1
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Affiliation(s)
- Finn Werner
- RNAP Laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London , Darwin Building, Gower Street, London WC1E 6BT, U.K
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2
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Gómez-Herreros F, de Miguel-Jiménez L, Morillo-Huesca M, Delgado-Ramos L, Muñoz-Centeno MC, Chávez S. TFIIS is required for the balanced expression of the genes encoding ribosomal components under transcriptional stress. Nucleic Acids Res 2012; 40:6508-19. [PMID: 22544605 PMCID: PMC3413141 DOI: 10.1093/nar/gks340] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Transcription factor IIS (TFIIS) stimulates RNA cleavage by RNA polymerase II by allowing backtracked enzymes to resume transcription elongation. Yeast cells do not require TFIIS for viability, unless they suffer severe transcriptional stress due to NTP-depleting drugs like 6-azauracil or mycophenolic acid. In order to broaden our knowledge on the role of TFIIS under transcriptional stress, we carried out a genetic screening for suppressors of TFIIS-lacking cells’ sensitivity to 6-azauracil and mycophenolic acid. Five suppressors were identified, four of which were related to the transcriptional regulation of those genes encoding ribosomal components [rRNAs and ribosomal proteins (RP)], including global regulator SFP1. This led us to discover that RNA polymerase II is hypersensitive to the absence of TFIIS under NTP scarcity conditions when transcribing RP genes. The absence of Sfp1 led to a profound alteration of the transcriptional response to NTP-depletion, thus allowing the expression of RP genes to resist these stressful conditions in the absence of TFIIS. We discuss the effect of transcriptional stress on ribosome biogenesis and propose that TFIIS contributes to prevent a transcriptional imbalance between rDNA and RP genes.
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Affiliation(s)
- Fernando Gómez-Herreros
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Avda Reina Mercedes 6. E-41012 Seville, Spain
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3
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Felle M, Exler JH, Merkl R, Dachauer K, Brehm A, Grummt I, Längst G. DNA sequence encoded repression of rRNA gene transcription in chromatin. Nucleic Acids Res 2010; 38:5304-14. [PMID: 20421213 PMCID: PMC2938192 DOI: 10.1093/nar/gkq263] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Eukaryotic genomes are packaged into nucleosomes that occlude DNA from interacting with most DNA-binding proteins. Nucleosome positioning and chromatin organization is critical for gene regulation. We have investigated the mechanism by which nucleosomes are positioned at the promoters of active and silent rRNA genes (rDNA). The reconstitution of nucleosomes on rDNA results in sequence-dependent nucleosome positioning at the rDNA promoter that mimics the chromatin structure of silent rRNA genes in vivo, suggesting that active mechanisms are required to reorganize chromatin structure upon gene activation. Nucleosomes are excluded from positions observed at active rRNA genes, resulting in transcriptional repression on chromatin. We suggest that the repressed state is the default chromatin organization of the rDNA and gene activation requires ATP-dependent chromatin remodelling activities that move the promoter-bound nucleosome about 22-bp upstream. We suggest that nucleosome remodelling precedes promoter-dependent transcriptional activation as specific inhibition of ATP-dependent chromatin remodelling suppresses the initiation of RNA Polymerase I transcription in vitro. Once initiated, RNA Polymerase I is capable of elongating through reconstituted chromatin without apparent displacement of the nucleosomes. The results reveal the functional cooperation of DNA sequence and chromatin remodelling complexes in nucleosome positioning and in establishing the epigenetic active or silent state of rRNA genes.
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Affiliation(s)
- Max Felle
- Institut für Biochemie III, Universität Regensburg, Universitätsstr. 31, 93053 Regensburg, Germany
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4
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The Paf1 complex is required for efficient transcription elongation by RNA polymerase I. Proc Natl Acad Sci U S A 2009; 106:2153-8. [PMID: 19164765 DOI: 10.1073/pnas.0812939106] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Regulation of RNA polymerase I (Pol I) transcription is critical for controlling ribosome synthesis. Most previous investigations into Pol I transcription regulation have focused on transcription initiation. To date, the factors involved in the control of Pol I transcription elongation are poorly understood. The Paf1 complex (Paf1C) is a well-defined factor that influences polymerase II (Pol II) transcription elongation. We found that Paf1C associates with rDNA. Deletion of genes for Paf1C subunits (CDC73, CTR9, or PAF1) reduces the rRNA synthesis rate; however, there is no significant alteration of rDNA copy number or Pol I occupancy of the rDNA. Furthermore, EM analysis revealed a substantial increase in the frequency of large gaps between transcribing polymerases in ctr9Delta mutant cells compared with WT. Together, these data indicate that Paf1C promotes Pol I transcription through the rDNA by increasing the net rate of elongation. Thus, the multifunctional, conserved transcription factor Paf1C plays an important role in transcription elongation by Pol I in vivo.
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5
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Ghavi-Helm Y, Michaut M, Acker J, Aude JC, Thuriaux P, Werner M, Soutourina J. Genome-wide location analysis reveals a role of TFIIS in RNA polymerase III transcription. Genes Dev 2008; 22:1934-47. [PMID: 18628399 DOI: 10.1101/gad.471908] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
TFIIS is a transcription elongation factor that stimulates transcript cleavage activity of arrested RNA polymerase II (Pol II). Recent studies revealed that TFIIS has also a role in Pol II transcription initiation. To improve our understanding of TFIIS function in vivo, we performed genome-wide location analysis of this factor. Under normal growth conditions, TFIIS was detected on Pol II-transcribed genes, and TFIIS occupancy was well correlated with that of Pol II, indicating that TFIIS recruitment is not restricted to NTP-depleted cells. Unexpectedly, TFIIS was also detected on almost all Pol III-transcribed genes. TFIIS and Pol III occupancies correlated well genome-wide on this novel class of targets. In vivo, some dst1 mutants were partly defective in tRNA synthesis and showed a reduced Pol III occupancy at the restrictive temperature. In vitro transcription assays suggested that TFIIS may affect Pol III start site selection. These data provide strong in vivo and in vitro evidence in favor of a role of TFIIS as a general Pol III transcription factor.
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6
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Alic N, Ayoub N, Landrieux E, Favry E, Baudouin-Cornu P, Riva M, Carles C. Selectivity and proofreading both contribute significantly to the fidelity of RNA polymerase III transcription. Proc Natl Acad Sci U S A 2007; 104:10400-5. [PMID: 17553959 PMCID: PMC1965525 DOI: 10.1073/pnas.0704116104] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We examine here the mechanisms ensuring the fidelity of RNA synthesis by RNA polymerase III (Pol III). Misincorporation could only be observed by using variants of Pol III deficient in the intrinsic RNA cleavage activity. Determination of relative rates of the reactions producing correct and erroneous transcripts at a specific position on a tRNA gene, combined with computational methods, demonstrated that Pol III has a highly efficient proofreading activity increasing its transcriptional fidelity by a factor of 10(3) over the error rate determined solely by selectivity (1.8 x 10(-4)). We show that Pol III slows down synthesis past a misincorporation to achieve efficient proofreading. We discuss our findings in the context of transcriptional fidelity studies performed on RNA Pols, proposing that the fidelity of transcription is more crucial for Pol III than Pol II.
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Affiliation(s)
- Nazif Alic
- Commissariat à l'Énergie Atomique, Institut de Biologie et de Technologies de Saclay, F-91191 Gif sur Yvette Cedex, France
| | - Nayla Ayoub
- Commissariat à l'Énergie Atomique, Institut de Biologie et de Technologies de Saclay, F-91191 Gif sur Yvette Cedex, France
| | - Emilie Landrieux
- Commissariat à l'Énergie Atomique, Institut de Biologie et de Technologies de Saclay, F-91191 Gif sur Yvette Cedex, France
| | - Emmanuel Favry
- Commissariat à l'Énergie Atomique, Institut de Biologie et de Technologies de Saclay, F-91191 Gif sur Yvette Cedex, France
| | - Peggy Baudouin-Cornu
- Commissariat à l'Énergie Atomique, Institut de Biologie et de Technologies de Saclay, F-91191 Gif sur Yvette Cedex, France
| | - Michel Riva
- Commissariat à l'Énergie Atomique, Institut de Biologie et de Technologies de Saclay, F-91191 Gif sur Yvette Cedex, France
- To whom correspondence should be addressed. E-mail:
| | - Christophe Carles
- Commissariat à l'Énergie Atomique, Institut de Biologie et de Technologies de Saclay, F-91191 Gif sur Yvette Cedex, France
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7
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Schneider DA, French SL, Osheim YN, Bailey AO, Vu L, Dodd J, Yates JR, Beyer AL, Nomura M. RNA polymerase II elongation factors Spt4p and Spt5p play roles in transcription elongation by RNA polymerase I and rRNA processing. Proc Natl Acad Sci U S A 2006; 103:12707-12. [PMID: 16908835 PMCID: PMC1568913 DOI: 10.1073/pnas.0605686103] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Previous investigations into the mechanisms that control RNA Polymerase (Pol) I transcription have primarily focused on the process of transcription initiation, thus little is known regarding postinitiation steps in the transcription cycle. Spt4p and Spt5p are conserved throughout eukaryotes, and they affect elongation by Pol II. We have found that these two proteins copurify with Pol I and associate with the rDNA in vivo. Disruption of the gene for Spt4p resulted in a modest decrease in growth and rRNA synthesis rates at the permissive temperature, 30 degrees C. Furthermore, biochemical and EM analyses showed clear defects in rRNA processing. These data suggest that Spt4p, Spt5p, and, potentially, other regulators of Pol I transcription elongation play important roles in coupling rRNA transcription to its processing and ribosome assembly.
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Affiliation(s)
- D. A. Schneider
- *Department of Biological Chemistry, University of California, Irvine, CA 92697-1700
| | - S. L. French
- Department of Microbiology, University of Virginia Health System, Charlottesville, VA 22908-0734; and
| | - Y. N. Osheim
- Department of Microbiology, University of Virginia Health System, Charlottesville, VA 22908-0734; and
| | - A. O. Bailey
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92130
| | - L. Vu
- *Department of Biological Chemistry, University of California, Irvine, CA 92697-1700
| | - J. Dodd
- *Department of Biological Chemistry, University of California, Irvine, CA 92697-1700
| | - J. R. Yates
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92130
| | - A. L. Beyer
- Department of Microbiology, University of Virginia Health System, Charlottesville, VA 22908-0734; and
- To whom correspondence may be addressed. E-mail:
or
| | - M. Nomura
- *Department of Biological Chemistry, University of California, Irvine, CA 92697-1700
- To whom correspondence may be addressed. E-mail:
or
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8
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Abstract
In the extensive network of interdependent biochemical processes required for cell growth and division, there is mounting evidence that ribosomal DNA transcription by RNA polymerase I (pol I) not only drives cell growth via its direct role in production of the ribosomal RNA (rRNA) component of the protein-synthesis machinery, but that it is also crucial in determining the fate of the cell. Considerable progress has been made in recent years towards understanding both the function of components of the pol I transcription machinery and how cells accomplish the tight control of pol I transcription, balancing the supply of rRNA with demand under different growth conditions.
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Affiliation(s)
- Jackie Russell
- Division of Gene Regulation and Expression, Wellcome Trust Biocentre, University of Dundee, Dundee DD1 5EH, Scotland, UK
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9
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Poole AM, Logan DT. Modern mRNA proofreading and repair: clues that the last universal common ancestor possessed an RNA genome? Mol Biol Evol 2005; 22:1444-55. [PMID: 15774424 PMCID: PMC7107533 DOI: 10.1093/molbev/msi132] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
RNA repair has now been demonstrated to be a genuine biological process and appears to be present in all three domains of life. In this article, we consider what this might mean for the transition from an early RNA-dominated world to modern cells possessing genetically encoded proteins and DNA. There are significant gaps in our understanding of how the modern protein-DNA world could have evolved from a simpler system, and it is currently uncertain whether DNA genomes evolved once or twice. Against this backdrop, the discovery of RNA repair in modern cells is timely food for thought and brings us conceptually one step closer to understanding how RNA genomes were replaced by DNA genomes. We have examined the available literature on multisubunit RNA polymerase structure and function and conclude that a strong case can be made that the Last Universal Common Ancestor (LUCA) possessed a repair-competent RNA polymerase, which would have been capable of acting on an RNA genome. However, while this lends credibility to the proposal that the LUCA had an RNA genome, the alternative, that LUCA had a DNA genome, cannot be completely ruled out.
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Affiliation(s)
- Anthony M Poole
- Department of Molecular Biology and Functional Genomics, Stockholm University, Stockholm, Sweden.
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10
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Adelman K, Marr MT, Werner J, Saunders A, Ni Z, Andrulis ED, Lis JT. Efficient release from promoter-proximal stall sites requires transcript cleavage factor TFIIS. Mol Cell 2005; 17:103-12. [PMID: 15629721 DOI: 10.1016/j.molcel.2004.11.028] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2004] [Revised: 09/21/2004] [Accepted: 10/22/2004] [Indexed: 11/28/2022]
Abstract
Uninduced heat shock genes are poised for rapid activation, with RNA polymerase II (Pol II) transcriptionally engaged, but paused or stalled, within the promoter-proximal region. Upon heat shock, this Pol II is promptly released from the promoter region and additional Pol II and transcription factors are robustly recruited to the gene. Regulation of the heat shock response relies upon factors that modify the efficiency of elongation through the initially transcribed sequence. Here, we report that Pol II is susceptible to transcription arrest within the promoter-proximal region of Drosophila hsp70 and that transcript cleavage factor TFIIS is essential for rapid induction of hsp70 RNA. Moreover, using a tandem RNAi-ChIP assay, we discovered that TFIIS is not required to establish the stalled Pol II, but that TFIIS is critical for efficient release of Pol II from the hsp70 promoter region and the subsequent recruitment of additional Pol II upon heat induction.
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Affiliation(s)
- Karen Adelman
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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11
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Németh A, Strohner R, Grummt I, Längst G. The chromatin remodeling complex NoRC and TTF-I cooperate in the regulation of the mammalian rRNA genes in vivo. Nucleic Acids Res 2004; 32:4091-9. [PMID: 15292447 PMCID: PMC514363 DOI: 10.1093/nar/gkh732] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The transcription termination factor (TTF)-I is a multifunctional nucleolar protein that terminates ribosomal gene transcription, mediates replication fork arrest and regulates RNA polymerase I transcription on chromatin. TTF-I plays a dual role in rDNA regulation, being involved in both activation and silencing of rDNA transcription. The N-terminal part of TTF-I contains a negative regulatory domain (NRD) that inhibits DNA binding. Here we show that interactions between the NRD and the C-terminal part of TTF-I mask the DNA-binding domain of TTF-I. However, interaction with TIP5, a subunit of the nucleolar chromatin remodeling complex, NoRC, recovers DNA-binding activity. We have mapped the protein domains that mediate the interaction between TTF-I and TIP5. The association of TIP5 with the NRD facilitates DNA binding of TTF-I and leads to the recruitment of NoRC to the rDNA promoter. Thus, TTF-I and NoRC act in concert to silence rDNA transcription.
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Affiliation(s)
- Attila Németh
- Adolf Butenandt Institut, Molekularbiologie, Ludwig-Maximilians-Universität München, Schillerstrasse 44, D-80336 München, Germany
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12
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Strohner R, Németh A, Nightingale KP, Grummt I, Becker PB, Längst G. Recruitment of the nucleolar remodeling complex NoRC establishes ribosomal DNA silencing in chromatin. Mol Cell Biol 2004; 24:1791-8. [PMID: 14749393 PMCID: PMC344174 DOI: 10.1128/mcb.24.4.1791-1798.2004] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The rRNA gene cluster consists of multiple transcription units. Half of these are active, while the other half are transcriptionally inactive. Previously, in vivo studies have demonstrated that silencing of ribosomal DNA (rDNA) is mediated by the chromatin remodeling NoRC (nucleolar remodeling complex). To explore the mechanisms underlying NoRC-directed silencing of rDNA transcription, we investigated the effect of recombinant NoRC on RNA polymerase I transcription on reconstituted chromatin templates. We show that NoRC interacts with the transcription terminator factor (TTF-I), and this interaction is required both for the binding of TTF-I to its promoter-proximal target site and for the recruitment of NoRC to the promoter. After association with the rDNA promoter, NoRC alters the position of the promoter-bound nucleosome, thereby repressing RNA polymerase I transcription. This NoRC-directed rDNA repression requires the N terminus of histone H4. Repression is effective before preinitiation complex formation and as such is unable to exert an effect upon activated rDNA genes. Furthermore, the early steps of rDNA repression do not depend on DNA and histone modifications. These results reveal an important role for TTF-I in recruiting NoRC to rDNA and an active role for NoRC in the establishment of rDNA silencing.
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MESH Headings
- Acetylation
- Adenosine Triphosphatases/genetics
- Adenosine Triphosphatases/metabolism
- Animals
- Cell Line
- Chromatin/genetics
- Chromatin/metabolism
- Chromatin Assembly and Disassembly
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- DNA Methylation
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal/metabolism
- DNA, Superhelical/chemistry
- DNA, Superhelical/genetics
- DNA, Superhelical/metabolism
- DNA-Binding Proteins/metabolism
- Gene Silencing
- Histones/chemistry
- Histones/metabolism
- Kinetics
- Macromolecular Substances
- Promoter Regions, Genetic/genetics
- Protein Binding
- RNA Polymerase I/metabolism
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- Templates, Genetic
- Transcription Factors
- Transcription, Genetic/genetics
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Affiliation(s)
- Ralf Strohner
- Adolf-Butenandt-Institut, Molekularbiologie, Ludwig Maximilians Universität, 80336 Munich. German
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13
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Krogan NJ, Peng WT, Cagney G, Robinson MD, Haw R, Zhong G, Guo X, Zhang X, Canadien V, Richards DP, Beattie BK, Lalev A, Zhang W, Davierwala AP, Mnaimneh S, Starostine A, Tikuisis AP, Grigull J, Datta N, Bray JE, Hughes TR, Emili A, Greenblatt JF. High-definition macromolecular composition of yeast RNA-processing complexes. Mol Cell 2004; 13:225-39. [PMID: 14759368 DOI: 10.1016/s1097-2765(04)00003-6] [Citation(s) in RCA: 301] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2003] [Revised: 11/18/2003] [Accepted: 11/24/2003] [Indexed: 11/29/2022]
Abstract
A remarkably large collection of evolutionarily conserved proteins has been implicated in processing of noncoding RNAs and biogenesis of ribonucleoproteins. To better define the physical and functional relationships among these proteins and their cognate RNAs, we performed 165 highly stringent affinity purifications of known or predicted RNA-related proteins from Saccharomyces cerevisiae. We systematically identified and estimated the relative abundance of stably associated polypeptides and RNA species using a combination of gel densitometry, protein mass spectrometry, and oligonucleotide microarray hybridization. Ninety-two discrete proteins or protein complexes were identified comprising 489 different polypeptides, many associated with one or more specific RNA molecules. Some of the pre-rRNA-processing complexes that were obtained are discrete sub-complexes of those previously described. Among these, we identified the IPI complex required for proper processing of the ITS2 region of the ribosomal RNA primary transcript. This study provides a high-resolution overview of the modular topology of noncoding RNA-processing machinery.
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Affiliation(s)
- Nevan J Krogan
- Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
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14
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Gromak N, Rideau A, Southby J, Scadden ADJ, Gooding C, Hüttelmaier S, Singer RH, Smith CWJ. The PTB interacting protein raver1 regulates alpha-tropomyosin alternative splicing. EMBO J 2003; 22:6356-64. [PMID: 14633994 PMCID: PMC291850 DOI: 10.1093/emboj/cdg609] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2003] [Revised: 09/19/2003] [Accepted: 10/13/2003] [Indexed: 01/09/2023] Open
Abstract
Regulated switching of the mutually exclusive exons 2 and 3 of alpha-tropomyosin (TM) involves repression of exon 3 in smooth muscle cells. Polypyrimidine tract-binding protein (PTB) is necessary but not sufficient for regulation of TM splicing. Raver1 was identified in two-hybrid screens by its interactions with the cytoskeletal proteins actinin and vinculin, and was also found to interact with PTB. Consistent with these interactions raver1 can be localized in either the nucleus or cytoplasm. Here we show that raver1 is able to promote the smooth muscle-specific alternative splicing of TM by enhancing PTB-mediated repression of exon 3. This activity of raver1 is dependent upon characterized PTB-binding regulatory elements and upon a region of raver1 necessary for interaction with PTB. Heterologous recruitment of raver1, or just its C-terminus, induced very high levels of exon 3 skipping, bypassing the usual need for PTB binding sites downstream of exon 3. This suggests a novel mechanism for PTB-mediated splicing repression involving recruitment of raver1 as a potent splicing co-repressor.
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Affiliation(s)
- Natalia Gromak
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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15
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Weilbaecher RG, Awrey DE, Edwards AM, Kane CM. Intrinsic transcript cleavage in yeast RNA polymerase II elongation complexes. J Biol Chem 2003; 278:24189-99. [PMID: 12692127 DOI: 10.1074/jbc.m211197200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transcript elongation can be interrupted by a variety of obstacles, including certain DNA sequences, DNA-binding proteins, chromatin, and DNA lesions. Bypass of many of these impediments is facilitated by elongation factor TFIIS through a mechanism that involves cleavage of the nascent transcript by the RNA polymerase II/TFIIS elongation complex. Highly purified yeast RNA polymerase II is able to perform transcript hydrolysis in the absence of TFIIS. The "intrinsic" cleavage activity is greatly stimulated at mildly basic pH and requires divalent cations. Both arrested and stalled complexes can carry out the intrinsic cleavage reaction, although not all stalled complexes are equally efficient at this reaction. Arrested complexes in which the nascent transcript was cleaved in the absence of TFIIS were reactivated to readthrough blocks to elongation. Thus, cleavage of the nascent transcript is sufficient for reactivating some arrested complexes. Small RNA products released following transcript cleavage in stalled ternary complexes differ depending upon whether the cleavage has been induced by TFIIS or has occurred in mildly alkaline conditions. In contrast, both intrinsic and TFIIS-induced small RNA cleavage products are very similar when produced from an arrested ternary complex. Although alpha-amanitin interferes with the transcript cleavage stimulated by TFIIS, it has little effect on the intrinsic cleavage reaction. A mutant RNA polymerase previously shown to be refractory to TFIIS-induced transcript cleavage is essentially identical to the wild type polymerase in all tested aspects of intrinsic cleavage.
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Affiliation(s)
- Rodney G Weilbaecher
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
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16
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Fish RN, Kane CM. Promoting elongation with transcript cleavage stimulatory factors. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1577:287-307. [PMID: 12213659 DOI: 10.1016/s0167-4781(02)00459-1] [Citation(s) in RCA: 182] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Transcript elongation by RNA polymerase is a dynamic process, capable of responding to a number of intrinsic and extrinsic signals. A number of elongation factors have been identified that enhance the rate or efficiency of transcription. One such class of factors facilitates RNA polymerase transcription through blocks to elongation by stimulating the polymerase to cleave the nascent RNA transcript within the elongation complex. These cleavage factors are represented by the Gre factors from prokaryotes, and TFIIS and TFIIS-like factors found in archaea and eukaryotes. High-resolution structures of RNA polymerases and the cleavage factors in conjunction with biochemical investigations and genetic analyses have provided insights into the mechanism of action of these elongation factors. However, there are yet many unanswered questions regarding the regulation of these factors and their effects on target genes.
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Affiliation(s)
- Rachel N Fish
- Department of Molecular and Cell Biology, University of California-Berkeley, 401 Barker Hall, Berkeley, CA 94720-3202, USA
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17
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Olson MOJ, Hingorani K, Szebeni A. Conventional and nonconventional roles of the nucleolus. INTERNATIONAL REVIEW OF CYTOLOGY 2002; 219:199-266. [PMID: 12211630 PMCID: PMC7133188 DOI: 10.1016/s0074-7696(02)19014-0] [Citation(s) in RCA: 144] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
As the most prominent of subnuclear structures, the nucleolus has a well-established role in ribosomal subunit assembly. Additional nucleolar functions, not related to ribosome biogenesis, have been discovered within the last decade. Built around multiple copies of the genes for preribosomal RNA (rDNA), nucleolar structure is largely dependent on the process of ribosome assembly. The nucleolus is disassembled during mitosis at which time preribosomal RNA transcription and processing are suppressed; it is reassembled at the end of mitosis in part from components preserved from the previous cell cycle. Expression of preribosomal RNA (pre-rRNA) is regulated by the silencing of individual rDNA genes via alterations in chromatin structure or by controlling RNA polymerase I initiation complex formation. Preribosomal RNA processing and posttranscriptional modifications are guided by a multitude of small nucleolar RNAs. Nearly completed ribosomal subunits are exported to the cytoplasm by an established nuclear export system with the aid of specialized adapter molecules. Some preribosomal and nucleolar components are transiently localized in Cajal bodies, presumably for modification or assembly. The nonconventional functions of nucleolus include roles in viral infections, nuclear export, sequestration of regulatory molecules, modification of small RNAs, RNP assembly, and control of aging, although some of these functions are not well established. Additional progress in defining the mechanisms of each step in ribosome biogenesis as well as clarification of the precise role of the nucleolus in nonconventional activities is expected in the next decade.
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Affiliation(s)
- Mark O J Olson
- Department of Biochemistry, University of Mississippi Medical Center, Jackson 39216, USA
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Hara R, Selby CP, Liu M, Price DH, Sancar A. Human transcription release factor 2 dissociates RNA polymerases I and II stalled at a cyclobutane thymine dimer. J Biol Chem 1999; 274:24779-86. [PMID: 10455150 DOI: 10.1074/jbc.274.35.24779] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
RNA polymerase II stalled at a lesion in the transcribed strand is thought to constitute a signal for transcription-coupled repair. Transcription factors that act on RNA polymerase in elongation mode potentially influence this mode of repair. Previously, it was shown that transcription elongation factors TFIIS and Cockayne's syndrome complementation group B protein did not disrupt the ternary complex of RNA polymerase II stalled at a thymine cyclobutane dimer, nor did they enable RNA polymerase II to bypass the dimer. Here we investigated the effect of the transcription factor 2 on RNA polymerase II and RNA polymerase I stalled at thymine dimers. Transcription factor 2 is known to release transcripts from RNA polymerase II early elongation complex generated by pulse-transcription. We found that factor 2 (which is also called release factor) disrupts the ternary complex of RNA polymerase II at a thymine dimer and surprisingly exerts the same effect on RNA polymerase I. These findings show that in mammalian cells a RNA polymerase I or RNA polymerase II transcript truncated by a lesion in the template strand may be discarded unless repair is accomplished rapidly by a mechanism that does not displace stalled RNA polymerases.
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Affiliation(s)
- R Hara
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
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19
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Reeder RH. Regulation of RNA polymerase I transcription in yeast and vertebrates. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1999; 62:293-327. [PMID: 9932458 DOI: 10.1016/s0079-6603(08)60511-5] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
This article focuses on what is currently known about the regulation of transcription by RNA polymerase I (pol I) in eukaryotic organisms at opposite ends of the evolutionary spectrum--a yeast, Saccharomyces cerevisiae, and vertebrates, including mice, frogs, and man. Contemporary studies that have defined the DNA sequence elements are described, as well as the majority of the basal transcription factors essential for pol I transcription. Situations in which pol I transcription is known to be regulated are reviewed and possible regulatory mechanisms are critically discussed. Some aspects of basal pol I transcription machinery appear to have been conserved from fungi to vertebrates, but other aspects have evolved, perhaps to meet the needs of a metazoan organism. Different parts of the pol I transcription machinery are regulatory targets depending on different physiological stimuli. This suggests that multiple signaling pathways may also be involved. The involvement of ribosomal genes and their transcripts in events such as mitosis, cancer, and aging is discussed.
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Affiliation(s)
- R H Reeder
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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20
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Polyakov A, Richter C, Malhotra A, Koulich D, Borukhov S, Darst SA. Visualization of the binding site for the transcript cleavage factor GreB on Escherichia coli RNA polymerase. J Mol Biol 1998; 281:465-73. [PMID: 9698562 DOI: 10.1006/jmbi.1998.1958] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The structure of Escherichia coli core RNA polymerase (RNAP) complexed with the transcript cleavage factor GreB was determined from electron micrographs of negatively stained, flattened helical crystals. A binding assay was developed to establish that GreB was incorporated into the RNA polymerase crystals with high occupancy through interactions between the globular C-terminal domain and the RNA polymerase. Comparison of the core RNAP:GreB structure with the previously determined structure of core RNAP located the GreB binding site on one face of the RNA polymerase, next to but not in the 25 A-diameter channel of RNA polymerase.
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Affiliation(s)
- A Polyakov
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10021, USA
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21
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Mote J, Reines D. Recognition of a human arrest site is conserved between RNA polymerase II and prokaryotic RNA polymerases. J Biol Chem 1998; 273:16843-52. [PMID: 9642244 PMCID: PMC3371603 DOI: 10.1074/jbc.273.27.16843] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA sequences that arrest transcription by either eukaryotic RNA polymerase II or Escherichia coli RNA polymerase have been identified previously. Elongation factors SII and GreB are RNA polymerase-binding proteins that enable readthrough of arrest sites by these enzymes, respectively. This functional similarity has led to general models of elongation applicable to both eukaryotic and prokaryotic enzymes. Here we have transcribed with phage and bacterial RNA polymerases, a human DNA sequence previously defined as an arrest site for RNA polymerase II. The phage and bacterial enzymes both respond efficiently to the arrest signal in vitro at limiting levels of nucleoside triphosphates. The E. coli polymerase remains in a template-engaged complex for many hours, can be isolated, and is potentially active. The enzyme displays a relatively slow first-order loss of elongation competence as it dwells at the arrest site. Bacterial RNA polymerase arrested at the human site is reactivated by GreB in the same way that RNA polymerase II arrested at this site is stimulated by SII. Very efficient readthrough can be achieved by phage, bacterial, and eukaryotic RNA polymerases in the absence of elongation factors if 5-Br-UTP is substituted for UTP. These findings provide additional and direct evidence for functional similarity between prokaryotic and eukaryotic transcription elongation and readthrough mechanisms.
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Affiliation(s)
| | - Daniel Reines
- To whom correspondence should be addressed. Tel.: 404-727-3361; Fax: 404-727-3452;
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22
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Längst G, Becker PB, Grummt I. TTF-I determines the chromatin architecture of the active rDNA promoter. EMBO J 1998; 17:3135-45. [PMID: 9606195 PMCID: PMC1170652 DOI: 10.1093/emboj/17.11.3135] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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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23
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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] [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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Abstract
Ternary complexes of DNA-dependent RNA polymerase with its DNA template and nascent transcript are central intermediates in transcription. In recent years, several unusual biochemical reactions have been discovered that affect the progression of RNA polymerase in ternary complexes through various transcription units. These reactions can be signaled intrinsically, by nucleic acid sequences and the RNA polymerase, or extrinsically, by protein or other regulatory factors. These factors can affect any of these processes, including promoter proximal and promoter distal pausing in both prokaryotes and eukaryotes, and therefore play a central role in regulation of gene expression. In eukaryotic systems, at least two of these factors appear to be related to cellular transformation and human cancers. New models for the structure of ternary complexes, and for the mechanism by which they move along DNA, provide plausible explanations for novel biochemical reactions that have been observed. These models predict that RNA polymerase moves along DNA without the constant possibility of dissociation and consequent termination. A further prediction of these models is that the polymerase can move in a discontinuous or inchworm-like manner. Many direct predictions of these models have been confirmed. However, one feature of RNA chain elongation not predicted by the model is that the DNA sequence can determine whether the enzyme moves discontinuously or monotonically. In at least two cases, the encounter between the RNA polymerase and a DNA block to elongation appears to specifically induce a discontinuous mode of synthesis. These findings provide important new insights into the RNA chain elongation process and offer the prospect of understanding many significant biological regulatory systems at the molecular level.
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Affiliation(s)
- S M Uptain
- Department of Molecular and Cell Biology, University of California at Berkeley 94720, USA.
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