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Kim JH, Nagaraja R, Ogurtsov AY, Noskov VN, Liskovykh M, Lee HS, Hori Y, Kobayashi T, Hunter K, Schlessinger D, Kouprina N, Shabalina SA, Larionov V. Comparative analysis and classification of highly divergent mouse rDNA units based on their intergenic spacer (IGS) variability. NAR Genom Bioinform 2024; 6:lqae070. [PMID: 38881577 PMCID: PMC11177557 DOI: 10.1093/nargab/lqae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/20/2024] [Accepted: 06/05/2024] [Indexed: 06/18/2024] Open
Abstract
Ribosomal DNA (rDNA) repeat units are organized into tandem clusters in eukaryotic cells. In mice, these clusters are located on at least eight chromosomes and show extensive variation in the number of repeats between mouse genomes. To analyze intra- and inter-genomic variation of mouse rDNA repeats, we selectively isolated 25 individual rDNA units using Transformation-Associated Recombination (TAR) cloning. Long-read sequencing and subsequent comparative sequence analysis revealed that each full-length unit comprises an intergenic spacer (IGS) and a ∼13.4 kb long transcribed region encoding the three rRNAs, but with substantial variability in rDNA unit size, ranging from ∼35 to ∼46 kb. Within the transcribed regions of rDNA units, we found 209 variants, 70 of which are in external transcribed spacers (ETSs); but the rDNA size differences are driven primarily by IGS size heterogeneity, due to indels containing repetitive elements and some functional signals such as enhancers. Further evolutionary analysis categorized rDNA units into distinct clusters with characteristic IGS lengths; numbers of enhancers; and presence/absence of two common SNPs in promoter regions, one of which is located within promoter (p)RNA and may influence pRNA folding stability. These characteristic features of IGSs also correlated significantly with 5'ETS variant patterns described previously and associated with differential expression of rDNA units. Our results suggest that variant rDNA units are differentially regulated and open a route to investigate the role of rDNA variation on nucleolar formation and possible associations with pathology.
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Affiliation(s)
- Jung-Hyun Kim
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
| | - Ramaiah Nagaraja
- National Institute of Aging, Laboratory of Genetics and Genomics, Baltimore, MD, USA
| | - Alexey Y Ogurtsov
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Vladimir N Noskov
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
| | - Mikhail Liskovykh
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
| | - Hee-Sheung Lee
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
| | - Yutaro Hori
- The University of Tokyo, Laboratory of Genome Regeneration, Tokyo 113-0032, Japan
| | - Takehiko Kobayashi
- The University of Tokyo, Laboratory of Genome Regeneration, Tokyo 113-0032, Japan
| | - Kent Hunter
- National Cancer Institute, Laboratory of Cancer Biology and Genetics, Bethesda, MD, USA
| | - David Schlessinger
- National Institute of Aging, Laboratory of Genetics and Genomics, Baltimore, MD, USA
| | - Natalay Kouprina
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Vladimir Larionov
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
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2
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Tseng H, Chou W, Wang J, Zhang X, Zhang S, Schultz RM. Mouse ribosomal RNA genes contain multiple differentially regulated variants. PLoS One 2008; 3:e1843. [PMID: 18365001 PMCID: PMC2266999 DOI: 10.1371/journal.pone.0001843] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Accepted: 02/12/2008] [Indexed: 11/22/2022] Open
Abstract
Previous cytogenetic studies suggest that various rDNA chromosomal loci are not equally active in different cell types. Consistent with this variability, rDNA polymorphism is well documented in human and mouse. However, attempts to identify molecularly rDNA variant types, which are regulated individually (i.e., independent of other rDNA variants) and tissue-specifically, have not been successful. We report here the molecular cloning and characterization of seven mouse rDNA variants (v-rDNA). The identification of these v-rDNAs was based on restriction fragment length polymorphisms (RFLPs), which are conserved among individuals and mouse strains. The total copy number of the identified variants is less than 100 and the copy number of each individual variant ranges from 4 to 15. Sequence analysis of the cloned v-rDNA identified variant-specific single nucleotide polymorphisms (SNPs) in the transcribed region. These SNPs were used to develop a set of variant-specific PCR assays, which permitted analysis of the v-rDNAs' expression profiles in various tissues. These profiles show that three v-rDNAs are expressed in all tissues (constitutively active), two are expressed in some tissues (selectively active), and two are not expressed (silent). These expression profiles were observed in six individuals from three mouse strains, suggesting the pattern is not randomly determined. Thus, the mouse rDNA array likely consists of genetically distinct variants, and some are regulated tissue-specifically. Our results provide the first molecular evidence for cell-type-specific regulation of a subset of rDNA.
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Affiliation(s)
- Hung Tseng
- Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
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3
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Ryu S, Do Y, Fitch DHA, Kim W, Mishra B. Dropout Alignment Allows Homology Recognition and Evolutionary Analysis of rDNA Intergenic Spacers. J Mol Evol 2008; 66:368-83. [DOI: 10.1007/s00239-008-9090-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Revised: 12/14/2007] [Accepted: 02/21/2008] [Indexed: 11/28/2022]
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4
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Grozdanov P, Georgiev O, Karagyozov L. Complete sequence of the 45-kb mouse ribosomal DNA repeat: analysis of the intergenic spacer. Genomics 2004; 82:637-43. [PMID: 14611805 DOI: 10.1016/s0888-7543(03)00199-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
DNA from a single bacterial artificial chromosome clone was used to sequence the mouse ribosomal DNA intergenic spacer from the 3' end of the 45S pre-RNA to the spacer promoter (Accession No. AF441733). This made possible the assembly of a complete mouse ribosomal DNA repeat unit (45309 bp long, TPA Accession No. BK000964). Analysis of the intergenic spacer (IGS) showed a high density of simple sequence repeats and transposable elements. The IGS contains two long sequence blocks, which are repeated tandemly. Some of the sequences in these blocks are also present in other parts of the IGS. A difference in the mutation rate along the mouse IGS was observed. The significance of sequence motifs in the IGS for transcription enhancement, transcription termination, origin of replication, and nucleolar organization is discussed.
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Affiliation(s)
- Petar Grozdanov
- Cell Biology Department, Institute of Molecular Biology, Acad. G Bonchev Street, Building 21, 1113 Sofia, Bulgaria
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5
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Hannan RD, Stefanovsky V, Taylor L, Moss T, Rothblum LI. Overexpression of the transcription factor UBF1 is sufficient to increase ribosomal DNA transcription in neonatal cardiomyocytes: implications for cardiac hypertrophy. Proc Natl Acad Sci U S A 1996; 93:8750-5. [PMID: 8710943 PMCID: PMC38745 DOI: 10.1073/pnas.93.16.8750] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The accelerated protein accumulation characteristic of cardiomyocyte hypertrophy results from increased cellular protein synthetic capacity (elevated ribosome content). The rate limiting step in ribosome accumulation is transcription of the rRNA genes. During neonatal cardiomyocyte hypertrophy induced by norepinephrine or spontaneous contraction, changes in the expression of a ribosomal DNA transcription factor, UBF, correlated with increased rates of ribosome biogenesis. We hypothesized that elevated expression of UBF was part of the mechanism by which these hypertrophic stimuli effected increases in the rate of transcription from the rDNA promoter. In this study, we have examined directly the effect of overexpressing UBF on rDNA transcription in neonatal cardiomyocytes in culture. In control experiments, a novel reporter construct for rDNA transcription (pSMECAT) showed similar increases in activity in response to hypertrophic stimuli (10(-4) M phenylephrine, 10(-7) M endothelin, and spontaneous contraction) as did the endogenous rRNA genes. When contraction-arrested cardiomyocytes were cotransfected with pSMECAT and increasing amounts of a UBF1 expression vector; a dose-dependent (3-5 fold) increase in rDNA transcription was observed. Western blot analysis confirmed that the overexpressed, FLAG-tagged UBF accumulated in the cardiomyocyte nuclei. The observation that overexpression of UBF1 is sufficient to increase rDNA transcription in neonatal cardiomyocytes provides evidence in support of the hypothesis that the regulation of UBF is a key component of the increased ribosome biogenesis and protein accumulation associated with cardiomyocyte hypertrophy.
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Affiliation(s)
- R D Hannan
- Sigfried and Janet Weis Center for Research, Geisinger Clinic, Danville, PA 17822, USA
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6
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Suzuki H, Hosoda T, Sakurai S, Tsuchiya K, Munechika I, Korablev VP. Phylogenetic relationship between the Iriomote cat and the leopard cat, Felis bengalensis, based on the ribosomal DNA. IDENGAKU ZASSHI 1994; 69:397-406. [PMID: 7946460 DOI: 10.1266/jjg.69.397] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We analyzed the restriction fragment length polymorphisms in the spacer regions of ribosomal DNA (rDNA), using twelve restriction enzymes, to examine whether the Iriomote cat is related to the leopard cat (Felis bengalensis). A restriction map for each taxon was constructed and the major taxon-specific types of repeating unit (repetypes) were characterized on the basis of the arrangements of restriction sites. The Iriomote cat and the leopard cat share a common repetype but this repetype is different from that of the domestic cat (F. catus) with an estimated sequence divergence of 1.5% and from that of the ocelot (F. paradalis) with an estimated sequence divergence of 2.5%. These results indicate that, phylogenetically, the Iriomote cat is closely related to the leopard cat and that the ancestral population moved from the continent to Iriomote Island quite recently. The rDNA arrays of the leopard cat exhibit considerable intragenomic size-variation, which is thought to have emerged as a result of differences in numbers of repeated DNA segments, whereas the extent of such size-variation is much lower in the rDNA of the Iriomote cat. It appears that, even though migration of the Iriomote cat occurred relatively recently, the population has diverged to some extent from its continental counterpart, perhaps via fixation of preexistent intraspecific variations rather than by generation of new variations.
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Affiliation(s)
- H Suzuki
- Division of Molecular Genetics, Jikei University School of Medicine, Tokyo, Japan
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7
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Pikaard CS. Ribosomal gene promoter domains can function as artificial enhancers of RNA polymerase I transcription, supporting a promoter origin for natural enhancers in Xenopus. Proc Natl Acad Sci U S A 1994; 91:464-8. [PMID: 8290549 PMCID: PMC42969 DOI: 10.1073/pnas.91.2.464] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Enhancers of RNA polymerase I transcription in higher eukaryotes are repetitive elements within the intergenic spacers of rRNA genes. In Xenopus and mouse, enhancers and the gene promoter bind the activator protein, upstream binding factor, and in Xenopus, enhancers also share sequence similarity with an upstream domain of the promoter. This upstream promoter domain can act as an efficient enhancer when polymerized and cloned adjacent to a ribosomal gene promoter injected into oocytes. A core promoter domain lacking similarity with spacer sequences in Xenopus laevis but analogous to a repeated sequence in Xenopus borealis can also function as an enhancer. These data demonstrate functional relatedness between the promoter and enhancers, supporting the hypothesis that enhancers could have evolved from duplicated promoter domains that bind essential transcription factors. The ability of upstream binding factor to bind enhancers inactivated by mutation suggests that upstream binding factor binding alone cannot explain enhancer function.
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Affiliation(s)
- C S Pikaard
- Biology Department, Washington University, St. Louis, MO 63130
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8
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SUZUKI H, HOSODA T, SAKURAI S, TSUCHIYA K, MUNECHIKA I, KORABLEV VP. Phylogenetic relationship between the Iriomote cat and the leopard cat, Felis bengalensis, based on the ribosomal DNA. Genes Genet Syst 1994. [DOI: 10.1266/ggs.69.397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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9
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Palmer TD, Miller AD, Reeder RH, McStay B. Efficient expression of a protein coding gene under the control of an RNA polymerase I promoter. Nucleic Acids Res 1993; 21:3451-7. [PMID: 8393988 PMCID: PMC331444 DOI: 10.1093/nar/21.15.3451] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
In mammalian cells, RNA polymerase I transcripts are uncapped and retain a polyphosphate 5' terminus. It is probably for this reason that they are poorly translated as messenger RNA. We show in this report that insertion of an Internal Ribosome Entry Site (IRES) into the 5' leader of an RNA polymerase I transcript overcomes the block to translation, presumably by substituting for the 5' trimethyl G cap. Addition of an SV40 polyA addition signal also enhances protein production from the RNA polymerase I transcript. RNA Polymerase I driven expression vectors containing both elements produce protein at levels comparable to that produced from RNA polymerase II driven expression vectors which utilize a retroviral LTR. RNA Polymerase I driven expression vectors may have a variety of uses both for basic research and for practical expression of recombinant proteins.
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Affiliation(s)
- T D Palmer
- Hutchinson Cancer Research Center, Seattle, WA 98104
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10
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Baldridge GD, Dalton MW, Fallon AM. Is higher-order structure conserved in eukaryotic ribosomal DNA intergenic spacers? J Mol Evol 1992; 35:514-23. [PMID: 1474605 DOI: 10.1007/bf00160212] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Computer-based structural analysis of the ribosomal DNA intergenic spacer (IGS) from the mosquito Aedes albopictus revealed a potential to form strong and extensive secondary structures throughout a 4.7-kilobase (kb) region. The predicted stability of secondary structures was particularly high within a 3.15-kb region containing 17 tandem 201 base-pair subrepeats. Similarly strong secondary structure potential was also found when IGS subrepeats were analyzed from 17 phylogenetically diverse eukaryotes, including vertebrates, invertebrates, and plants. Conservation of higher-order structure potential in the IGS region of ribosomal DNA may reflect evolutionary and functional constraints on chromatin organization, transcriptional regulation of the ribosomal RNA genes, and/or transcript processing and stability.
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Affiliation(s)
- G D Baldridge
- Department of Entomology, University of Minnesota, St. Paul 55108
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11
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Suzuki H, Sakurai S, Nishimura M, Kominami R, Moriwaki K. Compensatory changes in silver-stainability of nucleolar organizer regions in mice. IDENGAKU ZASSHI 1992; 67:217-32. [PMID: 1445722 DOI: 10.1266/jjg.67.217] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Silver-stainability of nucleolar organizer regions (NORs) that contain genes for ribosomal RNA (rDNA) was investigated using two mouse strains, BALB/cCrSlc and MOA, and their hybrid progeny. The patterns of segregation of the rDNA clusters were analyzed in terms of chromosomal C-banding and by use of a polymorphic probe for the variable region in backcrossed N2 and N3 individuals. The results indicate that the intensity of Ag-NOR staining is stably inherited in most of the rDNA clusters, irrespective of different genetic backgrounds. In some clusters, such as those on chromosome 12 of BALB/cCrSlc, a modulation of the intensity is observed. This modulation seems to be due to compensatory activation via a change in the number of actively transcribed genes. The change from silver-negative to silver-positive staining of the NOR of chromosome 12 of BALB/cCrSlc was correlated with demethylation of the genes.
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Affiliation(s)
- H Suzuki
- Division of Molecular Genetics, Jikei University School of Medicine, Tokyo, Japan
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12
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Kuhn A, Deppert U, Grummt I. A 140-base-pair repetitive sequence element in the mouse rRNA gene spacer enhances transcription by RNA polymerase I in a cell-free system. Proc Natl Acad Sci U S A 1990; 87:7527-31. [PMID: 2217183 PMCID: PMC54780 DOI: 10.1073/pnas.87.19.7527] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We show that the repetitive 140-base-pair (bp) elements present in the spacer of mouse rRNA genes function as enhancers for RNA polymerase I. Attachment of these elements to the rDNA promoter stimulates rRNA synthesis both in vivo and in vitro. The cis-activating effect of the spacer repeats is orientation-independent and increases with increasing numbers of the 140-bp elements. Competition experiments demonstrate that the spacer repeats bind one or more of the transcription factors interaction with the rDNA promoter. Both the 140-bp elements and the core promoter act cooperatively and thus are functionally linked. The 60/81-bp enhancer repeats from Xenopus laevis rDNA compete for a murine transcription factor(s) and stimulate transcription often fused to the mouse rDNA promoter. The results indicate that despite the marked species specificity of rDNA transcription initiation, common factors may interact with both the rDNA promoter and the enhancer.
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Affiliation(s)
- A Kuhn
- Institut für Biochemie, Würzburg, Federal Republic of Germany
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13
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Abstract
The intergenic spacer of the mouse ribosomal genes contains repetitive 140-base-pair (bp) elements which we show are enhancers for RNA polymerase I transcription analogous to the 60/81-bp repetitive enhancers (enhancers containing a 60-bp and an 81-bp element) previously characterized from Xenopus laevis. In rodent cell transfection assays, the 140-bp repeats stimulated an adjacent mouse polymerase I promoter when located in cis and competed with it when located in trans. Remarkably, in frog oocyte injection assays, the 140-bp repeats enhanced a frog ribosomal gene promoter as strongly as did the homologous 60/81-bp repeats. Mouse 140-bp repeats also competed against frog promoters in trans. The 140-bp repeats bound UBF, a DNA-binding protein we have purified from mouse extracts that is the mouse homolog of polymerase I transcription factors previously isolated from frogs and humans. The DNA-binding properties of UBF are conserved from the mouse to the frog. The same regulatory elements (terminators, gene and spacer promoters, and enhancers) have now been identified in both a mammalian and an amphibian spacer, and they are found in the same relative order. Therefore, this arrangement of elements probably is widespread in nature and has important functional consequences.
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14
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Pikaard CS, Pape LK, Henderson SL, Ryan K, Paalman MH, Lopata MA, Reeder RH, Sollner-Webb B. Enhancers for RNA polymerase I in mouse ribosomal DNA. Mol Cell Biol 1990; 10:4816-25. [PMID: 2388626 PMCID: PMC361088 DOI: 10.1128/mcb.10.9.4816-4825.1990] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The intergenic spacer of the mouse ribosomal genes contains repetitive 140-base-pair (bp) elements which we show are enhancers for RNA polymerase I transcription analogous to the 60/81-bp repetitive enhancers (enhancers containing a 60-bp and an 81-bp element) previously characterized from Xenopus laevis. In rodent cell transfection assays, the 140-bp repeats stimulated an adjacent mouse polymerase I promoter when located in cis and competed with it when located in trans. Remarkably, in frog oocyte injection assays, the 140-bp repeats enhanced a frog ribosomal gene promoter as strongly as did the homologous 60/81-bp repeats. Mouse 140-bp repeats also competed against frog promoters in trans. The 140-bp repeats bound UBF, a DNA-binding protein we have purified from mouse extracts that is the mouse homolog of polymerase I transcription factors previously isolated from frogs and humans. The DNA-binding properties of UBF are conserved from the mouse to the frog. The same regulatory elements (terminators, gene and spacer promoters, and enhancers) have now been identified in both a mammalian and an amphibian spacer, and they are found in the same relative order. Therefore, this arrangement of elements probably is widespread in nature and has important functional consequences.
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Affiliation(s)
- C S Pikaard
- Basic Sciences Division, Hutchinson Cancer Research Center, Seattle, Washington 98104
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15
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Swisshelm K, Disteche CM, Thorvaldsen J, Nelson A, Salk D. Age-related increase in methylation of ribosomal genes and inactivation of chromosome-specific rRNA gene clusters in mouse. Mutat Res 1990; 237:131-46. [PMID: 1700292 DOI: 10.1016/0921-8734(90)90019-n] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
An age-related increase in DNA methylation of the multicopy 18S and 28S ribosomal RNA genes was found in CBA/Ca mice beginning between 6 and 18 months of age at the 5' end of these genes in liver, brain and spleen. The highest level of age-associated hypermethylation was mapped to the proximal 5' spacer domain. Silver staining of actively transcribing ribosomal genes in metaphase chromosomes from stimulated spleen cells provided cytological evidence that these mice have 3 rRNA cistrons located on chromosomes 15, 16, and 18. The ribosomal gene cluster located on chromosome 16 was preferentially inactivated in older animals. Exposure of spleen cells from older individuals to 5-azacytidine appeared to both reactivate ribosomal gene clusters and reduce rRNA gene methylation.
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Affiliation(s)
- K Swisshelm
- Department of Pathology, University of Washington, Seattle 98195
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16
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Oyan AM, Lillehaug JR. Structural changes in the ribosomal genes of immortalized and transformed mouse embryo C3H/10T1/2 cell lines. APMIS 1990; 98:212-20. [PMID: 1969285 DOI: 10.1111/j.1699-0463.1990.tb01024.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Comparative studies of DNA isolated from adult C3H mouse liver, immortalized mouse embryo cells (C3H/10T1/2 Cl 8) and the tumorigenic methylcholanthrene transformed C3H/10T1/2 Cl 16 cell line have been carried out in order to analyze possible structural changes in the ribosomal genes associated with the immortalization and tumorigenic transformation of mouse cells. Southern blot hybridization experiments revealed a mutation hotspot within repetitive sequences 13 kb upstream from the 18S rRNA genes in the non-transcribed spacer (NTS). Other DNA changes were localized near the initiation and termination regions of rRNA transcription. The differences found in the restriction maps of the 5'-region resided 5 to 6 kd upstream from the 18S 5'-end and the changes located in the 3'-end mapped approximately 5 kb downstream from the 28S 3'-end. Thus, oncogenic transformation of the C3H/10T1/2 Cl 8 cells by methylcholanthrene treatment was associated with stable genetic changes in the 18S rRNA gene. There was no evidence for rRNA gene amplification.
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Affiliation(s)
- A M Oyan
- Department of Biochemistry, University of Bergen, Norway
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17
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Kominami R. A sensitive assay for detecting mutations resulting from unequal homologous recombination without phenotypic selection. Mutat Res 1990; 243:133-9. [PMID: 2304482 DOI: 10.1016/0165-7992(90)90035-i] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Naturally occurring mutations are composed of a large number of mutations of many types that include mutations resulting from unequal homologus recombination between repetitive elements. The present paper describes a sensitive method for detecting such mutations without phenotypic selection. This system utilizes a tandemly arranged Vr repetitive sequence comprising 6000 copies in the mouse genome that is present in the spacer of the ribosomal RNA gene. For HincII digests of FM3A cell DNA, the Vr probe provides 4 major bands of 2.7 kb, 1.7 kb, 1.6 kb and 1.35 kb and several minor bands. Newly induced mutations due to unequal homologous recombination are observed as disappearance of the minor bands and appearance of extra bands. With this method a spontaneous mutation was detected in 14 cell clones randomly isolated after 60 days of continuous growth. Exposure to 4 micrograms/ml of N-methyl-N'-nitro-N-nitrosoguanidine for 2 h revealed 4 mutations in 11 clones examined. Culturing the cells after treatment in the presence of 12-O-tetradecanoylphorbol 13-acetate enhanced the frequency, yielding 6 mutations in 5 clones. The assay can skip phenotypic selection prior to analysis of DNA changes and hence provides a direct method for monitoring mutations resulting from homologous recombination in non-biased cell populations.
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Affiliation(s)
- R Kominami
- First Department of Biochemistry, Niigata University School of Medicine, Japan
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18
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Sylvester JE, Petersen R, Schmickel RD. Human ribosomal DNA: novel sequence organization in a 4.5-kb region upstream from the promoter. Gene 1989; 84:193-6. [PMID: 2606358 DOI: 10.1016/0378-1119(89)90155-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We have investigated the molecular organization of a portion of the human ribosomal nontranscribed spacer, by determining the sequence of 4580 bp of DNA upstream from the promoter. This region contains two pairs of oppositely oriented Alu elements, each of which is separated by dA (or dT)-rich stretches. One dT-rich region extends over 800 bp and is of variable length in different ribosomal genes. This and other portions of the spacer consist of simple sequences reiterated many times: for instance, (TACAA)26, (TTTC)117, and (TTGC)47. We are able to position the distal junction of the ribosomal repeat and sequences that have the propensity to form alternate structures, such as Z-DNA and bent DNA. A complex DNA methylation pattern and the influence on transcription of analogous regions in other species, suggest that this upstream area may be important to the expression of the human gene.
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Affiliation(s)
- J E Sylvester
- Department of Human Genetics, University of Pennsylvania, Philadelphia 19104
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19
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An RNA polymerase I promoter located in the CHO and mouse ribosomal DNA spacers: functional analysis and factor and sequence requirements. Mol Cell Biol 1989. [PMID: 2725513 DOI: 10.1128/mcb.9.4.1513] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report results of experiments in which we demonstrated the existence of a polymerase I promoter within the ribosomal DNA spacer upstream from the rRNA initiation site in Chinese hamsters and mice. Transcription of the CHO spacer promoter was achieved by the same protein factors, C and D, that catalyzed transcription of the gene promoter, and these factors bound stably to the CHO spacer promoter in a preinitiation complex, just as they did to the gene promoter. In contrast to the CHO spacer promoter, which was transcribed in vitro nearly as efficiently as the gene promoter, the mouse spacer promoter was far less active; this low activity was attributable to the fact that the mouse spacer promoter bound factor D inefficiently. It is striking that the active CHO spacer promoter violated the otherwise universal rule that metazoan RNA polymerase I promoters all have a G residue at position -16. Sequence comparisons also revealed a great similarity between the CHO and mouse spacer promoter regions, yet there was much less similarity between the flanking sequences. There was also only limited homology between the spacer and gene promoter regions, but despite this the two kinds of initiation regions were organized similarly, both consisting of an essential core promoter domain and a stimulatory domain that extended upstream to approximately residue -135. Evolutionary considerations argue strongly that the presence of ribosomal DNA spacer promoters offers a significant selective advantage.
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20
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Mitotic recombination is responsible for the loss of heterozygosity in cultured murine cell lines. Mol Cell Biol 1989. [PMID: 2725499 DOI: 10.1128/mcb.9.3.1284] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Heterozygous mammalian cell lines normally express both parental alleles at most autosomal loci. However, mutants can be isolated that fail to express one of the alleles. Using a murine pre-B cell line that is heterozygous for several loci on chromosome 12, including one encoding the cell surface antigen Ly-18, we found that one of the two Ly-18 antigenic forms was lost at a rate of 1.5 x 10(-5) per cell per generation. Molecular analysis revealed that a genetic marker distal to Ly-18 became homozygous. Analysis of the genotype of the mutants at the rDNA cluster, located close to the centromere, strongly suggests that the mutants arose by mitotic recombination within this multicopy locus.
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21
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Tower J, Henderson SL, Dougherty KM, Wejksnora PJ, Sollner-Webb B. An RNA polymerase I promoter located in the CHO and mouse ribosomal DNA spacers: functional analysis and factor and sequence requirements. Mol Cell Biol 1989; 9:1513-25. [PMID: 2725513 PMCID: PMC362568 DOI: 10.1128/mcb.9.4.1513-1525.1989] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We report results of experiments in which we demonstrated the existence of a polymerase I promoter within the ribosomal DNA spacer upstream from the rRNA initiation site in Chinese hamsters and mice. Transcription of the CHO spacer promoter was achieved by the same protein factors, C and D, that catalyzed transcription of the gene promoter, and these factors bound stably to the CHO spacer promoter in a preinitiation complex, just as they did to the gene promoter. In contrast to the CHO spacer promoter, which was transcribed in vitro nearly as efficiently as the gene promoter, the mouse spacer promoter was far less active; this low activity was attributable to the fact that the mouse spacer promoter bound factor D inefficiently. It is striking that the active CHO spacer promoter violated the otherwise universal rule that metazoan RNA polymerase I promoters all have a G residue at position -16. Sequence comparisons also revealed a great similarity between the CHO and mouse spacer promoter regions, yet there was much less similarity between the flanking sequences. There was also only limited homology between the spacer and gene promoter regions, but despite this the two kinds of initiation regions were organized similarly, both consisting of an essential core promoter domain and a stimulatory domain that extended upstream to approximately residue -135. Evolutionary considerations argue strongly that the presence of ribosomal DNA spacer promoters offers a significant selective advantage.
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Affiliation(s)
- J Tower
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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22
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Nelson FK, Frankel W, Rajan TV. Mitotic recombination is responsible for the loss of heterozygosity in cultured murine cell lines. Mol Cell Biol 1989; 9:1284-8. [PMID: 2725499 PMCID: PMC362720 DOI: 10.1128/mcb.9.3.1284-1288.1989] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Heterozygous mammalian cell lines normally express both parental alleles at most autosomal loci. However, mutants can be isolated that fail to express one of the alleles. Using a murine pre-B cell line that is heterozygous for several loci on chromosome 12, including one encoding the cell surface antigen Ly-18, we found that one of the two Ly-18 antigenic forms was lost at a rate of 1.5 x 10(-5) per cell per generation. Molecular analysis revealed that a genetic marker distal to Ly-18 became homozygous. Analysis of the genotype of the mutants at the rDNA cluster, located close to the centromere, strongly suggests that the mutants arose by mitotic recombination within this multicopy locus.
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Affiliation(s)
- F K Nelson
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York 10461
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23
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Taira T, Kato A, Tanifuji S. Difference between two major size classes of carrot rDNA repeating units is due to reiteration of sequences of about 460 bp in the large spacer. MOLECULAR & GENERAL GENETICS : MGG 1988; 213:170-4. [PMID: 2851705 DOI: 10.1007/bf00333416] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Based on the previous observation that the different regions between two major size classes of carrot rRNA genes are located in their large spacer, detailed physical maps of the spacer region were constructed by cloning, followed by restriction analysis. As a result, the different regions were restricted to BamHI segments of 1.3 kb and 1.8 kb. Sequence analysis of these segments revealed that the shorter one carried one truncated and two complete copies of about 460 bp of repetitious sequences, while the longer one contained one truncated and three full copies of the repetitious sequences. S1 nuclease mapping data suggest that either transcription initiation sites or processing sites of precursor rRNA are located in the repetitious sequence closest to the 18 S rRNA coding region.
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Affiliation(s)
- T Taira
- Department of Pharmacy, College of Science and Technology, Nihon University, Tokyo, Japan
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24
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Braaten DC, Thomas JR, Little RD, Dickson KR, Goldberg I, Schlessinger D, Ciccodicola A, D'Urso M. Locations and contexts of sequences that hybridize to poly(dG-dT).(dC-dA) in mammalian ribosomal DNAs and two X-linked genes. Nucleic Acids Res 1988; 16:865-81. [PMID: 3267216 PMCID: PMC334724 DOI: 10.1093/nar/16.3.865] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Sequences located several kilobases both 5' and 3' of the stably transcribed portion of several genes hybridize to radio-labeled pure fragments of the alternating sequence poly (dG-dT) (dC-dA) ["poly(GT)"]. The genes include the ribosomal DNA of mouse, rat, and human, and also human glucose-6-phosphate dehydrogenase (G6PD) and mouse hypoxanthine-guanine phosphoribosyl transferase (HPRT). HPRT has additional hybridizing sequences in introns. Fragments that include the hybridizing sequences and up to 300 bp of adjoining DNA show perfect runs of poly(GT) (greater than 30bp) in all but the human 5' region of rDNA, which shows a somewhat different alternating purine:pyrimidine sequence, poly(GTAT) (36bp). Within 150 bp of these sequences in various instances are found a number of other sequences reported to affect DNA conformation in model systems. Most marked is an enhancement of sequences matching at least 67% to the consensus binding sequence for topoisomerase II. Two to ten-fold less of such sequences were found in other sequenced portions of the nontranscribed spacer or in the transcribed portion of rDNA. The conservation of the locations of tracts of alternating purine:pyrimidine between evolutionarily diverse species is consistent with a possible functional role for these sequences.
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Affiliation(s)
- D C Braaten
- Department of Microbiology and Immunology, Washington University School of Medicine, St Louis, MO 63110
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25
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Dvorák J, Jue D, Lassner M. Homogenization of tandemly repeated nucleotide sequences by distance-dependent nucleotide sequence conversion. Genetics 1987; 116:487-98. [PMID: 3609728 PMCID: PMC1203160 DOI: 10.1093/genetics/116.3.487] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Previous work revealed that recurrent mutations (= mutation occurring more than once) in the tandemly repeated arrays present in nontranscribed spacers (NTS) of ribosomal RNA genes (rDNA) are clustered, i.e., they most frequently occur in repeats with adjacent or alternate distribution. A possible explanation is that the likelihood of heteroduplex formation, a prerequisite of gene conversion, decreases with the distance between repeats. To test this possibility, evolution of an array of 11 initially homogeneous repeats was computer simulated using three models, two assuming that the likelihood of heteroduplex formation decreases with increasing distance between the repeats and one assuming that it is constant. Patterns of mutation distribution obtained in computer simulations were compared with the distribution of mutations found in the repeated arrays in the NTS of seven rDNA clones. The patterns of mutations generated by the models assuming that the likelihood of heteroduplex formation decreases as distance between the repeats increases agreed with the patterns observed in rDNA; the patterns generated by the model assuming that the likelihood is independent of distance between repeats disagreed with the patterns observed in the rDNA clones. The topology of the heteroduplex formed between DNA in adjacent repeats predicts that the most frequently occurring conversions in the NTS repeated arrays will be shorter than the length of the repeat. The topology of the heteroduplex also predicts that if the heteroduplex leads to crossing over a circular repeat is excised. It is speculated that the circle can transpose or can be amplified via rolling circle replication and subsequently transpose. It is also shown that homogenization of the NTS repeated arrays proceeds at different rates in different species.
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26
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Fry M, Sharf R, Weisman-Shomer P, Evers PC, Loeb LA. The DNA sequence specificity of stimulation of DNA polymerases by factor D. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)47495-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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27
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Abstract
The transcriptional activity of spacer sequences flanking the rat 45S ribosomal DNA (rDNA) gene were studied. Nascent RNA labeled in in vitro nuclear run-on reactions hybridized with both 5' and 3' spacer regions. The highest level of hybridization was seen with an rDNA fragment containing tandem repeats of a 130-base-pair sequence upstream of the 45S rRNA initiation site. Synthesis of RNA transcripts homologous to this internally repetitious spacer region was insensitive to high levels of alpha-amanitin, suggesting that it is mediated by RNA polymerase I. Analysis of steady-state RNA showed that these transcripts were present at extremely low levels in vivo relative to precursor rRNA transcripts. In contrast, precursor and spacer run-on RNAs were synthesized at similar levels. This suggests that spacer transcripts are highly unstable in vivo; therefore, it may be the process of transcription rather than the presence of spacer transcripts that is functionally important. Transcription in this upstream rDNA region may be involved in regulation of 45S rRNA synthesis in rodents, as has been suggested previously for frog rRNA. In addition, the presence of transcriptional activity in other regions of the spacer suggests that some polymerase I molecules may transcribe through the spacer from one 45S gene to the next on rodent rDNA.
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28
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Harrington CA, Chikaraishi DM. Transcription of spacer sequences flanking the rat 45S ribosomal DNA gene. Mol Cell Biol 1987; 7:314-25. [PMID: 3031466 PMCID: PMC365071 DOI: 10.1128/mcb.7.1.314-325.1987] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The transcriptional activity of spacer sequences flanking the rat 45S ribosomal DNA (rDNA) gene were studied. Nascent RNA labeled in in vitro nuclear run-on reactions hybridized with both 5' and 3' spacer regions. The highest level of hybridization was seen with an rDNA fragment containing tandem repeats of a 130-base-pair sequence upstream of the 45S rRNA initiation site. Synthesis of RNA transcripts homologous to this internally repetitious spacer region was insensitive to high levels of alpha-amanitin, suggesting that it is mediated by RNA polymerase I. Analysis of steady-state RNA showed that these transcripts were present at extremely low levels in vivo relative to precursor rRNA transcripts. In contrast, precursor and spacer run-on RNAs were synthesized at similar levels. This suggests that spacer transcripts are highly unstable in vivo; therefore, it may be the process of transcription rather than the presence of spacer transcripts that is functionally important. Transcription in this upstream rDNA region may be involved in regulation of 45S rRNA synthesis in rodents, as has been suggested previously for frog rRNA. In addition, the presence of transcriptional activity in other regions of the spacer suggests that some polymerase I molecules may transcribe through the spacer from one 45S gene to the next on rodent rDNA.
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30
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McStay B, Reeder RH. A termination site for Xenopus RNA polymerase I also acts as an element of an adjacent promoter. Cell 1986; 47:913-20. [PMID: 3779846 DOI: 10.1016/0092-8674(86)90806-8] [Citation(s) in RCA: 129] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
On the Xenopus laevis ribosomal genes, RNA polymerase traverses the entire repeating unit of gene plus spacer and terminates just upstream of the next gene promoter. A conserved 7 bp element located at about -200 is an essential part of this terminator. In this paper we show that, in addition to its termination function, this same sequence motif acts as an upstream element of the adjacent promoter and appears to contribute to the long-term stability of the transcription complex.
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31
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Rogers SO, Honda S, Bendich AJ. Variation in the ribosomal RNA genes among individuals of Vicia faba. PLANT MOLECULAR BIOLOGY 1986; 6:339-345. [PMID: 24307384 DOI: 10.1007/bf00034941] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/1985] [Revised: 02/05/1986] [Accepted: 02/13/1986] [Indexed: 06/02/2023]
Abstract
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.
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Affiliation(s)
- S O Rogers
- Department of Botany, University of Washington, 98195, Seattle, WA, USA
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32
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Lopata MA, Cleveland DW, Sollner-Webb B. RNA polymerase specificity of mRNA production and enhancer action. Proc Natl Acad Sci U S A 1986; 83:6677-81. [PMID: 3462718 PMCID: PMC386572 DOI: 10.1073/pnas.83.18.6677] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
To examine the RNA polymerase (EC 2.7.7.6) specificity of RNA maturation/utilization and transcriptional enhancement, we constructed a chimeric plasmid (pPolI-CAT) in which a promoter for mouse rRNA gene transcription was placed adjacent the coding sequences for chloramphenicol acetyltransferase (CAT; EC 2.3.1.28). A number of other constructs, including plasmids also containing a murine sarcoma virus enhancer or lacking any natural eukaryotic promoter sequences, were also prepared. In apparent agreement with earlier conclusions that an RNA polymerase I transcript can act as a messenger RNA, transient transfection of mouse L cells with pPolI-CAT yielded both high levels of transcription from the RNA polymerase I promoter and enzymatically active CAT protein. However, further examination revealed that CAT protein is not translated from RNA that begins at the normal rRNA transcription initiation site. Polysomal RNA is devoid of such RNA and instead consists of CAT-encoding transcripts that begin elsewhere in the mouse ribosomal DNA (rDNA) region. Since transcription of these aberrant RNAs is stimulated by the addition of a murine sarcoma virus enhancer segment, they are probably transcribed by RNA polymerase II. Transcripts that map to the authentic rRNA start site are not similarly enhanced. Moreover, unlike the RNAs deriving from the rRNA initiation site, these aberrant RNAs are more stable and the level of translatable CAT transcripts is suppressed by inclusion of larger segments of the rDNA promoter regions. Fortuitously initiated mRNAs are also formed in the absence of any natural eukaryotic promoter sequence. From these data we conclude that there is no evidence that normal RNA polymerase I transcription yields functional mRNA and that transcriptional enhancement appears to be RNA polymerase specific.
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33
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Lassner M, Dvorak J. Preferential homogenization between adjacent and alternate subrepeats in wheat rDNA. Nucleic Acids Res 1986; 14:5499-512. [PMID: 3737408 PMCID: PMC311555 DOI: 10.1093/nar/14.13.5499] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
DNA from the "non-transcribed spacer" (NTS) of two wheat ribosomal RNA gene (rDNA) clones was sequenced. The regions flanking the internal subrepeat arrays are highly conserved between the two clones; the nucleotide sequence differ by less than one-half percent. In contrast, the consensus sequences of the subrepeats in the two arrays differ by three percent. Mutations unique to each array, yet found in more than one subrepeat of the array, are preferentially found in adjacent and alternate subrepeats. The similarity of the DNA sequences of the flanking regions is consistent with a model of homogenization among rDNA gene units by intergenic conversion. We propose that a different mechanism, preferential conversion between neighboring subrepeats, is largely responsible for the homogenization of subrepeats within an array.
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34
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Toloczyki C, Feix G. Occurrence of 9 homologous repeat units in the external spacer region of a nuclear maize rRNA gene unit. Nucleic Acids Res 1986; 14:4969-86. [PMID: 3014440 PMCID: PMC311504 DOI: 10.1093/nar/14.12.4969] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
A 14 kb maize DNA fragment carrying nuclear rRNA genes and spacer regions was isolated and characterised by restriction enzyme mapping. A complete 3020 bp long external spacer region was sequenced and revealed 9 tandemly arranged 200 bp long repeat units with high homology. The repeat units lie upstream from two prominent S1 mapping signals. The sequence of a typical repeat unit is compared to a corresponding 130 bp long wheat repeat unit. The possible functional relevance of the repeat units is discussed.
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35
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Yavachev LP, Georgiev OI, Braga EA, Avdonina TA, Bogomolova AE, Zhurkin VB, Nosikov VV, Hadjiolov AA. Nucleotide sequence analysis of the spacer regions flanking the rat rRNA transcription unit and identification of repetitive elements. Nucleic Acids Res 1986; 14:2799-810. [PMID: 3960734 PMCID: PMC339699 DOI: 10.1093/nar/14.6.2799] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We investigated the organization of the rat rDNA non-transcribed spacer (NTS) by determining the sequence of large NTS segments located upstream (2501 bp) and downstream (4025 bp) from the rRNA transcription unit. We identified four B2-like and two ID mobile elements. They may be grouped in three pairs with the members of each pair located in the upstream and downstream NTS. The ID sequences are identical to the consensus sequence, while the pairs of B2-like elements show 85% and 50/65% homology to the consensus B2 sequence. The proximal part of the downstream NTS contains a region of widely diverged SalI tandem repeats. A considerable part of the analyzed upstream and downstream NTS sequences is constituted by different types of simple sequences and long poly(purine) X poly(pyrimidine) tracts. These data show that the rat rDNA NTS regions flanking the rRNA transcription unit are characterized by a combination of short interspersed (B2-superfamily) and various simple sequences.
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36
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Dumenco VM, Wejksnora PJ. Characterization of the region around the start point of transcription of ribosomal RNA in the Chinese hamster. Gene 1986; 46:227-35. [PMID: 3803927 DOI: 10.1016/0378-1119(86)90407-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The initiation site for ribosomal RNA transcription in the Chinese hamster was identified and the sequence around and upstream determined. The start point region shows considerable homology with comparable regions in the mouse and rat. In the Chinese hamster, the region between bp -700 and -200 consists of imperfect repeats approximately 120-130 bp in length which are flanked by T-rich regions. The region within each repeat which is homologous with an adjacent repeat decreases in length as the start point is approached. The final promoter-proximal repeat preserves only an 11-bp region of the promoter-distal repeats. This short sequence, termed the repeat core, appears with a periodicity of about 120-130 bp in the Chinese hamster, and is conserved in both mouse and rat. In humans, a short repeated sequence occupies similar positions, suggesting that while complete 120-130-bp repeats are not a feature of all mammalian RNA polymerase I promoter-proximal r X DNA spacers, a short sequence repeating with approximate 120-130-bp periodicity may be such a feature.
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37
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Thomas JR, Bolla RI, Rumbyrt JS, Schlessinger D. DNase I-resistant nontranscribed spacer segments of mouse ribosomal DNA contain poly(dG-dT).poly(dA-dC). Proc Natl Acad Sci U S A 1985; 82:7595-8. [PMID: 3865181 PMCID: PMC391379 DOI: 10.1073/pnas.82.22.7595] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The nontranscribed spacer regions (NTS) that adjoin the coding portion of mouse ribosomal DNA are protected in nucleoli against exhaustive DNase I digestion. Since these sequences are degraded by the enzyme after they are extracted by phenol, the protection is suggested to result from the binding of specific proteins. The nucleolar structure would thus be organized to protect NTS sequences and expose the coding sequences for transcription. We show here that these protected sequences include tracts of poly(dG-dT).poly(dA-dC). We also report that these sequences are localized in regions flanking the rRNA transcription unit. These sequences can potentially form Z-DNA. The organized DNase I-resistant NTS structure in which they participate could be involved in structuring the nucleolus or in regulating transcription because poly(dG-dT).poly(dA-dC) sequences and portions of spacer rDNA can serve as transcriptional enhancer elements.
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38
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Vance VB, Thompson EA, Bowman LH. Transfection of mouse ribosomal DNA into rat cells: faithful transcription and processing. Nucleic Acids Res 1985; 13:7499-513. [PMID: 2997749 PMCID: PMC322058 DOI: 10.1093/nar/13.20.7499] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Truncated mouse ribosomal DNA (rDNA) genes were stably incorporated into rat HTC-5 cells by DNA-mediated cell transfection techniques. The mouse rDNA genes were accurately transcribed in these rat cells indicating that there is no absolute species specificity of rDNA transcription between mouse and rat. No more than 170 nucleotides of the 5' nontranscribed spacer was required for the accurate initiation of mouse rDNA transcription in rat cells. Further, the mouse transcripts were accurately cleaved at the 5' end of the 18S rRNA sequence, even though these transcripts contained neither the 3' end of mouse 18S rRNA nor any other downstream mouse sequences. Thus, cleavage at the 5' end of 18S rRNA is not dependent on long range interactions involving these downstream sequences.
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39
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Kato A, Yakura K, Tanifuji S. Repeated DNA sequences found in the large spacer of Vicia faba rDNA. ACTA ACUST UNITED AC 1985. [DOI: 10.1016/0167-4781(85)90069-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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40
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La Volpe A, Simeone A, D'Esposito M, Scotto L, Fidanza V, de Falco A, Boncinelli E. Molecular analysis of the heterogeneity region of the human ribosomal spacer. J Mol Biol 1985; 183:213-23. [PMID: 2989541 DOI: 10.1016/0022-2836(85)90214-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The human ribosomal non-transcribed spacers are 30 X 10(3) base-pairs (or 30 kb) in length with a limited length heterogeneity localized in a specific region downstream from the 3' end of the transcribed region. Total DNA digested with EcoRI and BamHI and hybridized with a probe containing the 3' end of the 28 S ribosomal RNA coding region shows four major bands of 3.9 kb, 4.6 kb, 5.4 kb and 6.2 kb. The 5.4 kb band is the most abundant in every individual, followed by the 4.6 kb band. The longest and the shortest size classes are less well-represented and may even be absent. Every individual shows his own pattern of relative abundance of non-transcribed spacer length classes that can be followed through generations. We decided to investigate the molecular structure of the heterogeneity region, in order to cast light onto the mechanisms underlying the origin and maintenance of this length heterogeneity. Pertinent spacer regions of eight ribosomal clones from two human genomic libraries were subcloned and analyzed by restriction mapping and nucleotide sequencing. In the minimal length class, there is a sequence of 700 base-pairs that appears to be tandemly duplicated once, twice or three times in the other length classes. This repeated DNA module contains a region consisting of repetitions of simple pyrimidine groups like C-T, C-T-T-T or C-C-C-T. DNA module repeats may differ by the length of this pyrimidine-rich region. However, these length variations are not continuous, as revealed by Southern transfer analysis of several individuals and different cloned gene units: instead, the repeated modules fall into two discrete length classes of about 700 base-pairs and 800 base-pairs. An imperfect duplication of a short sequence of 86/89 base-pairs is present at the boundary between the heterogeneity region and the upstream flanking region, representing a very ancient duplication event.
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41
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Grummt I, Skinner JA. Efficient transcription of a protein-coding gene from the RNA polymerase I promoter in transfected cells. Proc Natl Acad Sci U S A 1985; 82:722-6. [PMID: 3856225 PMCID: PMC397118 DOI: 10.1073/pnas.82.3.722] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The activity of the mouse ribosomal promoter was examined after fusion to the gene coding for chloramphenicol acetyltransferase (CAT) and transfection into mouse cells. Very little CAT enzyme but high levels of CAT-specific RNA correctly initiated at the ribosomal DNA start site were synthesized. The amount of specific transcripts was neither influenced by long stretches of upstream spacer sequences nor by the insertion of the Moloney murine sarcoma virus enhancer. The deletion mutant pMr delta-39, which has been shown to be fully active in vitro, exhibited a 90% decrease in template activity in vivo. A mutant in which 22 base pairs of ribosomal DNA (between positions -35 and -14) were substituted by foreign DNA sequences proved transcriptionally inactive. The fusion genes were only transcribed in mouse cells, indicating that species-specific transcription factors are involved in ribosomal promoter recognition.
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42
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43
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Length heterogeneity of the large spacer of Vicia faba rDNA is due to the differing number of a 325 bp repetitive sequence elements. ACTA ACUST UNITED AC 1984. [DOI: 10.1007/bf00382075] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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44
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Mandal RK. The organization and transcription of eukaryotic ribosomal RNA genes. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1984; 31:115-60. [PMID: 6397769 DOI: 10.1016/s0079-6603(08)60376-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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45
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Abstract
A detailed restriction map was determined for a 10.9 KB region that contains the initiation site for 45S pre-rRNA and the first 1.7 KB of the 18S rRNA coding region. When the restriction pattern of the cloned rDNA was compared with that of total rat DNA, the rDNA regions of both Sprague-Dawley and BD-9 rats were identical to each other and to that of the cloned rDNA. However, both strains exhibit a major polymorphism consisting of an insertion of 0.9 KB of DNA in the nontranscribed spacer between 0.29 KB and 1.8 KB upstream from the 45S RNA initiation site. This region consists of tandem repeats approximately 130 base pairs in length. These repeats contain large poly T tracts and are similar in sequence to analogous elements 5' to the origin of mouse rRNA transcription. Regions containing highly repetitious DNA sequences were located at sites 2.8 KB and 4.3 KB upstream from the initiation site. The repetitive sequence at 2.8 KB from the initiation site anneal to a known Alu-equivalent type 2 sequence derived from the second intron of the rat growth hormone gene.
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