DNA shows only deletions when compared with the E.coli species.
Abstract: The nucleotide sequence of 23S rDNA from Zea mays chloroplasts has been determined. Alignment with 23S rDNA from E.coli reveals 71 percent homology when maize 4.5S rDNA is included as an equivalent of the 3' end of E.coli 23S rDNA. Among the conserved sequences are sites for base modification. Chloramphenicol sensitivity and ribosomal subunit interaction. A proposal for the base pairs formed between 16S and 23S rRNAs during the 30S/50S subunit interaction is presented. The alignment of maize 23S rDNA with that of E.coli reveals three small insertion sequences of 25, 65 and 78 base pairs, whereas maize 16S rDNA shows only deletions when compared with the E.coli species.
139 citations
TL;DR: The cell-free system somehow reflects the rRNA synthetic activity of the cell and will prove valuable for the identification and purification of the various factors that are involved in the specific read-out of rDNA and may play a central role in the regulation of transcription of the ribosomal genes.
Abstract: Cloned ribosomal DNA (rDNA) from mouse, which contains the initiation site of 45S pre-rRNA transcription and 5' flanking sequences, has been used as the template in an in vitro transcription system. In the presence of extracts from rapidly growing Ehrlich ascites cells, RNA polymerase I initiates specifically in that region of purified rDNA where the 5' end of 45S rRNA has been mapped. This is shown by electrophoretic analysis of the length of run-off transcripts synthesized from truncated templates, by S1 nuclease mapping, and by hybridization analysis of the in vitro products. The ability of the crude extracts to promote faithful transcription of mouse rDNA correlates with the proliferation rate of the cells. Only extracts prepared from exponentially growing mouse cells contain the factor(s) required for the faithful transcription of mouse ribosomal genes. Extracts from nongrowing or slowly growing mouse cells show very little activity. Thus, the cell-free system somehow reflects the rRNA synthetic activity of the cell and will prove valuable for the identification and purification of the various factors that are involved in the specific read-out of rDNA and may play a central role in the regulation of transcription of the ribosomal genes.
112 citations
TL;DR: The distributions of three human ribosomal gene polymorphisms among individual chromosomes containing nucleolus organizers were analyzed by using mouse--human hybrid cells, suggesting the occurrence of genetic exchanges among ribosome gene clusters on nonhomologous chromosomes less frequently in mice.
Abstract: The distributions of three human ribosomal gene polymorphisms among individual chromosomes containing nucleolus organizers were analyzed by using mouse--human hybrid cells. Different nucleolus organizers can contain the same variant, suggesting the occurrence of genetic exchanges among ribosomal gene clusters on nonhomologous chromosomes. Such exchanges appear to occur less frequently in mice. This difference is discussed in terms of the nucleolar organization and chromosomal location of ribosomal gene clusters in humans and mice.
97 citations
93 citations
TL;DR: It is demonstrated that although each nucleus contains methylated and unmethylated rDNA, only unmethylation genes are hypersensitive to DNAase I in Balb/c liver nuclei, consistent with the possibility that the methylated genes are transcriptionally inactive.
79 citations
TL;DR: Unlike the transcripts of the type I ribosomal DNA insertions, transcripts of type II insertions are found only in the nucleus and the proportion of the higher molecular weight transcripts to the 3.4 × 10 3 base transcripts is much higher in ovarian tissue than in embryos, larvae or pupae.
73 citations
TL;DR: Certain structural elements of the L1 binding sites in rRNA are also found in the initial segment of the polycistronic L11-L1 mRNA, providing support for the hypothesis that L1 participates in the regulation of ribosomal protein synthesis by specific interaction with its own mRNA.
Abstract: Ribosomal protein L1 from the prokaryote Escherichia coli has been shown to form a specific complex with 26S ribosomal RNA from the eukaryote Dictyostelium discoideum. The segment of Dictyostelium rRNA protected from ribonuclease digestion by L1 and the corresponding region in Dictyostelium rDNA were investigated by nucleotide sequence analysis, and an analogous section in rDNA from Xenopus laevis was identified. When the L1-specific segments from eukaryotic rRNA were compared with those from prokaryotic rRNA, striking similarities in both primary and secondary structure were apparent. These conserved features suggest a common structural basis for protein recognition and indicate that such regions became fixed at a very early stage in rRNA evolution. In addition, certain structural elements of the L1 binding sites in rRNA are also found in the initial segment of the polycistronic L11-L1 mRNA, providing support for the hypothesis that L1 participates in the regulation of ribosomal protein synthesis by specific interaction with its own mRNA.
72 citations
TL;DR: Cultures of Tetrahymena thermophila were deprived of nutrients and later refed with enriched medium to obtain partial synchrony of DNA replication, and electron microscopic data was consistent with an off-center origin of replication located approximatley 600 base pairs from the center of the rDNA of T. pyriformis.
Abstract: Cultures of Tetrahymena thermophila were deprived of nutrients and later refed with enriched medium to obtain partial synchrony of DNA replication. Preferential replication of the extrachromosomal, macronuclear ribosomal RNA genes (rDNA) was found to occur at 40-80 min after refeeding. The rDNA accounted for one half of the label incorporated into cellular DNA during this period. Electron microscopy of the purified rDNA showed 1% replicative intermediates. Their structure was that expected for bidirectional replication of the linear rDNA from an origin or origins located in the central nontranscribed region of the palindromic molecule. Similar forms had previously been observed for the rDNA of a related species, Tetrahymena pyriformis. The electron microscopic data was consistent with an origin of replication located approximatley 600 base pairs from the center of the rDNA of T. thermophila, in contrast to a more central location in the rDNA of T. pyriformis. One implication of an off-center origin of replication is that there are two such sequences per palindromic molecule.
71 citations
TL;DR: The organization of the genes coding for 18 S, 5·8 S and 26 S ribosomal RNAs in the nematode Caenorhabditis elegans is characterized and no difference is found in the major Ribosomal DNA restriction endonuclease cleavage patterns between two interbreeding strains of C. elegans.
Journal Article•
TL;DR: Comparisons by in situ hybridization of the amount of satellite DNA in Robertsonian translocation and "normal variant" chromosomes with that in their homologs are reported.
Abstract: Satellite III DNA has been located by in situ hybridization in chromosomes 1, 3--5, 7, 9, 10, 13--18, 20--22, and Y and ribosomal DNA (rDNA) in the acrocentric chromosomes 13--15, 21, and 22. In the acrocentric chromosomes, the satellite DNA is located in the short arm. Here we report comparisons by in situ hybridization of the amount of satellite DNA in Robertsonian translocation and "normal variant" chromosomes with that in their homologs. In almost all dicentric Robertsonian translocations, the amount of satellite DNA is less than that in the normal homologs, but it is rarely completely absent, indicating that satellite DNA is located between the centromere and the nucleolus organizer region (NOR) and that the breakpoints are within the satellite DNA. The amount of satellite DNA shows a range of variation in "normal" chromosomes, and this is still more extreme in "normal variant" chromosomes, those with large short arm (p+ or ph+) generally having more satellite DNA than those with small short arms (p- or ph-). The cytological satellites are heterogeneous in DNA content; some contain satellite DNA, others apparently do not, and the satellite DNA content is not related to the size or intensity of fluorescence of the satellites. The significance of these variations for the putative functions of satellite DNA is discussed.
TL;DR: The kinetics of appearance and synthesis of the 11 kb rDNA early in macronuclear development are consistent with its being an intermediate in rDNA amplification.
TL;DR: The 5'-terminal of Saccharomyces cerevisiae 18 S and 25 S rRNA and 37 S pre-rRNA are precisely mapped within the sequence of the rDNA repeating unit.
Abstract: The 5'-terminal of Saccharomyces cerevisiae 18 S and 25 S rRNA are precisely mapped within the sequence of the rDNA repeating unit. The 3'-terminal of 25 S rRNA and 37 S pre-rRNA are located within a 548 bp segment of the rDNA repeating unit by the use of a DNA polymerase I extension technique. The analysis of the rDNA sequences at the structural gene boundaries reveals the presence of oligonucleotide repeats which may be involved in transcription or processing control mechanisms. The sequence of rDNA in the transcription termination region is determined and possible mechanisms shaping the 3'-end of 25 S rRNA are discussed.
TL;DR: The interspersed repeated sequences studied are transcribed into rare, heterogeneous, poly(A)-lacking nuclear RNA molecules, and it is shown that both strands of a flanking sequence are transcribes, but to a different extent.
TL;DR: The ribosomal DNA amount of the flax variety ‘Stormont Cirrus’ was determined during its growth under inducing conditions and the rDNA amount increased while under a different set of conditions there was a decrease in this amount.
TL;DR: These findings suggest that most of the amplified human rRNA genes on the 14p+ chromosomes have been inactivated by a process involving DNA methylation.
Abstract: In two unrelated families, the short arm of a 14p+ marker chromosome contains an increased number of copies of the 18S+28S rRNA genes without a comparable increase in the transcriptional activity, as shown by silver staining. The DNA in this region is highly enriched in 5-methylcytosine, as shown by specific antibody binding. In contrast, the owl monkey and cat have a single major nucleolus organizer region (NOR) per haploid genome; these NORs contain about the same number of rRNA genes as the 14p+ chromosome but are not methylated. These findings suggest that most of the amplified human rRNA genes on the 14p+ chromosomes have been inactivated by a process involving DNA methylation.
TL;DR: The results of these two approaches indicate that the rRNA gene cluster consists of multiple units of replication, possibly one per gene unit, and show that the origins of replication are localized into the non-transcribed spacer.
Abstract: The study of the localization of the replication origins of rDNA in Xenopus laevis has been approached by two different methods.
1
The DNA of X. laevis larvae was fractionated by CsCI gradient centrifugation in bulk and ribosomal DNA and examined in the electron microscope. In bulk DNA, clusters of microbubbles, which are related with the origins of replication, appear to be spaced along the DNA molecules at intervals comparable with the size of the ‘average’ replicon of X. laevis. In ribosomal DNA, the distance between adjacent clusters is much shorter and corresponds to the size of the rDNA repeating unit. When ribosomal DNA was submitted to digestion with restriction enzymes (EcoRl or HindIII) the microbubbles are observed in the non-transcribed spacer-containing fragment.
2
Cultured cells of X. laevis were synchronized by mitotic selection and incubates: with 5-fluoro-2-deoxyuridine for a time longer than the G1 phase. This treatment synchronizes the replicons and allows them to start replicating very slowly. It was thus possible to obtain a preferential labelling of the regions containing the origins. The analysis by gel electrophoresis of the EcoRl-digested rDNA showed that the radioactivity was preferentially incorporated in the fragments which contain the non-transcribed spacer.
The results of these two approaches indicate that the rRNA gene cluster consists of multiple units of replication, possibly one per gene unit. Furthermore they show that the origins of replication are localized into the nontranscribed spacer.
TL;DR: The 5' end of 45S pre-rRNA has been located on a cloned rDNA fragment from mouse by r-loop mapping and the nuclease S1 protection technique, and the sequence of about 1100 nucleotides surrounding the initiation site for ribosomal RNA transcription has been determined.
Abstract: The 5' end of 45S pre-rRNA has been located on a cloned rDNA fragment from mouse by r-loop mapping and the nuclease S1 protection technique. 45S pre-rRNA could be shown to represent the primary transcript of the ribosomal genes because 5' polyphosphate termini have been detected by an enzymatic assay. The sequence of about 1100 nucleotides surrounding the initiation site for ribosomal RNA transcription has been determined. Features of this region of the ribosomal DNA will be discussed. A comparison of the nucleotide sequence with corresponding areas of ribosomal genes from other eukaryotes does not reveal significant homology in the region of transcription initiation.
TL;DR: A phage lambda recombinant library containing Euglena gracilis genomic DNA was screened for nuclear rDNA sequences and the 11.5-kb insert was shown to represent a complete rDNA repeat unit that carried the genes for the 19S, 25S, 5.8 S and 5 S cytoplasmic rRNAs.
TL;DR: Intraspecific differences occur in both ribosomal DNA cistron number (one or three) and structural organization among those strains designated as “strain Z” and bacillaris.
Abstract: Chloroplast DNAs from six different laboratory collections of Euglena gracilis “strain Z” and var. bacillaris were analyzed with restriction endonucleases EcoRI and Bam HI. The most variable portion of the organelle genome is the region containing the ribosomal cistrons. Intraspecific differences occur in both ribosomal DNA cistron number (one or three) and structural organization among those strains designated as “strain Z” and bacillaris. One culture previously designated as “Z” is most likely bacillaris.
TL;DR: It is suggested that even severely bobbed flies fail to utilize their interrupted rRNA genes, and these genes cannot be transcribed productively in D. melanogaster.
Abstract: We have shown earlier that interrupted rRNA genes in Drosophila melanogaster do not contribute significantly to rRNA production by a splicing mechanism (Long and Dawid 1979). In the work reported here the expression of interrupted rRNA genes was tested in several stocks that carry bobbed mutations, i.e., have partial deletions of their rRNA gene clusters. Transcripts of the major 5 kb type 1 insertion are very rare in bobbed flies as they are in the wild type, occurring at a concentration in embryos of less than one copy per nucleus. Transcripts of short type 1 insertions are more abundant in certain bobbed stocks, especially those carrying the car bb chromosome. However, other severely bobbed flies have no increase in these insertion transcripts over the low wild-type levels. Type 2 insertions are transcribed into very rare RNA molecules in the wild type and in the bobbed genotypes that were studied. From these results we conclude that interrupted rRNA genes are not expressed through a splicing mechanism into mature rRNA in mutant or wild-type flies. Since even severely bobbed flies fail to utilize their interrupted rRNA genes, we suggest that these genes cannot be transcribed productively in D. melanogaster.
TL;DR: The analysis of single and double digestions with Eco RI, Hind III, and Bam HI endonuclease restriction enzymes showed the presence of at least two types of repetitive units that were present in each single individual of Allium cepa analyzed.
Abstract: Southern blot hybridizations were performed to investigate the ribosomal DNA structure inAllium cepa (Liliaceae). The analysis of single and double digestions with Eco RI, Hind III, and Bam HI endonuclease restriction enzymes showed the presence of at least two types of repetitive units. The gene types were present in each single individual ofAllium cepa analyzed, notwithstanding the variation of the ribosomal gene number from 5,500 to 11,900 and the NOR number from 2 to 4. The first and the second gene type are 12.7 kb long and the first type is much more represented inAllium cepa genome. The differences between the two gene types consist in the position of the Hind III restriction sites in the external spacer.
TL;DR: Pyrimidine tract analysis gave no indication of relatedness between the spacer and satellite DNA sequences, and sequences in rDNA that encode 18S and 28S ribosomal RNA have been highly conserved during the divergence of Drosophila species; this is inferred from interspecific hybridizations involving ribosome RNA and a comparison of distributions of restriction enzyme cleavage sites in r DNA.
Abstract: Ribosomal DNA nontranscribed spacers in Drosophila virilis DNA have been examined in some detail by restriction site analysis of cloned segments of rDNA, nucleic acid hybridizations involving unfractionated rDNA, and base composition estimates. The overall G+C content of the spacer is 27–28%; this compares with 39% for rDNA as a whole, 40% for main band DNA, and 26% for the D. virilis satellites. Much of the spacer is comprised of 0.25 kb repeats revealed by digestion with Msp I, Fnu DII or Rsd I, which terminate very near the beginning of the template for the ribosomal RNA precursor. The spacers are heterogeneous in length among rDNA repeats, and this is largely accounted for by variation among rDNA units in the number of 0.25 kb elements per spacer. Despite its high A+T content and the repetitive nature of much of the spacer, and the proximity of rDNA and heterochromatin in Drosophila, pyrimidine tract analysis gave no indication of relatedness between the spacer and satellite DNA sequences. Species of Drosophila closely related to D. virilis have rDNA spacers that are homologous with those in D. virilis to the extent that hybridization of a cloned spacer segment of D. virilis rDNA to various DNA is comparable with hybridization to homologous DNA, and distributions of restriction enzyme cleavage sites are very similar (but not identical) among spacers of the various species. There is spacer length heterogeneity in the rDNA of all species, and each species has a unique major rDNA spacer length. Judging from Southern blot hybridization, D. hydei rDNA spacers have 20–30% sequence homology with D. virilis rDNA spacers, and a repetitive component is similarly sensitive to Msp I and Fnu DII digestion, D. melanogaster rDNA spacers have little or no homology with counterparts in D. virilis rDNA, despite a similar content of 0.25 kb repetitive elements. In contrast, sequences in rDNA that encode 18S and 28S ribosomal RNA have been highly conserved during the divergence of Drosophila species; this is inferred from interspecific hybridizations involving ribosomal RNA and a comparison of distributions of restriction enzyme cleavage sites in rDNA.
TL;DR: Two Charon 4A lambda bacteriophage clones were characterized which contain all and part of the 18S ribosomal DNA of the rat suggesting that there is heterogeneity in the non-transcribed spacer regions of rat ribosome genes.
Abstract: Two Charon 4A lambda bacteriophage clones were characterized which contain all and part of the 18S ribosomal DNA of the rat. One clone contained two Eco RI fragments which include the whole 18S ribosomal RNA region and part of 28S ribosomal RNA region. The other clone contained an Eco RI fragment which covers part of 18S ribosomal RNA region. There were differences between the two clones in the non-transcribed spacer regions suggesting that there is heterogeneity in the non-transcribed spacer regions of rat ribosomal genes. The restriction map of the cloned mouse ribosomal DNA. Eco RI, Hind III, Pst I, and Bam HI sites in 18S ribosomal RNA region were in the same places in mouse and rat DNA but the restriction sites in the 5′-spacer regions were different.
TL;DR: The X chromosomal nucleolus organizer of Drosophila hydei contains about 500 ribosomal RNA genes and the 28 S rRNA coding region of about 50% of these genes is interrupted by an intervening sequence of 6.0 × 10 3 basepairs.
TL;DR: The genes coding for ribosomal RNa in plasmodia of Physarum polycephalum are arranged palindromically on extrachromosomal rDNA molecules of 61 kb (kilobasepairs).
Abstract: The genes coding for ribosomal RNa in plasmodia of Physarum polycephalum are arranged palindromically on extrachromosomal rDNA molecules of 61 kb (kilobasepairs). Incubation of mildly extracted rDNA with the 125I Bolton-Hunter reagent results in incorporation of label not removed by SDS, CsCl, or various organic solvents. Labeled protein is preferentially associated with terminal rDNA restriction fragments, as detected after gel electrophoresis of the DNA. Antibody reaction with dinitrophenylated protein-rDNA complexes allows visualization of protein located from 1 to 2 kb from the termini, in a region containing multiple inverted repeat sequences and single-strand gaps. DNase I treatment of either rDNA or rDNA termini releases primarily two labeled protein bands of 5,000 and 13,000 daltons as well as less prominent bands of higher molecular weight. We discuss mechanisms for involvement of terminal protein in replication of 3' ends and chromosomal integration of the rDNA.
TL;DR: Interestingly, the intron + cistrons were shown to be clustered within the rDNA and to contain a different population of non-transcribed spacer/external transcribed spacer (NTS + ETS) regions to that seen amongst the introns − cistsrons.
TL;DR: Although each genotype is characterized by different frequencies of some spacer classes, the prominent spacer length heterogeneity pattern is similar among the different nucleolus organizers and, therefore, seems to be conserved during evolution.
Abstract: Drosophila hydei rRNA genes from different chromosomes and from different stocks have been studied by restriction enzyme analysis. In DNA from wild-type females, about half of the X chromosomal rRNA genes are interrupted by an intervening sequence within the 28S coding region. In contrast to D. melanogaster, the intervening sequences belong to a single size class of 6.0 kb. Although there are two nucleolus organizers on the Y chromosome, genes containing the intervening sequence seem to be restricted to the X chromosome. — As shown in four cloned rDNA fragments, the nontranscribed spacers differ in length by having varying numbers of a 242 base pair sequence located in tandem in the right section of the spacer. In genomic rDNA, the spacers also differ in length by a regular 0.25 kb interval. Spacers with between 5 and 15 subrepeats occur frequently within the X and Y chromosomal nucleolus organizers in different D. hydei stocks; shorter and longer spacers are also present but are relatively rare. — Although each genotype is characterized by different frequencies of some spacer classes, the prominent spacer length heterogeneity pattern is similar among the different nucleolus organizers and, therefore, seems to be conserved during evolution.
TL;DR: Data suggest that Drosophila rDNA interruptions arose as a transposable element, and that divergence had included length alterations generated by unequal crossing over.
Abstract: The nucleotide sequences at and around the termini of 5 kb type 1 interruptions in three separate clones of D. melanogaster rDNA repeats have been determined, and have been compared with the sequence of the corresponding region of an insertion-free rDNA repeat. All three interrupted rDNA repeats contain a small deletion of 28S rRNA coding material at the left coding/insertion sequence junction. A second deletion was found in one of the three clones, ad other aberrations were suggested by the results of restriction enzyme digestions of unfractionated rDNA. The termini of 5 kb type 1 rDNA insertions in D. melanogaster were also compared with the corresponding regions of 28S rDNA interruptions in D. virilis: the insertion site is identical in the two species, but the termini of the two species' interruptions show no homology. I sequenced a 1.1 kb region of the 5 kb type 1 D. melanogaster rDNA interruption that covers the sequences of the 1 kb and 0.5 kb insertions. There is 98% homology between the rightmost 1 kb of the 5 kb interruption and the sequences of the shorter insertions. Data suggest that Drosophila rDNA interruptions arose as a transposable element, and that divergence had included length alterations generated by unequal crossing over.