1
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Robinett CC, Dunaway M. Modeling transcriptional regulation using microinjection into Xenopus oocytes. Methods 1999; 17:151-60. [PMID: 10075893 DOI: 10.1006/meth.1998.0726] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Transcriptional regulation is a complex process that requires cooperation between specific DNA sequence elements, the DNA-binding proteins that bind to these sequences, the general transcriptional machinery, and chromatin. Oocyte microinjection offers a technique to study the integrated transcription process while still providing the opportunity to experimentally perturb this process. We describe here techniques for manipulating DNA templates and the protein complement of the oocyte to study multiple facets of transcriptional regulation. We present sample results showing that the GAL4-VP16 fusion activator is sensitive to distance in constructs containing only a minimal promoter, but can activate transcription at greater distances when proximal promoter elements are present.
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Affiliation(s)
- C C Robinett
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
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2
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Osheim YN, Mougey EB, Windle J, Anderson M, O'Reilly M, Miller OL, Beyer A, Sollner-Webb B. Metazoan rDNA enhancer acts by making more genes transcriptionally active. J Cell Biol 1996; 133:943-54. [PMID: 8655586 PMCID: PMC2120851 DOI: 10.1083/jcb.133.5.943] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Enhancers could, in principle, function by increasing the rate of reinitiation on individual adjacent active promoters or by increasing the probability that an adjacent promoter is activated for transcription. We have addressed this issue for the repetitive metazoan rDNA enhancer by microinjecting Xenopus oocytes with enhancer-less and enhancer-bearing genes and determining by EM the frequency that each gene type forms active transcription units and their transcript density. We use conditions where transcription requires the normal rDNA promoter and is stimulated 30-50-fold by the enhancer. (In contrast, at saturating template conditions as used in previous EM studies, an aberrant mode of transcription is activated that is not affected by the rDNA enhancer or by the generally recognized rDNA promoter). The active transcription units on enhancer-less genes are found to be as densely packed with nascent transcripts and polymerases as those on enhancer-bearing genes and on the endogenous rRNA genes. Significantly, the enhancer-bearing genes are approximately 30-50-fold more likely to form such active transcription units than enhancer-less genes, consistent with their amounts of transcript. Complementary studies confirm that the enhancer does not affect elongation rate, the stability of the transcription complex, or transcript half-life. These data demonstrate that the repetitive metazoan rDNA enhancer causes more genes to be actively transcribed and does not alter the reinitiation rate on individual active genes.
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Affiliation(s)
- Y N Osheim
- Department of Microbiology, University of Virginia School of Medicine, Charlottesville, 22908, USA
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3
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Paalman MH, Henderson SL, Sollner-Webb B. Stimulation of the mouse rRNA gene promoter by a distal spacer promoter. Mol Cell Biol 1995; 15:4648-56. [PMID: 7623857 PMCID: PMC230706 DOI: 10.1128/mcb.15.8.4648] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
We show that the mouse ribosomal DNA (rDNA) spacer promoter acts in vivo to stimulate transcription from a downstream rRNA gene promoter. This augmentation of mammalian RNA polymerase I transcription is observed in transient-transfection experiments with three different rodent cell lines, under noncompetitive as well as competitive transcription conditions, over a wide range of template concentrations, whether or not the enhancer repeats alone stimulate or repress expression from the downstream gene promoter. Stimulation of gene promoter transcription by the spacer promoter requires the rDNA enhancer sequences to be present between the spacer promoter and gene promoter and to be oriented as in native rDNA. Stimulation also requires that the spacer promoter be oriented toward the enhancer and gene promoter. However, stimulation does not correlate with transcription from the spacer promoter because the level of stimulation is not altered by either insertion of a functional mouse RNA polymerase I transcriptional terminator between the spacer promoter and enhancer or replacement with a much more active heterologous polymerase I promoter. Further analysis with a series of mutated spacer promoters indicates that the stimulatory activity does not reside in the major promoter domains but requires the central region of the promoter that has been correlated with enhancer responsiveness in vivo.
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Affiliation(s)
- M H Paalman
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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4
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Moss T, Stefanovsky VY. Promotion and regulation of ribosomal transcription in eukaryotes by RNA polymerase I. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1995; 50:25-66. [PMID: 7754036 DOI: 10.1016/s0079-6603(08)60810-7] [Citation(s) in RCA: 154] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- T Moss
- Cancer Research Centre, Laval University, Hôtel-Dieu de Québec, Canada
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5
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Lakshmikumaran M, Negi MS. Structural analysis of two length variants of the rDNA intergenic spacer from Eruca sativa. PLANT MOLECULAR BIOLOGY 1994; 24:915-927. [PMID: 8204828 DOI: 10.1007/bf00014445] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Restriction enzyme analysis of the rRNA genes of Eruca sativa indicated the presence of many length variants within a single plant and also between different cultivars which is unusual for most crucifers studied so far. Two length variants of the rDNA intergenic spacer (IGS) from a single individual E. sativa (cv. Itsa) plant were cloned and characterized. The complete nucleotide sequences of both the variants (3 kb and 4 kb) were determined. The intergenic spacer contains three families of tandemly repeated DNA sequences denoted as A, B and C. However, the long (4 kb) variant shows the presence of an additional repeat, denoted as D, which is a duplication of a 224 bp sequence just upstream of the putative transcription initiation site. Repeat units belonging to the three different families (A, B and C) were in the size range of 22 to 30 bp. Such short repeat elements are present in the IGS of most of the crucifers analysed so far. Sequence analysis of the variants (3 kb and 4 kb) revealed that the length heterogeneity of the spacer is located at three different regions and is due to the varying copy numbers of repeat units belonging to families A and B. Length variation of the spacer is also due to the presence of a large duplication (D repeats) in the 4 kb variant which is absent in the 3 kb variant. The putative transcription initiation site was identified by comparisons with the rDNA sequences from other plant species.
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Affiliation(s)
- M Lakshmikumaran
- Department of Biotechnology, Tata Energy Research Institute, New Delhi, India
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6
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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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7
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8
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Sollner-Webb B, Pape L, Ryan K, Mougey EB, Poretta R, Nikolov E, Paalman MH, Lazdins I, Martin C. Expression of mouse and frog rRNA genes: transcription and processing. Mol Cell Biochem 1991; 104:149-54. [PMID: 1921993 DOI: 10.1007/bf00229814] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
This article summarizes a number of lines of investigation of rRNA gene expression that are ongoing in the laboratory. These studies focus on mouse and frog, two distant vertebrate species. One major conclusion is that the basic properties of rRNA gene expression appear remarkably well conserved in evolution, with only relatively minor perturbations between frog and mouse, contrary to the common interpretation of the species-selectively between mouse and human rDNA transcription (e.g., 1). This is true both for the process of rDNA transcription and for the subsequent rRNA processing event.
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Affiliation(s)
- B Sollner-Webb
- Johns Hopkins University, School of Medicine, Baltimore, Maryland 21205
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9
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The mouse ribosomal DNA promoter has more stringent requirements in vivo than in vitro. Mol Cell Biol 1990. [PMID: 2388633 DOI: 10.1128/mcb.10.9.4970] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Using mouse ribosomal DNA templates bearing polymerase I terminators to prevent transcriptional interference (S. L. Henderson, K. Ryan, and B. Sollner-Webb, Genes Dev. 3:212-223, 1989) and facilitate promoter analysis in intact cells, we demonstrate that a -140 promoter domain (as well as the core region) is essential for appreciable levels of initiation in vivo. This in vivo polymerase I promoter can also be detected in vitro but only under very stringent conditions.
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10
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Henderson SL, Sollner-Webb B. The mouse ribosomal DNA promoter has more stringent requirements in vivo than in vitro. Mol Cell Biol 1990; 10:4970-3. [PMID: 2388633 PMCID: PMC361124 DOI: 10.1128/mcb.10.9.4970-4973.1990] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Using mouse ribosomal DNA templates bearing polymerase I terminators to prevent transcriptional interference (S. L. Henderson, K. Ryan, and B. Sollner-Webb, Genes Dev. 3:212-223, 1989) and facilitate promoter analysis in intact cells, we demonstrate that a -140 promoter domain (as well as the core region) is essential for appreciable levels of initiation in vivo. This in vivo polymerase I promoter can also be detected in vitro but only under very stringent conditions.
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Affiliation(s)
- S L Henderson
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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11
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McStay B, Reeder RH. An RNA polymerase I termination site can stimulate the adjacent ribosomal gene promoter by two distinct mechanisms in Xenopus laevis. Genes Dev 1990; 4:1240-51. [PMID: 2210376 DOI: 10.1101/gad.4.7.1240] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
On the ribosomal genes of Xenopus laevis, the T3 terminator is located approximately 60 bp upstream of the 5' boundary of the gene promoter. We have shown previously that mutation of the terminator simultaneously abolishes termination and impairs initiation by RNA polymerase I. Here, we show that the terminator influences the promoter by two distinct mechanisms. In one mechanism the terminator protects the promoter by preventing polymerase from reading through the initiation complex. In a second mechanism, the terminator interacts directly with the promoter, whether or not termination occurs. This positive interaction requires precise positioning of the terminator relative to the promoter and is sensitive to movement of the terminator by as little as 1 or 2 bp. We conclude that the terminator and promoter interact as one interdependent complex.
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Affiliation(s)
- B McStay
- Basic Sciences Division, Hutchinson Cancer Research Center, Seattle, Washington 98104
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12
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Piller KJ, Baerson SR, Polans NO, Kaufman LS. Structural analysis of the short length ribosomal DNA variant from Pisum sativum L. cv. Alaska. Nucleic Acids Res 1990; 18:3135-45. [PMID: 1972558 PMCID: PMC330916 DOI: 10.1093/nar/18.11.3135] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The genomic clone, RRNpss1, representing the short ribosomal DNA length variant in Pisum sativum L. cv. Alaska, has been isolated and the 2859 bp intergenic spacer, along with the 25S rRNA 3' border and 18S rRNA 5' border, has been sequenced. The intergenic spacer contains nine tandem repeats, approximately 180 bp in length, which show greater than 80% sequence homology to each other. The RNA polymerase I transcription start site and a processing site, located 776 bp and 536 bp upstream of the 5' end of 18S rRNA, respectively, have been determined using S1 analysis. The region surrounding the +1 site shows strong homology between the positions -6 to +10 to the rDNA sites of initiation in radish, maize, and wheat. The sequence CATGCAAA is located 19 bp upstream of the site of initiation, and appears once within each subrepeat and twice more between the end of the subrepeat array and the site of initiation. A previously characterized HpaII site which shows developmental regulation of methylation is located 31 bp downstream of the site of initiation. Using RFLP linkage analysis, the short rDNA length variant of cv. Alaska is assigned to Chromosome 4 where it is genetically independent of the long rDNA length variant which is putatively assigned to Chromosome 7.
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MESH Headings
- Base Sequence
- Chromosomes, Human, Pair 4
- Cloning, Molecular
- DNA, Ribosomal/genetics
- Fabaceae/genetics
- Genetic Linkage
- Humans
- Methylation
- Molecular Sequence Data
- Nucleic Acid Conformation
- Plants, Medicinal
- Polymorphism, Restriction Fragment Length
- RNA Polymerase I/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 18S/genetics
- Repetitive Sequences, Nucleic Acid
- Restriction Mapping
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- K J Piller
- Department of Biological Sciences, University of Illinois, Chicago 60680
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13
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Bell SP, Jantzen HM, Tjian R. Assembly of alternative multiprotein complexes directs rRNA promoter selectivity. Genes Dev 1990; 4:943-54. [PMID: 2384215 DOI: 10.1101/gad.4.6.943] [Citation(s) in RCA: 133] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
How can trans-activators with the same DNA binding specificity direct different transcriptional programs? The rRNA transcriptional apparatus offers a useful model system to address this question and to dissect the mechanisms that generate alternative transcription complexes. Here, we compare the mouse and human transcription factors that govern species-specific RNA polymerase I promoter recognition. We find that both human and mouse rRNA transcription is mediated by a specific multiprotein complex. One component of this complex is the DNA-binding transcription factor, UBF. Paradoxically, human and mouse UBF display identical DNA binding specificities even though transcription of rRNA is species specific. Promoter selectivity is conferred by a second essential factor, SL1, which, for humans, does not bind DNA independently but, instead, cooperates with UBF in the formation of high-affinity DNA-binding complexes. In contrast, mouse SL1 can selectively interact with DNA in the absence of UBF. Reconstituted transcription experiments establish that UBF and RNA polymerase I from the two species are functionally interchangeable, whereas mouse and human SL1 exhibit distinct DNA binding and transcription activities. Together, these results suggest a critical role for a specific multiprotein assembly in RNA polymerase I promoter recognition and reveal distinct mechanisms through which such complexes can generate functional diversity.
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Affiliation(s)
- S P Bell
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, University of California, Berkeley 94720
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14
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Perry KL, Palukaitis P. Transcription of tomato ribosomal DNA and the organization of the intergenic spacer. MOLECULAR & GENERAL GENETICS : MGG 1990; 221:103-12. [PMID: 2325628 DOI: 10.1007/bf00280374] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The organization of the intergenic spacer of a 9.04 kb tomato ribosomal RNA gene (rDNA) was determined. The 3258 bp spacer contains two major repeat elements enclosing a region which includes 351 bp of an 81.8% A --T rich sequence. A block of nine 53 bp repeats begins 388 bp downstream from the 3' end of the 25S rRNA. The A--T rich domain is followed by a block of six 141 bp repeats terminating 818 bp upstream from the 5' end of the 18S rRNA. Major pre-rRNAs of 7.6 and 6.5 kb were observed by Northern hybridization analysis. The 5' termini of these RNAs were identified through combined S1 nuclease and primer extension analyses. The 7.6 kb RNA is likely to be the primary transcript; its 5' terminus lies within a sequence motif. TATA(R)TA(N)GGG, conserved at the termini of transcripts mapped in three other plant species. The 6.5 kb RNA is interpreted as a 5' end processed transcript derived from the 7.6 kb RNA. Comparative analysis of transcribed sequences revealed a 25 bp domain of the intergenic spacer which is relatively conserved among five plant species. The conservation of spacer sequences in plants is in contrast to the extensive sequence divergence of the intergenic spacer in other non-plant systems and suggests a conserved function directed by these sequences.
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Affiliation(s)
- K L Perry
- Department of Plant Pathology, Cornell University, Ithaca, NY 14853-5908
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15
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The Xenopus ribosomal DNA 60- and 81-base-pair repeats are position-dependent enhancers that function at the establishment of the preinitiation complex: analysis in vivo and in an enhancer-responsive in vitro system. Mol Cell Biol 1990. [PMID: 2601710 DOI: 10.1128/mcb.9.11.5093] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Although it is generally believed that the 60- and 81-base-pair (60/81-bp) repeats of the Xenopus laevis ribosomal DNA (rDNA) spacer are position-independent transcriptional enhancers, this has not been shown directly. We have now developed a critical assay which proves that the 60/81-bp repeats do, in fact, stimulate transcription from promoters in cis and that they function in both orientations and when up to 1 kilobase pair from the initiation site. However, contrary to the widely accepted view, these elements are found to be highly position dependent, for they have no net effect when downstream of the initiation site within the transcribed region and they behave as transcriptional silencers of promoters in cis when moved greater than 2 kilobase pairs upstream of the initiation site. The 60/81-bp elements therefore are position-dependent 5' enhancers. We also found that this rDNA enhancer was polymerase I specific and that it was composed of duplicated, individually functional elements. Finally, we report an in vitro system that reproduces both cis enhancement and trans competition by the 60/81-bp repeats. Sequential-addition studies in this system demonstrated that the rDNA enhancer functions in trans at or before establishment of the stable transcription complex, not subsequently at each round of transcription.
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16
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Firek S, Read C, Smith DR, Moss T. Point mutation analysis of the Xenopus laevis RNA polymerase I core promoter. Nucleic Acids Res 1990; 18:105-9. [PMID: 2308816 PMCID: PMC330209 DOI: 10.1093/nar/18.1.105] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The core region of the Xenopus laevis pre-ribosomal RNA promoter was subjected to point mutation analysis. A total of 27 point mutants within a 78 base pair region from -64 to +14, (relative to the start of transcription at +1), were assayed by oocyte microinjection. The results locate the 3' boundary of the core promoter at +4 and the 5' boundary at between -33 and -39 and suggest that this region of the Xenopus promoter is generally similar in organisation to mammalian core promoters. In particular, the conserved guanidine nucleotides at -7 and -16 are clearly essential for promoter function. The data suggest that interactions between the transcription machinery and the promoter occur in four distinct regions around +2 to +4, -7, -17 to -20 and -28 to -33. This particular periodicity of functionally important nucleotides is consistent with a model in which all protein-DNA interactions take place from predominantly one side of the DNA helix.
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Affiliation(s)
- S Firek
- Biophysics Laboratories, Portsmouth Polytechnic, UK
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17
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Pape LK, Windle JJ, Sollner-Webb B. Half helical turn spacing changes convert a frog into a mouse rDNA promoter: a distant upstream domain determines the helix face of the initiation site. Genes Dev 1990; 4:52-62. [PMID: 2155160 DOI: 10.1101/gad.4.1.52] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Transcription of frog rDNA by mouse cell factors is the only documented exception to the observed species selectivity of rRNA gene expression. This heterologous transcription is authentic in that it uses the normal frog upstream and core promoter domains, as well as the normal mouse polymerase I transcription factors, but it initiates at residue -4. We now show that by introducing an insertion or deletion of approximately one-half helical turn anywhere within the 90-bp region between the upstream and core promoter domains, the initiation site moves to residue +1. Promoters bearing spacing changes of approximately one or two full helix turns do not initiate at residue +1, whereas a promoter with a one and one-half-turn helical turn spacing change again supports initiation at residue +1. Thus, the position of the upstream domain of the frog promoter shows a stereo-specific requirement relative to the core promoter domain and dictates the face of the DNA helix on which transcription initiates, 140 bp away. In contrast, relative to the core promoter domain, initiation can occur on either side of the DNA helix. Furthermore, the striking observation that several frog half helical turn spacing change mutants are stronger templates with the mouse factors than the homologous mouse rDNA suggests that the polymerase I transcriptional machinery of even distantly related species is far more similar than generally envisioned.
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Affiliation(s)
- L K Pape
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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18
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The Molecular Basis of Variation Affecting Gene Expression: Evidence from Studies on the Ribosmal RNA Gene Loci of Wheat. ACTA ACUST UNITED AC 1990. [DOI: 10.1007/978-1-4684-7047-5_22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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19
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Musters W, Knol J, Maas P, Dekker AF, van Heerikhuizen H, Planta RJ. Linker scanning of the yeast RNA polymerase I promoter. Nucleic Acids Res 1989; 17:9661-78. [PMID: 2690005 PMCID: PMC335205 DOI: 10.1093/nar/17.23.9661] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
To define the RNA polymerase I promoter in the rDNA of Saccharomyces cerevisiae more precisely, we have constructed a series of 5'- and 3'-deletion mutants in a novel, plasmid-borne rDNA minigene, that also contains the transcriptional enhancer. Our data show that the Pol I promoter, in this context, extends from position -155 to +27, with 5'-deletions up to -134 and 3'-deletions up to -2 removing essential sequence information. To investigate the internal organization of the yeast Pol I promoter, linker scanning mutants were constructed, that traverse the Pol I promoter region and comprise between 5 and 12 clustered point mutations. Analysis of minigene transcription in yeast cells transformed with these plasmids demonstrates that the pol I promoter consists of three domains. Mutations in Domain I (from position -28 to +8) and Domain II (-70 to -51) drastically reduce promoter activity, whereas clustered point mutations in Domain III (starts at position -146 and presumably extends to position -76) appear to have less effect. Furthermore, the insertion of 4 nt between Domains I and II diminishes minigene transcription, indicating that the relative positions of these domains is essential.
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Affiliation(s)
- W Musters
- Biochemisch Laboratorium, Vrije Universiteit, Amsterdam, The Netherlands
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20
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Bell SP, Pikaard CS, Reeder RH, Tjian R. Molecular mechanisms governing species-specific transcription of ribosomal RNA. Cell 1989; 59:489-97. [PMID: 2805069 DOI: 10.1016/0092-8674(89)90032-9] [Citation(s) in RCA: 120] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
An unusual property of ribosomal RNA transcription is the species specificity of promoter recognition. Unexpectedly, the sequence-specific RNA pol I transcription factors hUBF and xUBF, isolated from human and Xenopus cells, respectively, recognize the same DNA sequence elements. Despite this similarity in DNA binding activity, neither factor will functionally substitute for the other in reconstituted transcription assays, suggesting that the specificity of protein-DNA interactions cannot account for the species-specific activation of transcription by hUBF and xUBF. Interestingly, we find that hUBF and xUBF form distinctly different complexes with human SL1 at both the human and Xenopus promoters. Together these results strongly implicate specific protein-protein interactions between transcription factors as an important determinant of promoter selectivity and species specificity.
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Affiliation(s)
- S P Bell
- Howard Hughes Medical Institute, Department of Biochemistry, University of California, Berkeley 94720
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21
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Pape LK, Windle JJ, Mougey EB, Sollner-Webb B. The Xenopus ribosomal DNA 60- and 81-base-pair repeats are position-dependent enhancers that function at the establishment of the preinitiation complex: analysis in vivo and in an enhancer-responsive in vitro system. Mol Cell Biol 1989; 9:5093-104. [PMID: 2601710 PMCID: PMC363661 DOI: 10.1128/mcb.9.11.5093-5104.1989] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Although it is generally believed that the 60- and 81-base-pair (60/81-bp) repeats of the Xenopus laevis ribosomal DNA (rDNA) spacer are position-independent transcriptional enhancers, this has not been shown directly. We have now developed a critical assay which proves that the 60/81-bp repeats do, in fact, stimulate transcription from promoters in cis and that they function in both orientations and when up to 1 kilobase pair from the initiation site. However, contrary to the widely accepted view, these elements are found to be highly position dependent, for they have no net effect when downstream of the initiation site within the transcribed region and they behave as transcriptional silencers of promoters in cis when moved greater than 2 kilobase pairs upstream of the initiation site. The 60/81-bp elements therefore are position-dependent 5' enhancers. We also found that this rDNA enhancer was polymerase I specific and that it was composed of duplicated, individually functional elements. Finally, we report an in vitro system that reproduces both cis enhancement and trans competition by the 60/81-bp repeats. Sequential-addition studies in this system demonstrated that the rDNA enhancer functions in trans at or before establishment of the stable transcription complex, not subsequently at each round of transcription.
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Affiliation(s)
- L K Pape
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185
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22
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Dunaway M. A transcription factor, TFIS, interacts with both the promoter and enhancer of the Xenopus rRNA genes. Genes Dev 1989; 3:1768-78. [PMID: 2606346 DOI: 10.1101/gad.3.11.1768] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
An activity that binds sequence specifically to the enhancer of the Xenopus laevis rRNA genes has been highly purified. This activity stimulates transcription of coinjected rRNA templates in Xenopus oocytes and has been named TFIS, as it binds to the enhancer sequences within the intergenic spacer. In addition to its enhancer binding activity, TFIS binds to the promoter of the Xenopus rRNA genes, as predicted by models for enhancer action. DNase I footprinting on promoter mutants suggests that there are three TFIS-binding sites between -70 and -240 and that TFIS binding is unusually tolerant of mutations. The large region of protein-DNA interaction and the occurrence of DNase I enhancements at integral multiples of the helical repeat are consistent with the promoter and enhancer DNA wrapping around TFIS.
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Affiliation(s)
- M Dunaway
- Department of Molecular and Cell Biology, University of California, Berkeley 94720
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23
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Structural determinant of the species-specific transcription of the mouse rRNA gene promoter. Mol Cell Biol 1989. [PMID: 2927396 DOI: 10.1128/mcb.9.1.349] [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
Mammalian ribosomal DNA (rDNA) transcription has a certain species specificity such that, both in vivo and in vitro, human rDNA cannot be transcribed by mouse machinery and vice versa. This is due to a species-dependent transcription factor, TFID (Y. Mishima, I. Financsek, R. Kominami, and M. Muramatsu, Nucleic Acids Res. 10:6659-6670, 1982). On the basis of the information obtained from 5' and 3' substitution mutants, we prepared a chimeric gene in which the mouse sequence from positions -32 to -14 was inserted into the corresponding location of the human rDNA promoter. The chimeric gene could be transcribed by mouse extracts nearly as efficiently as the wild-type mouse promoter. The chimeric gene could also sequester transcription factor TFID at an efficiency similar to that for the mouse promoter. Partially purified mouse TFID that could not protect the human rDNA promoter against DNase I produced a clear footprint on this chimeric gene that was similar to that on mouse rDNA promoter. The basic structure of the mouse rDNA core promoter is discussed in relation to the interaction with TFID.
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24
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Specific Binding of Nuclear Proteins to the Promoter Region of a Maize Nuclear rRNA Gene Unit. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)94211-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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25
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Safrany G, Tanaka N, Kishimoto T, Ishikawa Y, Kato H, Kominami R, Muramatsu M. Structural determinant of the species-specific transcription of the mouse rRNA gene promoter. Mol Cell Biol 1989; 9:349-53. [PMID: 2927396 PMCID: PMC362182 DOI: 10.1128/mcb.9.1.349-353.1989] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Mammalian ribosomal DNA (rDNA) transcription has a certain species specificity such that, both in vivo and in vitro, human rDNA cannot be transcribed by mouse machinery and vice versa. This is due to a species-dependent transcription factor, TFID (Y. Mishima, I. Financsek, R. Kominami, and M. Muramatsu, Nucleic Acids Res. 10:6659-6670, 1982). On the basis of the information obtained from 5' and 3' substitution mutants, we prepared a chimeric gene in which the mouse sequence from positions -32 to -14 was inserted into the corresponding location of the human rDNA promoter. The chimeric gene could be transcribed by mouse extracts nearly as efficiently as the wild-type mouse promoter. The chimeric gene could also sequester transcription factor TFID at an efficiency similar to that for the mouse promoter. Partially purified mouse TFID that could not protect the human rDNA promoter against DNase I produced a clear footprint on this chimeric gene that was similar to that on mouse rDNA promoter. The basic structure of the mouse rDNA core promoter is discussed in relation to the interaction with TFID.
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Affiliation(s)
- G Safrany
- Department of Biochemistry, University of Tokyo Faculty of Medicine, Japan
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26
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Grimaldi G, Di Nocera PP. Multiple repeated units in Drosophila melanogaster ribosomal DNA spacer stimulate rRNA precursor transcription. Proc Natl Acad Sci U S A 1988; 85:5502-6. [PMID: 2840664 PMCID: PMC281785 DOI: 10.1073/pnas.85.15.5502] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Drosophila melanogaster ribosomal DNA (rDNA) transcriptional units are separated by nontranscribed spacer (NTS) segments consisting of tandemly arranged repeats 95, 330, and 240 base pairs long. NTS sequences stimulate transcription from the rRNA precursor (pre-rRNA) promoter. Primer extension analysis of RNA from cells cotransfected with plasmids carrying NTS sequences of various lengths shows that the activity of the pre-rRNA promoter is directly correlated with the number of 240-base-pair repeats; NTS sequences upstream of these units also stimulate pre-rRNA transcription. The NTS effect might depend upon transcription from duplicated promoters present within the 240- and 330-base-pair repeats. The strength of the pre-RNA promoter correlates in each construct with the level of spacer transcription. The action of spacer sequences, although able to take place over a large distance, is not independent of orientation: stimulation of pre-rRNA transcription is abolished in plasmids carrying inverted NTS segments. Removal of a putative transcription termination site located upstream of the pre-rRNA promoter has no effect on pre-rRNA initiation nor does it substantially alter spacer enhancement.
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Affiliation(s)
- G Grimaldi
- European Molecular Biology Laboratory, Heidelberg, Federal Republic of Germany
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27
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Slavicek JM, Krider HM. The organization and composition of the ribosomal RNA gene non-transcribed spacer of D. busckii is unique among the drosophilids. Genet Res (Camb) 1987; 50:173-80. [PMID: 3443288 DOI: 10.1017/s0016672300023661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
SummarySeveral ribosomal RNA (rRNA) genes fromD. busckiiwere cloned and characterized. The prominent repeat classes have lengths of 12·8 and 13·6 kb and lack 28S introns. rRNA genes were cloned containing 28S insertions which exhibit heterogeneity in size and sequence. The non-transcribed spacer (NTS) contains two regions composed of different repeated sequences that exhibit pronounced instability in HB 101. NTS region II, centrally located within the NTS, contains predominately 11 or 16HincII generated 160 bp repeats. NTS region III, next to the 18S gene, contains repeats that are variable in number, and are either heterogeneous in length or are dispersed within unique sequences. The organization and composition of the rRNA gene NTS ofD. busckiiis different in comparison to the NTSs of other drosophilids. In addition, the pronounced instability of two different NTS regions is unique in comparison to all other cloned rRNA genes.
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28
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Culotta VC, Wilkinson JK, Sollner-Webb B. Mouse and frog violate the paradigm of species-specific transcription of ribosomal RNA genes. Proc Natl Acad Sci U S A 1987; 84:7498-502. [PMID: 3478707 PMCID: PMC299323 DOI: 10.1073/pnas.84.21.7498] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Transcription of ribosomal RNA genes by RNA polymerase I is generally accepted as being highly species specific, a conclusion based on numerous reports that rRNA genes of one species are not transcribed by factors of even closely related species. It thus was striking to find that cloned rDNA from the frog Xenopus laevis is specifically transcribed in extracts prepared from mouse cells. The data in this paper demonstrate that this heterologous transcription is due to a normal initiation process and not to a fortuitous event. Transcription of Xenopus rDNA in the mouse cell extract is directed by the same large promoter (residue-141 to +6) that is utilized to promote the synthesis of frog rRNA in homologous Xenopus systems. Moreover, the same factors of the mouse cell extract that transcribe the homologous mouse rDNA also catalyze transcription from the X. laevis rDNA promoter. We conclude that polymerase I transcriptional machinery does not evolve as rapidly as prior studies would suggest.
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Affiliation(s)
- V C Culotta
- John Hopkins School of Medicine, Department of Biological Chemistry, Baltimore, MD 21205
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29
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Reeder RH, Pennock D, McStay B, Roan J, Tolentino E, Walker P. Linker scanner mutagenesis of the Xenopus laevis ribosomal gene promoter. Nucleic Acids Res 1987; 15:7429-41. [PMID: 3658698 PMCID: PMC306258 DOI: 10.1093/nar/15.18.7429] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We have assayed a series of linker scanner mutants which cover the Xenopus laevis ribosomal gene promoter at approximately ten base pair intervals. All of these mutations adversely affect promoter activity with the exception of one mutation which stimulates activity. Thus, none are neutral. We show that most of the mutations can be partially rescued by ligating a block of enhancer elements upstream of the promoter. In addition, we have made extracts from liver nuclei which produce DNaseI protection footprints over the promoter. Analysis of both strands reveals a prominent footprinting domain from about -5 to -30. However, lesser changes in the digestion pattern are detected over most of the promoter. Previously published analyses have suggested that this promoter might be composed of three functional domains. The experiments presented here suggest that either 1) the three putative domains are so closely arranged that the boundaries are difficult to discern, or 2) the situation is more complex.
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Affiliation(s)
- R H Reeder
- Hutchinson Cancer Research Center, Seattle, WA 98104
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30
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Briner G, Müller E, Neuhaus H, Back E, Müller F, Tobler H. Localization of the in vivo and in vitro transcription initiation site and comparative analysis of the flanking sequences in the two main size classes of Ascaris lumbricoides rDNA. Nucleic Acids Res 1987; 15:6515-38. [PMID: 3502712 PMCID: PMC306120 DOI: 10.1093/nar/15.16.6515] [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: 01/06/2023] Open
Abstract
An accurate in vitro transcription system which utilizes the cloned 8.8 and 8.4 kb size classes of Ascaris rRNA genes (pAlr8 and pAlr13) and two kinds of cellular extracts from Ascaris oogonia has been established. Both rDNA containing plasmids are efficiently transcribed in vitro by RNA polymerase I from a unique site of rDNA which corresponds to the in vivo initiation site. The in vitro transcription product has a triphosphorylated 5'-end and starts on a G localized 414 bp (pAlr8) upstream of the beginning of the mature 18S rRNA. The promoter region has been delimited by testing the in vitro template activity of a series of restriction fragments. The region essential for the accuracy of initiation is contained within nucleotides -72 to +65, but full efficiency of transcription requires the additional presence of the region from nucleotides +66 to +84. The sequences upstream from position -72 do not appear to modulate the efficiency of specific in vitro initiation. Furthermore, the sequences flanking the transcription initiation site from position -1500 to +570 have been determined in the two cloned representatives of the two rDNA main size classes.
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31
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A 12-base-pair sequence is an essential element of the ribosomal gene terminator in Xenopus laevis. Mol Cell Biol 1987. [PMID: 3600650 DOI: 10.1128/mcb.7.5.1900] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
rRNA transcription in Xenopus laevis terminates near a 7-base-pair (bp) conserved sequence (T3 box) located 200 bp upstream of the site of transcription initiation for the adjacent gene promoter. We present evidence here that a 12-bp element containing the T3 box is an essential part of the terminator. Using an oocyte injection assay, we found that the 12-bp element (but not the T3 box alone) severely reduced the amount of RNA detectable at sites downstream from itself and that the T3 box within the 12-bp element was required to specify the formation of correct 3' ends. This requirement for the 12-bp element was also seen in pulse-label experiments by using a homogenate of oocyte nuclei, but the present data did not allow us to determine the exact mechanism by which the 12-bp element acts. Removal of the T3 region from its normal location allowed a significant amount of readthrough transcripts to accumulate, indicating that additional sequences may be required for complete terminator function.
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32
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Koller HT, Frondorf KA, Maschner PD, Vaughn JC. In vivo transcription from multiple spacer rRNA gene promoters during early development and evolution of the intergenic spacer in the brine shrimp Artemia. Nucleic Acids Res 1987; 15:5391-411. [PMID: 3037491 PMCID: PMC305968 DOI: 10.1093/nar/15.13.5391] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The control of ribosomal RNA (rRNA) gene expression during development can be productively studied by examination of the relationship between promoter structure and function as well as the processing of primary transcripts. Toward this end total cell RNA was extracted from embryos at various stages and probed with cloned rRNA genes using the "dot blot" method. This exercise showed that rRNA gene expression is a stage-specific process and is thus under developmental control. S1 nuclease protection experiments localized fourteen different upstream DNA sites encoding 5'-termini of pre-rRNAs during this synthetic phase of development. There is no indication of any spacer fail-safe terminator function. The S1 approach contributed to the sequencing of several of the sites. Comparative sequence alignments reveal short conserved regions in DNAs corresponding to these sites, which are shown to fall into two structural classes. Sites 3, 4, 6 and 9 are proposed to function in transcription initiation and are found to have the consensus sequence 5'...T-A-T-A-T-Pu-Pu-Pu-G-Pu-Pu-G-T-C-A 3'. Sites 1, 2, 5 and 8 which are proposed to function in 5'-processing have the consensus sequence; 5'...Pu-G-T-Pu-T-T-G 3'. These short sequence conserved regions are hypothesized to serve as recognition signals for proteins within the rDNA transcription initiation complex and for 5'-processing enzymes, respectively. Sequencing of the intergenic spacer region from which a model for spacer evolution is derived shows that tandem ca 600 bp subrepeats explain much of the multiplicity observed within control sites.
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33
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Labhart P, Reeder RH. Ribosomal precursor 3' end formation requires a conserved element upstream of the promoter. Cell 1987; 50:51-7. [PMID: 3594564 DOI: 10.1016/0092-8674(87)90661-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In Xenopus laevis the 3' end of the longest intact ribosomal RNA precursor is formed by a processing event at site T2, which is located 7860 bp downstream of the site of transcription initiation. Processing at T2 is eliminated by mutations within the T2 box, a 7 nucleotide conserved element, GACTTGC, located 15 bp downstream of the 3' ends. The same conserved box is also present at T3, a site 60 bp upstream of the gene promoter and that is part of a termination site. Surprisingly, mutations within the T3 box also eliminate processing at T2. To obtain proper T2 function, T3 can be at any distance but must be in the correct orientation upstream of a ribosomal gene promoter.
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34
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Labhart P, Reeder RH. A 12-base-pair sequence is an essential element of the ribosomal gene terminator in Xenopus laevis. Mol Cell Biol 1987; 7:1900-5. [PMID: 3600650 PMCID: PMC365294 DOI: 10.1128/mcb.7.5.1900-1905.1987] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
rRNA transcription in Xenopus laevis terminates near a 7-base-pair (bp) conserved sequence (T3 box) located 200 bp upstream of the site of transcription initiation for the adjacent gene promoter. We present evidence here that a 12-bp element containing the T3 box is an essential part of the terminator. Using an oocyte injection assay, we found that the 12-bp element (but not the T3 box alone) severely reduced the amount of RNA detectable at sites downstream from itself and that the T3 box within the 12-bp element was required to specify the formation of correct 3' ends. This requirement for the 12-bp element was also seen in pulse-label experiments by using a homogenate of oocyte nuclei, but the present data did not allow us to determine the exact mechanism by which the 12-bp element acts. Removal of the T3 region from its normal location allowed a significant amount of readthrough transcripts to accumulate, indicating that additional sequences may be required for complete terminator function.
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35
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Two distant and precisely positioned domains promote transcription of Xenopus laevis rRNA genes: analysis with linker-scanning mutants. Mol Cell Biol 1987. [PMID: 3796610 DOI: 10.1128/mcb.6.12.4585] [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
To examine the internal organization of the promoter of the Xenopus laevis rRNA gene, we constructed a series of linker-scanning mutants that traverse the rDNA initiation region. The mutant genes, which have 3 to 11 clustered base substitutions set within an otherwise unaltered rDNA promoter sequence, were injected into Xenopus oocyte nuclei, and their transcriptional capacity was assessed by S1 nuclease analysis of the resultant RNA. The data demonstrate that there are two essential promoter domains, the distal boundaries of which coincide with the promoter boundaries established previously by analysis of 5' and 3' deletion mutants. The upstream promoter domain is relatively small and extends from residues ca. -140 to -128. The downstream domain is considerably larger, encompassing residues ca. -36 to +10, and exactly corresponds in both size and position to the mammalian minimal promoter region. The Xenopus rDNA sequence between these two essential domains has a much smaller effect on the level of transcriptional initiation. In light of the fact that a large portion of this intervening region consists of a segment (residues -114 to -72) that is duplicated many times in the upstream spacer to form an rDNA enhancer sequence, it is noteworthy that a "-115/-77 linker scanner," in which virtually this entire segment is replaced by a polylinker sequence, has full promoter activity in the injected Xenopus borealis oocytes. Analysis of a parallel series of spacing change linker-scanning mutants revealed the unexpected result that the relative positions of the upstream and downstream promoter domains are very critical: all spacing alterations of more than 2 base pairs within this 100-base-pair region virtually abolish promoter activity. We conclude that the factors that bind to these two distant promoter domains must interact in a very precise stereospecific manner.
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36
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Identification of primary transcriptional start sites of mouse mitochondrial DNA: accurate in vitro initiation of both heavy- and light-strand transcripts. Mol Cell Biol 1987. [PMID: 3785171 DOI: 10.1128/mcb.6.5.1446] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The major transcriptional control sequences of vertebrate mitochondrial DNA lie within the displacement loop region. Transcription events initiating in the displacement loop sequence of the mouse genome were identified by 5' end mapping of primary transcripts by S1 nuclease protection and primer extension techniques. Light-strand transcription initiates at a single site, 165 nucleotides upstream of the major heavy-strand origin of replication. Transcription of the heavy strand occurs at two distinct sites, 5 and 13 nucleotides upstream of the gene for phenylalanyl-tRNA, the first heavy-strand-encoded gene. This spatial relationship of the two transcriptional start sites with each other and with the origin of heavy-strand replication and the gene for tRNAPhe is quite similar to that for human mitochondrial DNA. The predominant form of primary heavy-strand transcript in mouse is a short, ca. 75-nucleotide, RNA containing the sequences of tRNAPhe and a few additional nucleotides at the 5' end of tRNAPhe, suggesting that the processing of tRNA involves independent cleavages at the 5' and 3' ends of tRNA sequences.
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37
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Two distinct promoter elements in the human rRNA gene identified by linker scanning mutagenesis. Mol Cell Biol 1987. [PMID: 3785147 DOI: 10.1128/mcb.6.1.227] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A cell-free RNA polymerase I transcription system was used to evaluate the transcription efficiency of 21 linker scanning mutations that span the human rRNA gene promoter. Our analysis revealed the presence of two major control elements, designated the core and upstream elements, that affect the level of transcription initiation. The core element extends from -45 to +18 relative to the RNA start site, and transcription is severely affected (up to 100-fold) by linker scanning mutations in this region. Linker scanning and deletion mutations in the upstream element, located between nucleotides -156 and -107, cause a three- to fivefold reduction in transcription. Under certain reaction conditions, such as the presence of a high ratio of protein to template or supplementation of the reaction with partially purified protein fractions, sequences upstream of the core element can have an even greater effect (20- to 50-fold) on RNA polymerase I transcription. Primer extension analysis showed that RNA synthesized from all of these mutant templates is initiated at the correct in vivo start site. To examine the functional relationship between the core and the upstream region, mutant promoters were constructed that alter the orientation, distance, or multiplicity of these control elements relative to each other. The upstream control element appears to function in only one orientation, and its position relative to the core is constrained within a fairly narrow region. Moreover, multiple core elements in close proximity to each other have an inhibitory effect on transcription.
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38
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Upstream domains of the Xenopus laevis rDNA promoter are revealed in microinjected oocytes. Mol Cell Biol 1987. [PMID: 3785161 DOI: 10.1128/mcb.6.4.1228] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The DNA sequences involved in promoting transcription of the Xenopus laevis rRNA genes were determined by microinjecting a series of deletion mutants into oocyte nuclei. A very small promoter region is sufficient to direct efficient transcription when templates are microinjected at high rDNA concentration, since 5'delta- 9 and 3'delta +6 templates are fully active. However, as the concentration of injected template is decreased, an increasing requirement for upstream domains, extending to nucleotide approximately -170, is observed. The major downstream border of the required region does not change. This apparently expanding 5' promoter border results from the fact that, as the rDNA concentration is decreased, transcription from templates lacking the upstream promoter domain falls off much more sharply than does transcription from a complete promoter. In fact, the deleted promoters are virtually inactive below a threshold rDNA concentration. It is indeed the rDNA concentration that is important, for coinjected vector DNA does not increase the level of transcription obtained from low concentrations of the 5' deletions. From these data we conclude that polymerase I transcription factors can recognize and initiate transcription from a small core promoter domain, but that sequences extending upstream to nucleotide approximately -170 increase the efficiency of initiation. A model is presented that could account for these results.
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39
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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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40
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Grummt I, Kuhn A, Bartsch I, Rosenbauer H. A transcription terminator located upstream of the mouse rDNA initiation site affects rRNA synthesis. Cell 1986; 47:901-11. [PMID: 3779845 DOI: 10.1016/0092-8674(86)90805-6] [Citation(s) in RCA: 138] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Mouse ribosomal genes have a short sequence upstream of the transcription initiation site that is related in structure and function to the terminator boxes previously identified at the 3' end of the transcription unit. This upstream terminator recognizes the same protein factor as the 3'-terminal sites and is able to terminate RNA polymerase I transcription in vitro. S1 mapping and nucleolar run-on experiments reveal the presence of 5'-terminal spacer transcripts that are terminated at this site. These transcripts probably derive from spacer promoters, one of which has been identified approximately 2 kb upstream of the pre-rRNA start site. The interaction of a specific nuclear factor with the upstream terminator increases the efficiency of initiation, suggesting that transcription termination and initiation at the adjacent promoter work in an interrelated fashion.
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41
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Precise assignment of the heavy-strand promoter of mouse mitochondrial DNA: cognate start sites are not required for transcriptional initiation. Mol Cell Biol 1986. [PMID: 3785226 DOI: 10.1128/mcb.6.9.3262] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcription of the heavy strand of mouse mitochondrial DNA starts from two closely spaced, distinct sites located in the displacement loop region of the genome. We report here an analysis of regulatory sequences required for faithful transcription from these two sites. Data obtained from in vitro assays demonstrated that a 51-base-pair region, encompassing nucleotides -40 to +11 of the downstream start site, contains sufficient information for accurate transcription from both start sites. Deletion of the 3' flanking sequences, including one or both start sites to -17, resulted in the initiation of transcription by the mitochondrial RNA polymerase from alternative sites within vector DNA sequences. This feature places the mouse heavy-strand promoter uniquely among other known mitochondrial promoters, all of which absolutely require cognate start sites for transcription. Comparison of the heavy-strand promoter with those of other vertebrate mitochondrial DNAs revealed a remarkably high rate of sequence divergence among species.
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42
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Precise assignment of the light-strand promoter of mouse mitochondrial DNA: a functional promoter consists of multiple upstream domains. Mol Cell Biol 1986. [PMID: 3023972 DOI: 10.1128/mcb.6.9.3253] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Using deletion mutagenesis we localized the promoter for the light strand of mouse mitochondrial DNA to a 97-base-pair region, from -88 to +9 nucleotides of the transcriptional initiation site. Within this region the light-strand promoter could be dissected into at least three different functional domains. The specificity region, a maximum of 19 base pairs between -10 and +9 of the transcriptional initiation site, was essential and sufficient for accurate transcriptional initiation. A second region, extending to -29 nucleotides from the initiation site, facilitated the formation of a preinitiation complex between the template DNA and factor(s) present in the mitochondrial RNA polymerase fraction and was required for efficient transcription. A third, ill-defined upstream region, which extended up to -88 nucleotides from the initiation site, appeared to influence template transcriptional efficiencies in competition assays. Without the specificity domain, the upstream regions were incapable of supporting any transcription. The presence of multiple upstream domains was confirmed by disrupting nucleotide sequences in the upstream region by using linker insertion and linker replacement techniques.
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43
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Windle JJ, Sollner-Webb B. Two distant and precisely positioned domains promote transcription of Xenopus laevis rRNA genes: analysis with linker-scanning mutants. Mol Cell Biol 1986; 6:4585-93. [PMID: 3796610 PMCID: PMC367243 DOI: 10.1128/mcb.6.12.4585-4593.1986] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
To examine the internal organization of the promoter of the Xenopus laevis rRNA gene, we constructed a series of linker-scanning mutants that traverse the rDNA initiation region. The mutant genes, which have 3 to 11 clustered base substitutions set within an otherwise unaltered rDNA promoter sequence, were injected into Xenopus oocyte nuclei, and their transcriptional capacity was assessed by S1 nuclease analysis of the resultant RNA. The data demonstrate that there are two essential promoter domains, the distal boundaries of which coincide with the promoter boundaries established previously by analysis of 5' and 3' deletion mutants. The upstream promoter domain is relatively small and extends from residues ca. -140 to -128. The downstream domain is considerably larger, encompassing residues ca. -36 to +10, and exactly corresponds in both size and position to the mammalian minimal promoter region. The Xenopus rDNA sequence between these two essential domains has a much smaller effect on the level of transcriptional initiation. In light of the fact that a large portion of this intervening region consists of a segment (residues -114 to -72) that is duplicated many times in the upstream spacer to form an rDNA enhancer sequence, it is noteworthy that a "-115/-77 linker scanner," in which virtually this entire segment is replaced by a polylinker sequence, has full promoter activity in the injected Xenopus borealis oocytes. Analysis of a parallel series of spacing change linker-scanning mutants revealed the unexpected result that the relative positions of the upstream and downstream promoter domains are very critical: all spacing alterations of more than 2 base pairs within this 100-base-pair region virtually abolish promoter activity. We conclude that the factors that bind to these two distant promoter domains must interact in a very precise stereospecific manner.
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Clos J, Normann A, Ohrlein A, Grummt I. The core promoter of mouse rDNA consists of two functionally distinct domains. Nucleic Acids Res 1986; 14:7581-95. [PMID: 3774539 PMCID: PMC311782 DOI: 10.1093/nar/14.19.7581] [Citation(s) in RCA: 42] [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
We have determined the sequences constituting the minimal promoter of mouse rDNA. A very small region immediately upstream of the transcription start site (from -1 to -39) is sufficient to direct correct transcription initiation. Sequences immediately downstream of the transcription start site (+1 to +11) increase the efficiency of transcription initiation. Point mutations within the core promoter have been generated and assayed for their effects on template activity and on interaction with the pol I specific transcription factor TIF-IB. The core promoter element appears to consist of two functionally different domains. The distal sequence motif from position -22 to -16 is recognized by factor TIF-IB. Mutations within this region lead to similar changes of both template activity and binding of TIF-IB. Two point mutations within the proximal sequence motif from -15 to -1 do not affect TIF-IB binding although they severely impair transcription initiation. It is suggested, that this proximal region plays a role in the assembly of functional transcription initiation complexes rather than in the primary binding of TIF-IB.
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Chang DD, Clayton DA. Precise assignment of the light-strand promoter of mouse mitochondrial DNA: a functional promoter consists of multiple upstream domains. Mol Cell Biol 1986; 6:3253-61. [PMID: 3023972 PMCID: PMC367063 DOI: 10.1128/mcb.6.9.3253-3261.1986] [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
Using deletion mutagenesis we localized the promoter for the light strand of mouse mitochondrial DNA to a 97-base-pair region, from -88 to +9 nucleotides of the transcriptional initiation site. Within this region the light-strand promoter could be dissected into at least three different functional domains. The specificity region, a maximum of 19 base pairs between -10 and +9 of the transcriptional initiation site, was essential and sufficient for accurate transcriptional initiation. A second region, extending to -29 nucleotides from the initiation site, facilitated the formation of a preinitiation complex between the template DNA and factor(s) present in the mitochondrial RNA polymerase fraction and was required for efficient transcription. A third, ill-defined upstream region, which extended up to -88 nucleotides from the initiation site, appeared to influence template transcriptional efficiencies in competition assays. Without the specificity domain, the upstream regions were incapable of supporting any transcription. The presence of multiple upstream domains was confirmed by disrupting nucleotide sequences in the upstream region by using linker insertion and linker replacement techniques.
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Chang DD, Clayton DA. Precise assignment of the heavy-strand promoter of mouse mitochondrial DNA: cognate start sites are not required for transcriptional initiation. Mol Cell Biol 1986; 6:3262-7. [PMID: 3785226 PMCID: PMC367064 DOI: 10.1128/mcb.6.9.3262-3267.1986] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Transcription of the heavy strand of mouse mitochondrial DNA starts from two closely spaced, distinct sites located in the displacement loop region of the genome. We report here an analysis of regulatory sequences required for faithful transcription from these two sites. Data obtained from in vitro assays demonstrated that a 51-base-pair region, encompassing nucleotides -40 to +11 of the downstream start site, contains sufficient information for accurate transcription from both start sites. Deletion of the 3' flanking sequences, including one or both start sites to -17, resulted in the initiation of transcription by the mitochondrial RNA polymerase from alternative sites within vector DNA sequences. This feature places the mouse heavy-strand promoter uniquely among other known mitochondrial promoters, all of which absolutely require cognate start sites for transcription. Comparison of the heavy-strand promoter with those of other vertebrate mitochondrial DNAs revealed a remarkably high rate of sequence divergence among species.
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Chang DD, Clayton DA. Identification of primary transcriptional start sites of mouse mitochondrial DNA: accurate in vitro initiation of both heavy- and light-strand transcripts. Mol Cell Biol 1986; 6:1446-53. [PMID: 3785171 PMCID: PMC367669 DOI: 10.1128/mcb.6.5.1446-1453.1986] [Citation(s) in RCA: 17] [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 major transcriptional control sequences of vertebrate mitochondrial DNA lie within the displacement loop region. Transcription events initiating in the displacement loop sequence of the mouse genome were identified by 5' end mapping of primary transcripts by S1 nuclease protection and primer extension techniques. Light-strand transcription initiates at a single site, 165 nucleotides upstream of the major heavy-strand origin of replication. Transcription of the heavy strand occurs at two distinct sites, 5 and 13 nucleotides upstream of the gene for phenylalanyl-tRNA, the first heavy-strand-encoded gene. This spatial relationship of the two transcriptional start sites with each other and with the origin of heavy-strand replication and the gene for tRNAPhe is quite similar to that for human mitochondrial DNA. The predominant form of primary heavy-strand transcript in mouse is a short, ca. 75-nucleotide, RNA containing the sequences of tRNAPhe and a few additional nucleotides at the 5' end of tRNAPhe, suggesting that the processing of tRNA involves independent cleavages at the 5' and 3' ends of tRNA sequences.
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Windle J, Sollner-Webb B. Upstream domains of the Xenopus laevis rDNA promoter are revealed in microinjected oocytes. Mol Cell Biol 1986; 6:1228-34. [PMID: 3785161 PMCID: PMC367634 DOI: 10.1128/mcb.6.4.1228-1234.1986] [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 DNA sequences involved in promoting transcription of the Xenopus laevis rRNA genes were determined by microinjecting a series of deletion mutants into oocyte nuclei. A very small promoter region is sufficient to direct efficient transcription when templates are microinjected at high rDNA concentration, since 5'delta- 9 and 3'delta +6 templates are fully active. However, as the concentration of injected template is decreased, an increasing requirement for upstream domains, extending to nucleotide approximately -170, is observed. The major downstream border of the required region does not change. This apparently expanding 5' promoter border results from the fact that, as the rDNA concentration is decreased, transcription from templates lacking the upstream promoter domain falls off much more sharply than does transcription from a complete promoter. In fact, the deleted promoters are virtually inactive below a threshold rDNA concentration. It is indeed the rDNA concentration that is important, for coinjected vector DNA does not increase the level of transcription obtained from low concentrations of the 5' deletions. From these data we conclude that polymerase I transcription factors can recognize and initiate transcription from a small core promoter domain, but that sequences extending upstream to nucleotide approximately -170 increase the efficiency of initiation. A model is presented that could account for these results.
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De Winter RF, Moss T. Spacer promoters are essential for efficient enhancement of X. laevis ribosomal transcription. Cell 1986; 44:313-8. [PMID: 3943126 DOI: 10.1016/0092-8674(86)90765-8] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The X. laevis ribosomal DNA spacer contains duplicated RNA polymerase I "spacer promoters" and an array of repeated 60/81 bp promoter-related sequences. The latter have been shown to enhance transcription from a 40S preribosomal RNA promoter in cis. Here we present evidence that at least one spacer promoter is also necessary for efficient enhancement. Deletion of the spacer promoter sequences in a construct carrying only one such promoter reduces 40S RNA transcription to approximately 10% of wild type. This effect apparently is caused by inactivation of the spacer promoter, since mutants in which 4-177 bp of the spacer promoter and adjacent sequences are deleted are functionally equivalent. Spacer promoters and 60/80 bp arrays therefore probably act together to enhance 40S pre-RNA transcription in X. laevis.
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