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Kreiner G, Bierhoff H, Armentano M, Rodriguez-Parkitna J, Sowodniok K, Naranjo JR, Bonfanti L, Liss B, Schütz G, Grummt I, Parlato R. A neuroprotective phase precedes striatal degeneration upon nucleolar stress. Cell Death Differ 2013; 20:1455-64. [PMID: 23764776 PMCID: PMC3792439 DOI: 10.1038/cdd.2013.66] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 05/03/2013] [Accepted: 05/16/2013] [Indexed: 01/17/2023] Open
Abstract
The nucleolus is implicated in sensing and responding to cellular stress by stabilizing p53. The pro-apoptotic effect of p53 is associated with several neurodegenerative disorders, including Huntington's disease (HD), which is characterized by the progressive loss of medium spiny neurons (MSNs) in the striatum. Here we show that disruption of nucleolar integrity and function causes nucleolar stress and is an early event in MSNs of R6/2 mice, a transgenic model of HD. Targeted perturbation of nucleolar function in MSNs by conditional knockout of the RNA polymerase I-specific transcription initiation factor IA (TIF-IA) leads to late progressive striatal degeneration, HD-like motor abnormalities and molecular signatures. Significantly, p53 prolongs neuronal survival in TIF-IA-deficient MSNs by transient upregulation of phosphatase and tensin homolog deleted on chromosome 10 (PTEN), a tumor suppressor that inhibits mammalian target of rapamycin signaling and induces autophagy. The results emphasize the initial role of nucleolar stress in neurodegeneration and uncover a p53/PTEN-dependent neuroprotective response.
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Affiliation(s)
- G Kreiner
- 1] Department of Molecular Biology of the Cell I, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany [2] Department of Brain Biochemistry, Institute of Pharmacology, Polish Academy of Sciences, Cracow, Poland
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2
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Bierhoff H, Schmitz K, Maass F, Ye J, Grummt I. Noncoding transcripts in sense and antisense orientation regulate the epigenetic state of ribosomal RNA genes. Cold Spring Harb Symp Quant Biol 2011; 75:357-64. [PMID: 21502405 DOI: 10.1101/sqb.2010.75.060] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Alternative transcription of the same gene in sense and antisense orientation regulates expression of protein-coding genes. Here we show that noncoding RNA (ncRNA) in sense and antisense orientation also controls transcription of rRNA genes (rDNA). rDNA exists in two types of chromatin--a euchromatic conformation that is permissive to transcription and a heterochromatic conformation that is transcriptionally silent. Silencing of rDNA is mediated by NoRC, a chromatin-remodeling complex that triggers heterochromatin formation. NoRC function requires RNA that is complementary to the rDNA promoter (pRNA). pRNA forms a DNA:RNA triplex with a regulatory element in the rDNA promoter, and this triplex structure is recognized by DNMT3b. The results imply that triplex-mediated targeting of DNMT3b to specific sequences may be a common pathway in epigenetic regulation. We also show that rDNA is transcribed in antisense orientation. The level of antisense RNA (asRNA) is down-regulated in cancer cells and up-regulated in senescent cells. Ectopic asRNA triggers trimethylation of histone H4 at lysine 20 (H4K20me3), suggesting that antisense transcripts guide the histone methyltransferase Suv4-20 to rDNA. The results reveal that noncoding RNAs in sense and antisense orientation are important determinants of the epigenetic state of rDNA.
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Affiliation(s)
- H Bierhoff
- Division of Molecular Biology of the Cell II, German Cancer Research Center, DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
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3
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Grummt I. Non-coding RNA and chromatin remodeling: intergenic transcripts regulate the epigenetic state of rRNA genes. EJC Suppl 2008. [DOI: 10.1016/s1359-6349(08)71180-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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4
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Abstract
The target of rapamycin (TOR) signal-transduction pathway is an important mechanism by which eucaryotic cells adjust their protein biosynthetic capacity to nutrient availability. Both in yeast and in mammals, the TOR pathway regulates the synthesis of ribosomal components, including transcription and processing of pre-rRNA, expression of ribosomal proteins and the synthesis of 5S rRNA. Expression of the genes encoding the numerous constituents of ribosomes requires transcription by all three classes of nuclear RNA polymerases. In this review, we summarize recent advances in understanding the interplay among nutrient availability, transcriptional control and ribosome biogenesis. We focus on transcription in response to nutrients, detailing the relevant downstream targets of TOR in yeast and mammals. The critical role of TOR in linking environmental queues to ribosome biogenesis provides an efficient means by which cells alter their overall protein biosynthetic capacity.
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Affiliation(s)
- C Mayer
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
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5
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Voit R, Grummt I. Phosphorylation of UBF at serine 388 is required for interaction with RNA polymerase I and activation of rDNA transcription. Proc Natl Acad Sci U S A 2001; 98:13631-6. [PMID: 11698641 PMCID: PMC61092 DOI: 10.1073/pnas.231071698] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2001] [Indexed: 11/18/2022] Open
Abstract
Modulation of the activity of the upstream binding factor (UBF) plays a key role in cell cycle-dependent regulation of rRNA synthesis. Activation of rDNA transcription on serum stimulation requires phosphorylation of UBF at serine 484 by G(1)-specific cyclin-dependent kinase (cdk)/cyclin complexes. After G(1) progression UBF is phosphorylated at serine 388 by cdk2/cyclin E and cdk2/cyclin A. Conversion of serine 388 to glycine abolishes UBF activity, whereas substitution by aspartate enhances the transactivating function of UBF. Protein-protein interaction studies reveal that phosphorylation at serine 388 is required for the interaction between RNA polymerase I and UBF. The results suggest that phosphorylation of UBF represents a powerful means of modulating the assembly of the transcription initiation complex in a proliferation- and cell cycle-dependent fashion.
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Affiliation(s)
- R Voit
- Division of Molecular Biology of the Cell II, German Cancer Research Center, D-69120 Heidelberg, Germany.
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6
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Ciarmatori S, Scott PH, Sutcliffe JE, McLees A, Alzuherri HM, Dannenberg JH, te Riele H, Grummt I, Voit R, White RJ. Overlapping functions of the pRb family in the regulation of rRNA synthesis. Mol Cell Biol 2001; 21:5806-14. [PMID: 11486020 PMCID: PMC87300 DOI: 10.1128/mcb.21.17.5806-5814.2001] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2001] [Accepted: 05/07/2001] [Indexed: 12/25/2022] Open
Abstract
The "pocket" proteins pRb, p107, and p130 are a family of negative growth regulators. Previous studies have demonstrated that overexpression of pRb can repress transcription by RNA polymerase (Pol) I. To assess whether pRb performs this role under physiological conditions, we have examined pre-rRNA levels in cells from mice lacking either pRb alone or combinations of the three pocket proteins. Pol I transcription was unaffected in pRb-knockout fibroblasts, but specific disruption of the entire pRb family deregulated rRNA synthesis. Further analysis showed that p130 shares with pRb the ability to repress Pol I transcription, whereas p107 is ineffective in this system. Production of rRNA is abnormally elevated in Rb(-/-) p130(-/-) fibroblasts. Furthermore, overexpression of p130 can inhibit an rRNA promoter both in vitro and in vivo. This reflects an ability of p130 to bind and inactivate the upstream binding factor, UBF. The data imply that rRNA synthesis in living cells is subject to redundant control by endogenous pRb and p130.
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Affiliation(s)
- S Ciarmatori
- Division of Molecular Biology of the Cell II, German Cancer Research Centre, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
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7
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Abstract
Epigenetic control mechanisms silence about half of ribosomal RNA genes (rDNA) in metabolically active cells. In the mouse, 40% of rDNA repeats are methylated and can be activated by 5-azacytidine treatment. In exploring the effect of methylation on rDNA transcription, we found that methylation of a single CpG dinucleotide within the upstream control element of the rDNA promoter (at -133) abrogates rDNA transcription both in transfection experiments and in in vitro assays using chromatin templates. Chromatin immunoprecipitation assays demonstrate that methylation of the cytosine at -133 inhibits binding of the transcription factor UBF to nucleosomal rDNA, thereby preventing initiation complex formation. Thus, methylation may be a mechanism to inactivate rDNA genes and propagate transcriptional silencing through cell division.
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Affiliation(s)
- R Santoro
- Division of Molecular Biology of the Cell II, German Cancer Research Center, D-69120 Heidelberg, Germany
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8
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Abstract
Mammalian RNA polymerase I (Pol I) is a multisubunit enzyme that is decorated with accessory proteins, termed PAFs (polymerase-associated factors). The presence or absence of distinct PAFs may account for the functional differences of distinct fractions of cellular Pol I, and suggests that PAFs could be targets of regulatory pathways. Here we describe and functionally characterize PAF67, a novel 67 kDa protein that is tightly associated with a subpopulation of cellular Pol I. Both PAF67-containing and -deficient Pol I transcribe non-specific templates with similar efficiency, however, only the enzyme that contains PAF67 is capable of specifically transcribing rDNA templates. PAF67 co-localizes with Pol I in the nucleolus at sites of active rDNA transcription, indicating that PAF67 serves a role in rDNA transcription initiation. The results suggest that association of PAF67 with the 'core' enzyme endows Pol I with the capability to assemble into a productive transcription initiation complex at the rDNA promoter.
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Affiliation(s)
- P Seither
- German Cancer Research Center, Molecular Biology of the Cell II, Heidelberg
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9
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Jansa P, Burek C, Sander EE, Grummt I. The transcript release factor PTRF augments ribosomal gene transcription by facilitating reinitiation of RNA polymerase I. Nucleic Acids Res 2001; 29:423-9. [PMID: 11139612 PMCID: PMC29675 DOI: 10.1093/nar/29.2.423] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Termination of murine rDNA transcription by RNA polymerase I (Pol I) requires pausing of Pol I by terminator-bound TTF-I (transcription termination factor for Pol I), followed by dissociation of the ternary complex by PTRF (Pol I and transcript release factor). To examine the functional correlation between transcription termination and initiation, we have compared transcription on terminator-containing and terminator-less rDNA templates. We demonstrate that terminated RNA molecules are more efficiently synthesized than run-off transcripts, indicating that termination facilitates reinitiation. Transcriptional enhancement is observed in multiple- but not single-round transcription assays measuring either promoter-dependent or promoter-independent Pol I transcription. Increased synthesis of terminated transcripts is observed in crude extracts but not in a PTRF-free reconstituted transcription system, indicating that PTRF-mediated release of pre-rRNA is responsible for transcriptional enhancement. Consistent with PTRF serving an important role in modulating the efficiency of rRNA synthesis, PTRF exhibits pronounced charge heterogeneity, is phosphorylated at multiple sites and fractionates into transcriptionally active and inactive forms. The results suggest that regulation of PTRF activity may be an as yet unrecognized means to control the efficiency of ribosomal RNA synthesis.
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Affiliation(s)
- P Jansa
- Division of Molecular Biology of the Cell II, German Cancer Research Center, D-69120 Heidelberg, Germany
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10
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Bodem J, Dobreva G, Hoffmann-Rohrer U, Iben S, Zentgraf H, Delius H, Vingron M, Grummt I. TIF-IA, the factor mediating growth-dependent control of ribosomal RNA synthesis, is the mammalian homolog of yeast Rrn3p. EMBO Rep 2000; 1:171-5. [PMID: 11265758 PMCID: PMC1084264 DOI: 10.1093/embo-reports/kvd032] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2000] [Revised: 06/19/2000] [Accepted: 06/28/2000] [Indexed: 11/13/2022] Open
Abstract
Cells carefully modulate the rate of rRNA transcription in order to prevent an overinvestment in ribosome synthesis under less favorable nutritional conditions. In mammals, growth-dependent regulation of RNA polymerase I (Pol I) transcription is mediated by TIF-IA, an essential initiation factor that is active in extracts from growing but not starved or cycloheximide-treated mammalian cells. Here we report the molecular cloning and functional characterization of recombinant TIF-IA, which turns out to be the mammalian homolog of the yeast factor Rrn3p. We demonstrate that TIF-IA interacts with Pol I in the absence of template DNA, augments Pol I transcription in vivo and rescues transcription in extracts from growth-arrested cells in vitro.
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Affiliation(s)
- J Bodem
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg
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11
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Jansa P, Grummt I. Mechanism of transcription termination: PTRF interacts with the largest subunit of RNA polymerase I and dissociates paused transcription complexes from yeast and mouse. Mol Gen Genet 1999; 262:508-14. [PMID: 10589839 DOI: 10.1007/s004380051112] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Transcription termination by RNA polymerase I (Pol I) is a stepwise process. First the elongating RNA polymerase is forced to pause by DNA-bound transcription termination factor (TTF-I). Then the ternary transcription complex is dissociated by PTRF, a novel factor that promotes release of both nascent transcripts and Pol I from the template. In this study we have investigated the ability of PTRF to liberate transcripts from ternary transcription complexes isolated from yeast and mouse. Using immobilized, tailed templates that contain terminator sequences from Saccharomyces cerevisiae and mouse, respectively, we demonstrate that PTRF promotes release of terminated transcripts, irrespective of whether mouse Pol I has interacted with the murine termination factor TTF-I or its yeast homolog Reb1p. In contrast, mouse Pol I paused by the lac repressor remains bound to the template both in the presence and absence of PTRF. We demonstrate that PTRF interacts with the largest subunit of murine Pol I, with TTF-I and Reb1p, but not the lac repressor. The results imply that Pol I transcription termination in yeast and mouse is mediated by conserved interactions between Pol I, Reb1p/TTF-I and PTRF.
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Affiliation(s)
- P Jansa
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg
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12
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Klein J, Grummt I. Cell cycle-dependent regulation of RNA polymerase I transcription: the nucleolar transcription factor UBF is inactive in mitosis and early G1. Proc Natl Acad Sci U S A 1999; 96:6096-101. [PMID: 10339547 PMCID: PMC26841 DOI: 10.1073/pnas.96.11.6096] [Citation(s) in RCA: 133] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/1999] [Indexed: 01/15/2023] Open
Abstract
Transcription of ribosomal RNA genes by RNA polymerase (pol) I oscillates during the cell cycle, being maximal in S and G2 phase, repressed during mitosis, and gradually recovering during G1 progression. We have shown that transcription initiation factor (TIF)-IB/SL1 is inactivated during mitosis by cdc2/cyclin B-directed phosphorylation of TAFI110. In this study, we have monitored reactivation of transcription after exit from mitosis. We demonstrate that the pol I factor UBF is also inactivated by phosphorylation but recovers with different kinetics than TIF-IB/SL1. Whereas TIF-IB/SL1 activity is rapidly regained on entry into G1, UBF is reactivated later in G1, concomitant with the onset of pol I transcription. Repression of pol I transcription in mitosis and early G1 can be reproduced with either extracts from cells synchronized in M or G1 phase or with purified TIF-IB/SL1 and UBF isolated in the presence of phosphatase inhibitors. The results suggest that two basal transcription factors, e.g., TIF-IB/SL1 and UBF, are inactivated at mitosis and reactivated by dephosphorylation at the exit from mitosis and during G1 progression, respectively.
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Affiliation(s)
- J Klein
- Division of Molecular Biology of the Cell II, German Cancer Research Center, D-69120 Heidelberg, Germany
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13
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Abstract
Transcription of rRNA genes by RNA polymerase I increases following serum stimulation of quiescent NIH 3T3 fibroblasts. To elucidate the mechanism underlying transcriptional activation during progression through the G1 phase of the cell cycle, we have analyzed the activity and phosphorylation pattern of the nucleolar transcription factor upstream binding factor (UBF). Using a combination of tryptic phosphopeptide mapping and site-directed mutagenesis, we have identified Ser484 as a direct target for cyclin-dependent kinase 4 (cdk4)-cyclin D1- and cdk2-cyclin E-directed phosphorylation. Mutation of Ser484 impairs rDNA transcription in vivo and in vitro. The data demonstrate that UBF is regulated in a cell cycle-dependent manner and suggest a link between G1 cdks-cyclins, UBF phosphorylation and rDNA transcription activation.
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Affiliation(s)
- R Voit
- Division of Molecular Biology of the Cell II, German Cancer Research Center, D-69120 Heidelberg, Germany.
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14
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Abstract
All cells, from prokaryotes to vertebrates, synthesize vast amounts of ribosomal RNA to produce the several million new ribosomes per generation that are required to maintain the protein synthetic capacity of the daughter cells. Ribosomal gene (rDNA) transcription is governed by RNA polymerase I (Pol I) assisted by a dedicated set of transcription factors that mediate the specificity of transcription and are the targets of the pleiotrophic pathways the cell uses to adapt rRNA synthesis to cell growth. In the past few years we have begun to understand the specific functions of individual factors involved in rDNA transcription and to elucidate on a molecular level how transcriptional regulation is achieved. This article reviews our present knowledge of the molecular mechanism of rDNA transcriptional regulation.
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Affiliation(s)
- I Grummt
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
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15
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Abstract
Induction of the tumor suppressor protein p53 restricts cellular proliferation. Since actively growing cells require the ongoing synthesis of ribosomal RNA to sustain cellular biosynthesis, we studied the effect of p53 on ribosomal gene transcription by RNA polymerase I (Pol I). We have measured rDNA transcriptional activity in different cell lines which either lack or overexpress p53 and demonstrate that wild-type but not mutant p53 inhibits cellular pre-rRNA synthesis. Conversely, pre-rRNA levels are elevated both in cells which express mutant p53 and in fibroblasts from p53 knock-out mice. Transient transfection assays with a set of rDNA deletion mutants demonstrate that intergenic spacer sequences are dispensable and the minimal rDNA promoter is sufficient for p53-mediated repression of Pol I transcription. However, in a cell-free transcription system, recombinant p53 does not inhibit rDNA transcription, indicating that p53 does not directly interfere with the basal Pol I transcriptional machinery. Thus, repression of Pol I transcription by p53 may be a consequence of p53-induced growth arrest.
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Affiliation(s)
- A Budde
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg
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16
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Heix J, Vente A, Voit R, Budde A, Michaelidis TM, Grummt I. Mitotic silencing of human rRNA synthesis: inactivation of the promoter selectivity factor SL1 by cdc2/cyclin B-mediated phosphorylation. EMBO J 1998; 17:7373-81. [PMID: 9857193 PMCID: PMC1171082 DOI: 10.1093/emboj/17.24.7373] [Citation(s) in RCA: 118] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have used a reconstituted cell-free transcription system to investigate the molecular basis of mitotic repression of RNA polymerase I (pol I) transcription. We demonstrate that SL1, the TBP-containing promoter-binding factor, is inactivated by cdc2/cyclin B-directed phosphorylation, and reactivated by dephosphorylation. Transcriptional inactivation in vitro is accompanied by phosphorylation of two subunits, e.g. TBP and hTAFI110. To distinguish whether transcriptional repression is due to phosphorylation of TBP, hTAFI110 or both, SL1 was purified from two HeLa cell lines that express either full-length or the core domain of TBP only. Both TBP-TAFI complexes exhibit similar activity and both are repressed at mitosis, indicating that the variable N-terminal domain which contains multiple target sites for cdc2/cyclin B phosphorylation is dispensable for mitotic repression. Protein-protein interaction studies reveal that mitotic phosphorylation impairs the interaction of SL1 with UBF. The results suggest that phosphorylation of SL1 is used as a molecular switch to prevent pre-initiation complex formation and to shut down rDNA transcription at mitosis.
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Affiliation(s)
- J Heix
- Division of Molecular Biology of the Cell II, German Cancer Research Center, D-69120 Heidelberg, Germany
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17
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Abstract
Entry into mitosis is accompanied by a global repression of transcription. To investigate the molecular mechanisms which shut-down rRNA synthesis during mitosis, we have compared RNA polymerase I (Pol I) transcription in extracts from asynchronous and mitotic HeLa cells. We show by several experimental approaches that phosphorylation by cdc2/cyclin B inactivates the TBP-containing factor SL1 and thus abrogates Pol I transcription during mitosis. This finding links the cell's cycle with the transcriptional activity of Pol I and suggests a common mechanism for mitotic silencing of all three classes of nuclear RNA polymerases, i.e. reversible inactivation of the respective TBP-TAF complexes by (a) mitotic kinase(s).
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Affiliation(s)
- A Kuhn
- German Cancer Research Center, Heidelberg, D-69120, Germany
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18
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Stegh AH, Schickling O, Ehret A, Scaffidi C, Peterhänsel C, Hofmann TG, Grummt I, Krammer PH, Peter ME. DEDD, a novel death effector domain-containing protein, targeted to the nucleolus. EMBO J 1998; 17:5974-86. [PMID: 9774341 PMCID: PMC1170924 DOI: 10.1093/emboj/17.20.5974] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The CD95 signaling pathway comprises proteins that contain one or two death effector domains (DED), such as FADD/Mort1 or caspase-8. Here we describe a novel 37 kDa protein, DEDD, that contains an N-terminal DED. DEDD is highly conserved between human and mouse (98. 7% identity) and is ubiquitously expressed. Overexpression of DEDD in 293T cells induced weak apoptosis, mainly through its DED by which it interacts with FADD and caspase-8. Endogenous DEDD was found in the cytoplasm and translocated into the nucleus upon stimulation of CD95. Immunocytological studies revealed that overexpressed DEDD directly translocated into the nucleus, where it co-localizes in the nucleolus with UBF, a basal factor required for RNA polymerase I transcription. Consistent with its nuclear localization, DEDD contains two nuclear localization signals and the C-terminal part shares sequence homology with histones. Recombinant DEDD binds to both DNA and reconstituted mononucleosomes and inhibits transcription in a reconstituted in vitro system. The results suggest that DEDD is a final target of a chain of events by which the CD95-induced apoptotic signal is transferred into the nucleolus to shut off cellular biosynthetic activities.
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Affiliation(s)
- A H Stegh
- Tumor Immunology Program, German Cancer Research Center, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
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19
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Abstract
Transcription of ribosomal genes assembled into chromatin requires binding of the transcription termination factor TTF-I to the promoter-proximal terminator T0. To analyze the mechanism of TTF-I-mediated transcriptional activation, we have used mutant templates with altered sequence, polarity and distance of T0 with respect to the transcription start site. Transcription activation by TTF-I is chromatin specific and requires the precise positioning of the terminator relative to the promoter. Whereas termination by TTF-I depends on the correct orientation of a terminator, TTF-I-mediated transcriptional activation is orientation independent. TTF-I can bind to nucleosomal DNA in the absence of enzymatic activities that destabilize nucleosome structure. Chromatin-bound TTF-I synergizes with ATP-dependent cofactors present in extracts of Drosophila embryos and mouse cells to position a nucleosome over the rDNA promoter and the transcription start site. Nucleosome positioning correlates tightly with the activation of rDNA transcription. We suggest that transcriptional activation by TTF-I is a stepwise process involving the creation of a defined promoter architecture and that the positioning of a nucleosome is compatible with, if not a prerequisite for, transcription initiation from rDNA chromatin.
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Affiliation(s)
- G Längst
- German Cancer Research Center, Division of Molecular Biology of the Cell II, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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20
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Jansa P, Mason SW, Hoffmann-Rohrer U, Grummt I. Cloning and functional characterization of PTRF, a novel protein which induces dissociation of paused ternary transcription complexes. EMBO J 1998; 17:2855-64. [PMID: 9582279 PMCID: PMC1170626 DOI: 10.1093/emboj/17.10.2855] [Citation(s) in RCA: 120] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Termination of transcription by RNA polymerase I (Pol I) is a two-step process which involves pausing of elongating transcription complexes and release of both pre-rRNA and Pol I from the template. In mouse, pausing of elongation complexes is mediated by the transcription termination factor TTF-I bound to the 'Sal box' terminator downstream of the rDNA transcription unit. Dissociation of paused ternary complexes requires a cellular factor, termed PTRF for Pol I and transcript release factor. Here we describe the molecular cloning of a cDNA corresponding to murine PTRF. Recombinant PTRF is capable of dissociating ternary Pol I transcription complexes in vitro as revealed by release of both Pol I and nascent transcripts from the template. Consistent with its function in transcription termination, PTRF interacts with both TTF-I and Pol I. Moreover, we demonstrate specific binding of PTRF to transcripts containing the 3' end of pre-rRNA. Substitution of 3'-terminal uridylates by guanine residues abolishes PTRF binding and impairs release activity. The results reveal a network of protein-protein and protein-nucleic acid interactions that governs termination of Pol I transcription.
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Affiliation(s)
- P Jansa
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
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21
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Abstract
Transcription initiation of ribosomal RNA genes requires RNA polymerase I (Pol I) and auxiliary factors which either bind directly to the rDNA promoter, e.g. TIF-IB/SL1 and UBF, or are assembled into productive transcription initiation complexes via interaction with Pol I, e.g. TIF-IA, and TIF-IC. Here we show that all components required for specific rDNA transcription initiation are capable of physical interaction with Pol I in the absence of DNA and can be co-immunoprecipitated with antibodies against defined subunits of murine Pol I. Sucrose gradient centrifugation and fractionation on gel filtration columns reveals that approximately 10% of cellular Pol I elutes as a defined complex with an apparent molecular mass of > 2000 kDa. The large Pol I complex contains saturating levels of TIF-IA, TIF-IB and UBF, but limiting amounts of TIF-IC. In support of the existence of a functional complex between Pol I and basal factors, the large complex is transcriptionally active after complementation with TIF-IC. The results suggest that, analogous to class II gene transcription, a pre-assembled complex, the "Pol I holoenzyme", exists that appears to be the initiation-competent form of Pol I.
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Affiliation(s)
- P Seither
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg.p6
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22
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Abstract
Mouse RNA polymerase I (Pol I) is composed of 14 polypeptides, 3 of which are thought to be loosely associated with, and may be dislodged from, Pol I. To find out whether these polymerase-associated factors (PAF53, 51, and 49) serve a role in growth-dependent control of rDNA transcription, we generated polyclonal antibodies against three subunits of murine Pol I, RPA116, RPA40 and PAF53, and used different experimental approaches, e.g. immunoblot analysis, immunoprecipitation and immunofluorescence studies, to compare the stoichiometry of individual subunits both in different Pol I preparations and in extracts from cells grown under different conditions. This comparative analysis reveals that the molar ratio of the second largest subunit RPA116 to PAF53 is the same, irrespective of whether crude extracts or highly purified Pol I fractions are analyzed. Significantly, the relative level of PAF53 was comparable in exponentially growing or growth-arrested cells, indicating that growth-dependent fluctuations in Pol I activity are not accompanied by alterations in the amount of PAF53. In addition, we show by high resolution immunofluorescence analysis that, under conditions of repressed rDNA transcription, including serum starvation, actinomycin treatment und during mitosis, PAF53 remains attached to the transcriptional machinery. The finding that the Mr 53,000 protein remains in the multiprotein complex under all experimental conditions tested indicates that PAF53 is not a loosely associated regulatory factor but a bona fide subunit of Pol I.
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Affiliation(s)
- P Seither
- Division of Molecular Biology of the Cell II, German Cancer Research Center, D-69120 Heidelberg, Germany
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23
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Gerber JK, Gögel E, Berger C, Wallisch M, Müller F, Grummt I, Grummt F. Termination of mammalian rDNA replication: polar arrest of replication fork movement by transcription termination factor TTF-I. Cell 1997; 90:559-67. [PMID: 9267035 DOI: 10.1016/s0092-8674(00)80515-2] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A replication fork barrier (RFB) at the 3' end of eukaryotic ribosomal RNA genes blocks bidirectional fork progression and limits DNA replication to the same direction as transcription. We have reproduced the RFB in vitro in HeLa cell extracts using 3' terminal murine rDNA fused to an SV40 origin-based vector. The RFB is polar and modularly organized, requiring both the Sal box transcription terminator and specific flanking sequences. Mutations within the terminator element, depletion of the RNA polymerase I-specific transcription termination factor TTF-I, or deletion of the termination domain of TTF-I abolishes RFB activity. Thus, the same factor that blocks elongating RNA polymerase I prevents head-on collision between the DNA replication apparatus and the transcription machinery.
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Affiliation(s)
- J K Gerber
- Institute of Biochemistry, University of Würzburg, Germany
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24
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Abstract
The retinoblastoma susceptibility gene product pRb restricts cellular proliferation by affecting gene expression by all three classes of nuclear RNA polymerases. To elucidate the molecular mechanisms underlying pRb-mediated repression of ribosomal DNA (rDNA) transcription by RNA polymerase I, we have analyzed the effect of pRb in a reconstituted transcription system. We demonstrate that pRb, but not the related protein p107, acts as a transcriptional repressor by interfering with the assembly of transcription initiation complexes. The HMG box-containing transcription factor UBF is the main target for pRb-induced transcriptional repression. UBF and pRb form in vitro complexes involving the C-terminal part of pRb and HMG boxes 1 and 2 of UBF. We show that the interactions between UBF and TIF-IB and between UBF and RNA polymerase I, respectively, are not perturbed by pRb. However, the DNA binding activity of UBF to both synthetic cruciform DNA and the rDNA promoter is severely impaired in the presence of pRb. These studies reveal another mechanism by which pRb suppresses cell proliferation, namely, by direct inhibition of cellular rRNA synthesis.
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Affiliation(s)
- R Voit
- German Cancer Research Center, Division of Molecular Biology of the Cell II, Heidelberg
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25
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Seither P, Coy JF, Pouska A, Grummt I. Molecular cloning and characterization of the cDNA encoding the largest subunit of mouse RNA polymerase I. Mol Gen Genet 1997; 255:180-6. [PMID: 9236775 DOI: 10.1007/s004380050487] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We describe the cloning and analysis of mRPA1, the cDNA encoding the largest subunit (RPA194) of murine RNA polymerase I. The coding region comprises an open reading frame of 5151 bp that encodes a polypeptide of 1717 amino acids with a calculated molecular mass of 194 kDa. Alignment of the deduced protein sequence reveals homology to the beta' subunit of Escherichia coli RNA polymerase in the conserved regions a-h present in all large subunits of RNA polymerases. However, the overall sequence homology among the conserved regions of RPA1 from different species is significantly lower than that observed in the corresponding beta'-like subunits of class II and III RNA polymerase. We have raised two types of antibodies which are directed against the conserved regions c and f of RPA194. Both antibodies are monospecific for RPA194 and do not cross-react with subunits of RNA polymerase II or III. Moreover, these antibodies immunoprecipitate RNA polymerase I both from murine and human cell extracts and, therefore, represent an invaluable tool for the identification of RNA polymerase I-associated proteins.
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Affiliation(s)
- P Seither
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
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26
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Abstract
Termination of RNA polymerase I (Pol I) transcription requires the interaction of a specific DNA binding factor with terminator elements downstream of the pre-rRNA coding region. Both the terminator elements and the respective termination factors are distinct in yeast and mammals, and differences in the mechanism of transcription termination have been postulated. We have compared in vitro transcription termination of yeast and mouse Pol I using both the murine factor TTF-I, and the yeast homolog Reb1p. We show that, similar to TTF-I, Reb1p was sufficient for pausing of Pol I from either species, but was unable to cause release of the nascent transcripts from the paused ternary complex. The deficiency of Reb1p to mediate transcript release from Pol I of either species was complemented by the recently characterized murine release factor. Thus, both yeast and mouse Pol I termination requires a trans-acting factor that, in conjunction with the T-rich flanking sequence, releases the transcripts and Pol I from the template. The observation that the murine factor causes dissociation of ternary transcription complexes arrested by Reb1p suggests that the mechanism of Pol I termination is highly conserved from yeast to mammals.
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Affiliation(s)
- S W Mason
- German Cancer Research Center, Division of Molecular Biology of the Cell II, Heidelberg
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27
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Falciola L, Spada F, Calogero S, Langst G, Voit R, Grummt I, Bianchi ME. High mobility group 1 protein is not stably associated with the chromosomes of somatic cells. J Cell Biol 1997; 137:19-26. [PMID: 9105033 PMCID: PMC2139855 DOI: 10.1083/jcb.137.1.19] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
High mobility group 1 (HMG1) protein is an abundant and conserved component of vertebrate nuclei and has been proposed to play a structural role in chromatin organization, possibly similar to that of histone H1. However, a high abundance of HMG1 had also been reported in the cytoplasm and on the surface of mammalian cells. We conclusively show that HMG1 is a nuclear protein, since several different anti-HMG1 antibodies stain the nucleoplasm of cultured cells, and epitope-tagged HMG1 is localized in the nucleus only. The protein is excluded from nucleoli and is not associated to specific nuclear structures but rather appears to be uniformly distributed. HMG1 can bind in vitro to reconstituted core nucleosomes but is not stably associated to chromatin in live cells. At metaphase, HMG1 is detached from condensed chromosomes, contrary to histone H1. During interphase, HMG1 readily diffuses out of nuclei after permeabilization of the nuclear membranes with detergents, whereas histone H1 remains associated to chromatin. These properties exclude a shared function for HMG1 and H1 in differentiated cells, in spite of their similar biochemical properties. HMG1 may be stably associated only to a very minor population of nucleosomes or may interact transiently with nucleosomes during dynamic processes of chromatin remodeling.
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Affiliation(s)
- L Falciola
- Dipartimento di Genetica e di Biologia dei Microrganismi, Universitá di Milano, Italy
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28
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Sander EE, Grummt I. Oligomerization of the transcription termination factor TTF-I: implications for the structural organization of ribosomal transcription units. Nucleic Acids Res 1997; 25:1142-7. [PMID: 9092622 PMCID: PMC146573 DOI: 10.1093/nar/25.6.1142] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Mammalian ribosomal genes are flanked at their 5'and 3'ends by terminator sequences which are recognized by the transcription termination factor TTF-I. The occurrence of the same binding site upstream and downstream of the gene raises the possibility that TTF-I can interact with both sequences simultaneously and thus brings the terminator in the vicinity of the gene promoter by looping out the pre-rRNA coding sequence. To test this model, we have examined the ability of TTF-I to oligomerize and found that both full-length and N-terminally truncated versions of TTF-I form stable oligomeric structures. At least two domains of TTF-I located within the 184 N-terminal and 445 C-terminal amino acids, respectively, mediate the self-association of several TTF-I molecules. In support of the looping model, TTF-I is capable of linking two separate DNA fragments via binding to the target sites. This result indicates that in addition to its function in transcription termination, TTF-I may serve a role in the structural organization of the ribosomal genes which may be important for maintaining the high loading density of RNA polymerase I on active rRNA genes.
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Affiliation(s)
- E E Sander
- Division of Molecular Biology of the Cell II, German Cancer Research Center, D-69120 Heidelberg, Germany
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29
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Heix J, Zomerdijk JC, Ravanpay A, Tjian R, Grummt I. Cloning of murine RNA polymerase I-specific TAF factors: conserved interactions between the subunits of the species-specific transcription initiation factor TIF-IB/SL1. Proc Natl Acad Sci U S A 1997; 94:1733-8. [PMID: 9050847 PMCID: PMC19985 DOI: 10.1073/pnas.94.5.1733] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Promoter selectivity for all three classes of eukaryotic RNA polymerases is brought about by multimeric protein complexes containing TATA box binding protein (TBP) and specific TBP-associated factors (TAFs). Unlike class II- and III-specific TBP-TAF complexes, the corresponding murine and human class I-specific transcription initiation factor TIF-IB/SL1 exhibits a pronounced selectivity for its homologous promoter. As a first step toward understanding the molecular basis of species-specific promoter recognition, we cloned the cDNAs encoding the three mouse pol I-specific TBP-associated factors (TAFIs) and compared the amino acid sequences of the murine TAFIs with their human counterparts. The four subunits from either species can form stable chimeric complexes that contain stoichiometric amounts of TBP and TAFIs, demonstrating that differences in the primary structure of human and mouse TAFIs do not dramatically alter the network of protein-protein contacts responsible for assembly of the multimeric complex. Thus, primate vs. rodent promoter selectivity mediated by the TBP-TAFI complex is likely to be the result of cumulative subtle differences between individual subunits that lead to species-specific properties of RNA polymerase I transcription.
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Affiliation(s)
- J Heix
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg
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30
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Längst G, Blank TA, Becker PB, Grummt I. RNA polymerase I transcription on nucleosomal templates: the transcription termination factor TTF-I induces chromatin remodeling and relieves transcriptional repression. EMBO J 1997; 16:760-8. [PMID: 9049305 PMCID: PMC1169677 DOI: 10.1093/emboj/16.4.760] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Eukaryotic ribosomal gene promoters are preceded by a terminator element which is recognized by the transcription termination factor TTF-I. We have studied the function of this promoter-proximal terminator and show that binding of TTF-I is the key event which leads to ATP-dependent nucleosome remodeling and transcriptional activation of mouse rDNA pre-assembled into chromatin. We have analyzed TTF-I mutants for their ability to bind to free or nucleosomal DNA, and show that the DNA binding domain of TTF-I on its own is not sufficient for interaction with chromatin, indicating that specific protein features exist that endow a transcription factor with chromatin binding and remodeling properties. This first analysis of RNA polymerase I transcription in chromatin provides a clue for the function of the upstream terminator and establishes a dual role for TTF-I both as a termination factor and a chromatin-specific transcription activator.
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Affiliation(s)
- G Längst
- German Cancer Research Center, Division of Molecular Biology of the Cell II, Heidelberg, Germany
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31
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Längst G, Schätz T, Langowski J, Grummt I. Structural analysis of mouse rDNA: coincidence between nuclease hypersensitive sites, DNA curvature and regulatory elements in the intergenic spacer. Nucleic Acids Res 1997; 25:511-7. [PMID: 9016589 PMCID: PMC146485 DOI: 10.1093/nar/25.3.511] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We have analyzed the chromatin structure of mouse ribosomal RNA genes (rDNA) by partial digestion of genomic DNA with micrococcal nuclease (MNase), DNase I and identified hypersensitive sites by indirect end-labeling. This analysis has revealed defined regions of nuclease hypersensitivity in the intergenic spacer which in turn coincide with regulatory elements. Hypersensitive sites map to the transcription initiation site, the enhancer repeats, the spacer promoter and two sequence elements which coincide with amplification-promoting sequences. Analysis of the DNA curvature by computer modeling uncovered a striking correlation between sequence-directed structural features of regulatory regions and the position of nuclease hypersensitive sites. Moreover, we demonstrate that nucleosomes are specifically positioned upstream and downstream of the transcription start site. In vitro studies using chromatin assembled in the presence of Drosophila embryo extracts show that binding of the transcription termination factor TTF-I to the upstream terminator mediates this specific nucleosome positioning at the rDNA promoter in an ATP- dependent fashion.
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Affiliation(s)
- G Längst
- German Cancer Research Center, Division of Molecular Biology of the Cell II, 69120 Heidelberg, Germany
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32
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Mason SW, Sander EE, Grummt I. Identification of a transcript release activity acting on ternary transcription complexes containing murine RNA polymerase I. EMBO J 1997; 16:163-72. [PMID: 9009277 PMCID: PMC1169623 DOI: 10.1093/emboj/16.1.163] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Termination of mammalian ribosomal gene transcription by RNA polymerase I (Pol I) requires binding of the nucleolar factor TTF-I (transcription termination factor for Pol I) to specific rDNA terminator elements. We have used recombinant murine TTF-I in an immobilized tailed template assay to analyze individual steps of the termination reaction. We demonstrate that, besides the TTF-I-DNA complex which stops elongating Pol I, an additional activity is required to release both the nascent transcript and Pol I from the template. Moreover, transcript release, but not TTF-I-directed pausing, depends on upstream sequences directly flanking the terminator element. Together, complete termination of Pol I transcription requires TTF-I bound to the terminator DNA, a stretch of thymidine residues upstream of the TTF-I-mediated pause site and an activity which releases the RNA transcript and Pol I from the DNA template.
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Affiliation(s)
- S W Mason
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg
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33
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Sander EE, Mason SW, Munz C, Grummt I. The amino-terminal domain of the transcription termination factor TTF-I causes protein oligomerization and inhibition of DNA binding. Nucleic Acids Res 1996; 24:3677-84. [PMID: 8871544 PMCID: PMC146174 DOI: 10.1093/nar/24.19.3677] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The transcription termination factor TTF-I binds specifically to an 18 bp DNA element in the murine ribosomal gene spacer and mediates termination of RNA polymerase I transcription. In this study, we have compared DNA binding and termination activity of recombinant full-length TTF-I (TTF-Ip130) with two deletion mutants lacking 184 and 322 N-terminal amino acids, respectively. All three proteins exhibit similar termination activity, but the DNA binding of TTF-Ip130 is at least one order of magnitude lower than that of the deletion mutants, indicating that the N-terminus represses the interaction of TTF-I with DNA. The inhibitory effect of the N-terminus can be transferred to a heterologous DNA binding domain and is separable from other activities of TTF-I. We show by several methods that TTF-Ip130, the N-terminal domain alone, and fusions of the N-terminus with the DNA binding domain of Oct2.2 form stable oligomers in solution. Thus, in contrast to previous studies suggesting that activation of TTF-I occurs through proteolysis, we demonstrate that full-length TTF-I mediates termination of rDNA transcription in vivo and in vitro and that the oligomerization state of TTF-I may influence its DNA binding activity.
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Affiliation(s)
- E E Sander
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
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34
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Abstract
We have cloned the cDNA encoding the second largest subunit of RNA polymerase I, termed RPA2, from mouse cells. The cDNA has a 3978-nucleotide open reading frame encoding a polypeptide of 1136 amino acids with a calculated molecular mass of 128 kDa. A sequence alignment of mouse RPA2 with the corresponding gene from Drosophila melanogaster and yeast reveals a much lower sequence similarity of this subunit of RNA polymerase I (Pol I) compared to the second largest subunit of other eukaryotic RNA polymerases. Four Pol I-specific regions, termed I alpha-I delta, are conserved in the N-terminal part of RPA2. The structural features of the different domains as well as the homology to essential functional domains found in other RNA polymerases are discussed.
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Affiliation(s)
- P Seither
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
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35
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Schnapp G, Graveley BR, Grummt I. TFIIS binds to mouse RNA polymerase I and stimulates transcript elongation and hydrolytic cleavage of nascent rRNA. Mol Gen Genet 1996; 252:412-9. [PMID: 8879242 DOI: 10.1007/bf02173006] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Efficient transcription elongation by RNA polymerase I (Pol I) requires a specific Pol I-associated factor, termed TIF-IC. Here we show that TFIIS, a factor that has previously been shown to promote read-through past many types of blocks to elongation by RNA polymerase II, also enhances Pol I-directed transcription elongation. In a reconstituted transcription system containing purified proteins, TFIIS stimulates Pol I transcription by increasing the overall rate of RNA chain elongation. As with Pol II, ternary Pol I complexes cleave the 3' end of the nascent transcripts in response to TFIIS. The truncated RNAs remain bound to the template, are subject to pyrophosphorolysis, and can be chased into longer transcripts. Moreover, we show by immunoprecipitation and specific affinity chromatography that TFIIS physically interacts with Pol I. The results suggest that nascent transcript cleavage by TFIIS or a TFIIS-related factor may be a general mechanism by which both Pol I and Pol II can bypass transcriptional impediments.
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Affiliation(s)
- G Schnapp
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
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36
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Abstract
We have used nascent strand determination analysis to map start sites of DNA replication in the mouse ribosomal gene cluster in which individual copies of the ribosomal genes are separated by intergenic spacer regions. One origin of bidirectional replication (OBR) was localized within a 3 kb region centered about 1.6 kb upstream of the rDNA transcription start site. At least one additional initiation site is situated near the 3' end of the transcription unit. Adjacent to the OBR at the transcription start site are located two amplification-promoting sequences, i.e., APS1 and APS2. Nuclease-hypersensitive sites were identified in both of the two APSs as well as in the OBR region, thus indicating that these sequences have an altered chromatin structure. In the OBR an intrinsically bent region, a purine-rich element and other prospective initiation zone components are found.
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Affiliation(s)
- E Gögel
- Institut für Biochemie, Universität Würzburg, Biozentrum, D-97074 Würzburg, Germany
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37
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Eberhard D, Grummt I. Species specificity of ribosomal gene transcription: a factor associated with human RNA polymerase I prevents transcription of mouse rDNA. DNA Cell Biol 1996; 15:167-73. [PMID: 8634144 DOI: 10.1089/dna.1996.15.167] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
An intrinsic property of class I gene transcription by RNA polymerase I (Pol I) is the species specificity of the initiation reaction. Previous studies have demonstrated that species-specific rDNA promoter recognition is brought about by a TBP-TAF complex, termed TIF-IB in mouse and SL1 in man. We have compared the ability of affinity-purified TIF-IB and SL1 to direct transcription from the homologous rDNA template both in a reconstituted transcription system and in nuclear extracts prepared from mouse and human cells. We show that Pol I from both species and the individual transcription factors, with the exception of TIF-IB/SL1, are functionally interchangeable in the reconstituted transcription system containing purified proteins. In nuclear extracts, however, species-specific differences are obvious. Whereas SL1 reprograms a heterologous mouse extract to recognize the human promoter, TIF-IB fails to reprogram a human extract unless it is complemented with mouse Pol I. Crude human, but not mouse, Pol I exhibits species-specific differences that disappear after purification. We propose that in extracts and less purified fractions human Pol I exists as 'holoenzyme' containing associated protein(s) that prevent assembly of TIF-IB-directed initiation complexes at the murine rDNA promoter.
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Affiliation(s)
- D Eberhard
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
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38
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Affiliation(s)
- A Schnapp
- Division of Molecular Biology of the Cell II/0120, German Cancer Research Center, Heidelberg, Germany
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39
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Abstract
An unusual property of ribosomal gene transcription is its marked species specificity. This results from distinct promoter-recognition properties of the RNA polymerase I transcription apparatus. The purification and functional characterization of TIF-IB/SL1, a promoter-recognition factor containing the TATA-binding protein, as well as the recent cloning of cDNAs encoding the three subunits (TAF(I)s) of the respective human and mouse factor, will facilitate the molecular analysis of the mechanisms underlying species-specific rDNA transcription and reveal how the basal transcriptional machinery has evolved.
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Affiliation(s)
- J Heix
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
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40
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Voit R, Kuhn A, Sander EE, Grummt I. Activation of mammalian ribosomal gene transcription requires phosphorylation of the nucleolar transcription factor UBF. Nucleic Acids Res 1995; 23:2593-9. [PMID: 7651819 PMCID: PMC307079 DOI: 10.1093/nar/23.14.2593] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The nucleolar factor UBF is phosphorylated by casein kinase II (CKII) at serine residues within the C-terminal acidic domain which is required for transcription activation. To investigate the biological significance of UBF modification, we have compared the trans-activating properties of cellular UBF and recombinant UBF expressed in Escherichia coli. Using a variety of assays we demonstrate that unphosphorylated UBF is transcriptionally inactive and has to be phosphorylated at multiple sites to stimulate transcription. Examination of cDNA mutants in which the serine residues within the C-terminal domain were altered by site-directed mutagenesis demonstrates that CKII-mediated phosphorylations of UBF contribute to, but are not sufficient for, transcriptional activation. Besides CKII, other cellular protein kinases phosphorylate UBF at distinct sites in a growth-dependent manner. The marked differences in the tryptic peptide maps of UBF from growing and serum-starved cells suggest that alterations in the degree of UBF phosphorylation may modulate rRNA synthetic activity in response to extracellular signals.
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Affiliation(s)
- R Voit
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg
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41
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Evers R, Grummt I. Molecular coevolution of mammalian ribosomal gene terminator sequences and the transcription termination factor TTF-I. Proc Natl Acad Sci U S A 1995; 92:5827-31. [PMID: 7597036 PMCID: PMC41594 DOI: 10.1073/pnas.92.13.5827] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Both the DNA elements and the nuclear factors that direct termination of ribosomal gene transcription exhibit species-specific differences. Even between mammals--e.g., human and mouse--the termination signals are not identical and the respective transcription termination factors (TTFs) which bind to the terminator sequence are not fully interchangeable. To elucidate the molecular basis for this species-specificity, we have cloned TTF-I from human and mouse cells and compared their structural and functional properties. Recombinant TTF-I exhibits species-specific DNA binding and terminates transcription both in cell-free transcription assays and in transfection experiments. Chimeric constructs of mouse TTF-I and human TTF-I reveal that the major determinant for species-specific DNA binding resides within the C terminus of TTF-I. Replacing 31 C-terminal amino acids of mouse TTF-I with the homologous human sequences relaxes the DNA-binding specificity and, as a consequence, allows the chimeric factor to bind the human terminator sequence and to specifically stop rDNA transcription.
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Affiliation(s)
- R Evers
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg
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42
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Evers R, Smid A, Rudloff U, Lottspeich F, Grummt I. Different domains of the murine RNA polymerase I-specific termination factor mTTF-I serve distinct functions in transcription termination. EMBO J 1995; 14:1248-56. [PMID: 7720715 PMCID: PMC398203 DOI: 10.1002/j.1460-2075.1995.tb07108.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Termination of mouse ribosomal gene transcription by RNA polymerase I (Pol I) requires the specific interaction of a DNA binding protein, mTTF-I, with an 18 bp sequence element located downstream of the rRNA coding region. Here we describe the molecular cloning and functional characterization of the cDNA encoding this transcription termination factor. Recombinant mTTF-I binds specifically to the murine terminator elements and terminates Pol I transcription in a reconstituted in vitro system. Deletion analysis has defined a modular structure of mTTF-I comprising a dispensable N-terminal half, a large C-terminal DNA binding region and an internal domain which is required for transcription termination. Significantly, the C-terminal region of mTTF-I reveals striking homology to the DNA binding domains of the proto-oncogene c-Myb and the yeast transcription factor Reb1p. Site-directed mutagenesis of one of the tryptophan residues that is conserved in the homology region of c-Myb, Reb1p and mTTF-I abolishes specific DNA binding, a finding which underscores the functional relevance of these residues in DNA-protein interactions.
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Affiliation(s)
- R Evers
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg
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43
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Abstract
DNA-dependent protein kinase (DNA-PK) comprises a catalytic subunit of approximately 350 kD (p350) and a DNA-binding component termed Ku. Although DNA-PK can phosphorylate many transcription factors, no function for this enzyme in transcription has been reported thus far. Here, we show that DNA-PK strongly represses transcription by RNA polymerase I (Pol I). Transcriptional repression by DNA-PK requires ATP hydrolysis, and DNA-PK must be colocalized on the same DNA molecule as the Pol I transcription machinery. Consistent with DNA-PK requiring DNA ends for activity, transcriptional inhibition only occurs effectively on linearized templates. Mechanistic studies including single-round transcriptions, abortive initiation assays, and factor-independent transcription on a tailed template demonstrate that DNA-PK inhibits initiation (i.e., the formation of the first phosphodiester bonds) but does not affect transcription elongation. Repression of transcription involves phosphorylation of the transcription initiation complex, and rescue experiments reveal that the inactivated factor remains bound to the promoter and thus prevents initiation complex formation. We discuss the possible relevance of these findings in regard to the control of rRNA synthesis in vivo.
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Affiliation(s)
- A Kuhn
- German Cancer Research Centre, Heidelberg
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44
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Rudloff U, Stunnenberg HG, Keaveney M, Grummt I. Yeast TBP can replace its human homologue in the RNA polymerase I-specific multisubunit factor SL1. J Mol Biol 1994; 243:840-5. [PMID: 7966304 DOI: 10.1006/jmbi.1994.1686] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Basic mechanisms of transcription initiation are conserved from yeast to man. However, in contrast to genes transcribed by RNA polymerases II and III, ribosomal gene transcription by RNA polymerase I (Pol I) is species-specific. Promoter selectivity is mediated by SL1/TIF-IB, a multiprotein complex containing the TATA-binding protein (TBP) and TBP-associated factors (TAFs) which bind to DNA and nucleate the assembly of initiation complexes. Using a human cell line that expresses epitope-tagged yeast TBP, we have isolated a chimeric complex consisting of yeast TBP and human TAFs which faithfully promotes human rDNA transcription in vitro. This result argues that specific interactions between TBP and Pol I-specific TAFs have been evolutionarily conserved between distant species. In addition, this finding also underscores the importance of TAFs in determining promoter selectivity of Pol I.
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Affiliation(s)
- U Rudloff
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg
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45
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Abstract
We have characterized a transcription factor from Ehrlich ascites cells that is required for ribosomal gene transcription by RNA polymerase I (Pol I). This factor, termed TIF-IC, has a native molecular mass of 65 kDa, associates with Pol I, and is required both for the assembly of Sarkosyl-resistant initiation complexes and for the formation of the first internucleotide bonds. In addition to its function in transcription initiation, TIF-IC also plays a role in elongation of nascent RNA chains. At suboptimal levels of TIF-IC, transcripts with heterogeneous 3' ends are formed which are chased into full-length transcripts by the addition of more TIF-IC. Moreover, on a tailed template, which allows initiation in the absence of auxiliary factors, TIF-IC was found to stimulate the overall rate of transcription elongation and suppress pausing of Pol I. Thus TIF-IC appears to serve a function similar to the Pol II-specific factor TFIIF which is required for Pol II transcription initiation and elongation.
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Affiliation(s)
- G Schnapp
- Institute of Cell and Tumor Biology, German Cancer Research Center, Heidelberg
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46
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Rudloff U, Eberhard D, Grummt I. The conserved core domain of the human TATA binding protein is sufficient to assemble the multisubunit RNA polymerase I-specific transcription factor SL1. Proc Natl Acad Sci U S A 1994; 91:8229-33. [PMID: 8058785 PMCID: PMC44579 DOI: 10.1073/pnas.91.17.8229] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The human ribosomal RNA polymerase (Pol) I promoter selectivity factor SL1 is a complex consisting of the TATA binding protein (TBP) and three TBP-associated factors (TAFs). We have investigated which elements of TBP are involved in the assembly of Pol I-specific TBP-TAF complexes by comparing SL1 isolated from two human cell lines, one expressing epitope-tagged full-length TBP and another expressing a deletion of nearly the entire N-terminal domain (e delta NTBP). We have immunopurified epitope-tagged full-length TBP- and e delta NTBP-TAF complexes and show that e delta NTBP reconstitutes SL1 activity almost as well as full-length TBP. Moreover, e delta NTBP is shown to be associated with all three Pol I-specific TAFs. Thus, the core of TBP alone is sufficient for the correct assembly of the Pol I-specific TBP-TAF complex, and the variable N-terminal region of human TBP is not required for transcriptional activity. We also demonstrate by an in vitro protein-protein interaction assay that TBP directly interacts with the smallest TAF, TAFI48.
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Affiliation(s)
- U Rudloff
- German Cancer Research Center, Division of Molecular Biology of the Cell II, Heidelberg
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47
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Rudloff U, Eberhard D, Tora L, Stunnenberg H, Grummt I. TBP-associated factors interact with DNA and govern species specificity of RNA polymerase I transcription. EMBO J 1994; 13:2611-6. [PMID: 8013460 PMCID: PMC395135 DOI: 10.1002/j.1460-2075.1994.tb06551.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Unlike genes transcribed by RNA polymerases II and III, transcription by RNA polymerase I is highly species-specific. Ribosomal promoter selectivity is brought about by a multisubunit transcription factor (SL1/TIF-IB) which consists of the TATA-binding protein (TBP) and three TBP-associated factors (TAFs). To determine the basis for the inability of SL1/TIF-IB to recognize heterologous rDNA, the transcriptional properties and the subunit composition of the murine and the human factor, as well as a chimeric complex containing epitope-tagged human TBP and murine TAFs, have been compared. We show that TBP can be exchanged between the human and mouse factor indicating that the variable N-terminal domain of TBP does not play a significant role in rDNA promoter selectivity. Instead, DNA binding is brought about by the TAFs. UV crosslinking experiments demonstrate that binding to the ribosomal gene promoter is mediated by two TAFs (TAFI48 and TAFI68) which have the same electrophoretic mobility in the human and mouse factor. The largest TAF is different in both species and is suggested to play a role in the species-specific assembly of productive preinitiation complexes. Thus, evolutionary changes of rDNA promoter sequences have been accompanied by changes in specific TAFs.
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Affiliation(s)
- U Rudloff
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg
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48
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Lescure A, Lutz Y, Eberhard D, Jacq X, Krol A, Grummt I, Davidson I, Chambon P, Tora L. The N-terminal domain of the human TATA-binding protein plays a role in transcription from TATA-containing RNA polymerase II and III promoters. EMBO J 1994; 13:1166-75. [PMID: 7510635 PMCID: PMC394926 DOI: 10.1002/j.1460-2075.1994.tb06366.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In eukaryotes, the TATA box binding protein (TBP) is an integral component of the transcription initiation complexes of all three classes of nuclear RNA polymerases. In this study we have investigated the role of the N-terminal region of human TBP in transcription initiation from RNA polymerase (Pol) I, II and III promoters by using three monoclonal antibodies (mAbs). Each antibody recognizes a distinct epitope in the N-terminal domain of human TBP. We demonstrate that these antibodies differentially affect transcription from distinct classes of promoters. One antibody, mAb1C2, and a synthetic peptide comprising its epitope selectively inhibited in vitro transcription from TATA-containing, but not from TATA-less promoters, irrespective of whether they were transcribed by Pol II or Pol III. Transcription by Pol I, on the other hand, was not affected. Two other antibodies and their respective epitope peptides did not affect transcription from any of the promoters tested. Order of addition experiments indicate that mAb1C2 did not prevent binding of TBP to the TATA box or the formation of the TBP-TFIIA-TFIIB complex but rather inhibited a subsequent step of preinitiation complex formation. These data suggest that a defined region within the N-terminal domain of human TBP may be involved in specific protein-protein interactions required for the assembly of functional preinitiation complexes on TATA-containing, but not on TATA-less promoters.
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Affiliation(s)
- A Lescure
- LGME du CNRS, U 184 de l'INSERM, Faculté de Médecine, Strasbourg, France
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49
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Kuhn A, Voit R, Stefanovsky V, Evers R, Bianchi M, Grummt I. Functional differences between the two splice variants of the nucleolar transcription factor UBF: the second HMG box determines specificity of DNA binding and transcriptional activity. EMBO J 1994; 13:416-24. [PMID: 8313887 PMCID: PMC394823 DOI: 10.1002/j.1460-2075.1994.tb06276.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The nucleolar transcription factor UBF consists of two proteins, UBF1 and UBF2, which originate by alternative splicing. Here we show that deletion of 37 amino acids within the second of five HMG box motifs in UBF2 is important for the dual role of UBF as transcriptional activator and antirepressor. UBF1 is a potent antirepressor and transcriptional activator, whereas the ability of UBF2 to counteract histone H1-mediated repression and to stimulate ribosomal gene transcription both in vivo and in vitro is at least one order of magnitude lower. The difference in transcriptional activity between UBF1 and UBF2 is due to their different binding to the ribosomal gene promoter and enhancer. Apparently, the presence of an intact HMG box2 modulates the sequence-specific binding of UBF to rDNA control elements. However, the interaction of UBF with rDNA does not entirely depend on sequence recognition. Both UBF isoforms bind efficiently to four-way junction DNA, indicating that they recognize defined DNA structures rather than specific sequences. The results demonstrate that the HMG boxes are functionally diverse and that HMG box2 plays an important role in specific binding of UBF to rDNA.
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Affiliation(s)
- A Kuhn
- German Cancer Research Center, Heidelberg
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50
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Schnapp G, Santori F, Carles C, Riva M, Grummt I. The HMG box-containing nucleolar transcription factor UBF interacts with a specific subunit of RNA polymerase I. EMBO J 1994; 13:190-9. [PMID: 8306961 PMCID: PMC394792 DOI: 10.1002/j.1460-2075.1994.tb06248.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mammalian transcription activator protein UBF contains five tandemly repeated HMG homology domains which are required for DNA binding. We have used highly purified RNA polymerase I (Pol I) and upstream binding factor (UBF) and investigated whether these two proteins interact in solution. We show by a variety of different experimental approaches, such as immunoprecipitation, glycerol gradient sedimentation, affinity chromatography and protein blotting, that UBF physically associates with Pol I. Mutational analysis reveals that the HMG boxes play an important role in this specific interaction. UBF binds to mouse and yeast Pol I, demonstrating that the interaction of UBF with Pol I has been conserved during evolution. Interestingly, in both species one Pol I-specific subunit (34.5 kDa in yeast and 62 kDa in mouse) was recognized by UBF. No specific interaction was observed with Pol II. Unexpectedly, UBF was found to associate also with a unique subunit of yeast Pol III. This apparent specific interaction of UBF with the two classes of RNA polymerases may reflect functionally important interactions of HMG box-containing transcription factors with the transcriptional apparatus.
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Affiliation(s)
- G Schnapp
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg
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