1
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Yague-Sanz C. Shaping the chromatin landscape at rRNA and tRNA genes, an emerging new role for RNA polymerase II transcription? Yeast 2024; 41:135-147. [PMID: 38126234 DOI: 10.1002/yea.3921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/17/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
Eukaryotic genes must be condensed into chromatin while remaining accessible to the transcriptional machinery to support gene expression. Among the three eukaryotic RNA polymerases (RNAP), RNAPII is unique, partly because of the C-terminal domain (CTD) of its largest subunit, Rpb1. Rpb1 CTD can be extensively modified during the transcription cycle, allowing for the co-transcriptional recruitment of specific interacting proteins. These include chromatin remodeling factors that control the opening or closing of chromatin. How the CTD-less RNAPI and RNAPIII deal with chromatin at rRNA and tRNA genes is less understood. Here, we review recent advances in our understanding of how the chromatin at tRNA genes and rRNA genes can be remodeled in response to environmental cues in yeast, with a particular focus on the role of local RNAPII transcription in recruiting chromatin remodelers at these loci. In fission yeast, RNAPII transcription at tRNA genes is important to re-establish a chromatin environment permissive to tRNA transcription, which supports growth from stationary phase. In contrast, local RNAPII transcription at rRNA genes correlates with the closing of the chromatin in starvation in budding and fission yeast, suggesting a role in establishing silent chromatin. These opposite roles might support a general model where RNAPII transcription recruits chromatin remodelers to tRNA and rRNA genes to promote the closing and reopening of chromatin in response to the environment.
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Affiliation(s)
- Carlo Yague-Sanz
- Damien Hermand's Laboratory, URPhyM-GEMO, The University of Namur, Namur, Belgium
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2
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Huffines AK, Schneider DA. Hmo1 Promotes Efficient Transcription Elongation by RNA Polymerase I in Saccharomyces cerevisiae. Genes (Basel) 2024; 15:247. [PMID: 38397236 PMCID: PMC10888141 DOI: 10.3390/genes15020247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
RNA polymerase I (Pol I) is responsible for synthesizing the three largest eukaryotic ribosomal RNAs (rRNAs), which form the backbone of the ribosome. Transcription by Pol I is required for cell growth and, therefore, is subject to complex and intricate regulatory mechanisms. To accomplish this robust regulation, the cell engages a series of trans-acting transcription factors. One such factor, high mobility group protein 1 (Hmo1), has long been established as a trans-acting factor for Pol I in Saccharomyces cerevisiae; however, the mechanism by which Hmo1 promotes rRNA synthesis has not been defined. Here, we investigated the effect of the deletion of HMO1 on transcription elongation by Pol I in vivo. We determined that Hmo1 is an important activator of transcription elongation, and without this protein, Pol I accumulates across rDNA in a sequence-specific manner. Our results demonstrate that Hmo1 promotes efficient transcription elongation by rendering Pol I less sensitive to pausing in the G-rich regions of rDNA.
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Affiliation(s)
| | - David A. Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
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3
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Boltengagen M, Verhagen D, Wolff MR, Oberbeckmann E, Hanke M, Gerland U, Korber P, Mueller-Planitz F. A single fiber view of the nucleosome organization in eukaryotic chromatin. Nucleic Acids Res 2024; 52:166-185. [PMID: 37994698 PMCID: PMC10783498 DOI: 10.1093/nar/gkad1098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 10/13/2023] [Accepted: 10/31/2023] [Indexed: 11/24/2023] Open
Abstract
Eukaryotic cells are thought to arrange nucleosomes into extended arrays with evenly spaced nucleosomes phased at genomic landmarks. Here we tested to what extent this stereotypic organization describes the nucleosome organization in Saccharomyces cerevisiae using Fiber-Seq, a long-read sequencing technique that maps entire nucleosome arrays on individual chromatin fibers in a high throughput manner. With each fiber coming from a different cell, Fiber-Seq uncovers cell-to-cell heterogeneity. The long reads reveal the nucleosome architecture even over repetitive DNA such as the ribosomal DNA repeats. The absolute nucleosome occupancy, a parameter that is difficult to obtain with conventional sequencing approaches, is a direct readout of Fiber-Seq. We document substantial deviations from the stereotypical nucleosome organization with unexpectedly long linker DNAs between nucleosomes, gene bodies missing entire nucleosomes, cell-to-cell heterogeneity in nucleosome occupancy, heterogeneous phasing of arrays and irregular nucleosome spacing. Nucleosome array structures are indistinguishable throughout the gene body and with respect to the direction of transcription arguing against transcription promoting array formation. Acute nucleosome depletion destroyed most of the array organization indicating that nucleosome remodelers cannot efficiently pack nucleosomes under those conditions. Given that nucleosomes are cis-regulatory elements, the cell-to-cell heterogeneity uncovered by Fiber-Seq provides much needed information to understand chromatin structure and function.
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Affiliation(s)
- Mark Boltengagen
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
| | - Daan Verhagen
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
- Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Michael Roland Wolff
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
- Physics of Complex Biosystems, Physics Department, Technical University of Munich, Garching, Germany
| | - Elisa Oberbeckmann
- Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Matthias Hanke
- Physics of Complex Biosystems, Physics Department, Technical University of Munich, Garching, Germany
| | - Ulrich Gerland
- Physics of Complex Biosystems, Physics Department, Technical University of Munich, Garching, Germany
| | - Philipp Korber
- Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Felix Mueller-Planitz
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
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4
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Schwank K, Schmid C, Fremter T, Engel C, Milkereit P, Griesenbeck J, Tschochner H. Features of yeast RNA polymerase I with special consideration of the lobe binding subunits. Biol Chem 2023; 404:979-1002. [PMID: 37823775 DOI: 10.1515/hsz-2023-0184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/13/2023] [Indexed: 10/13/2023]
Abstract
Ribosomal RNAs (rRNAs) are structural components of ribosomes and represent the most abundant cellular RNA fraction. In the yeast Saccharomyces cerevisiae, they account for more than 60 % of the RNA content in a growing cell. The major amount of rRNA is synthesized by RNA polymerase I (Pol I). This enzyme transcribes exclusively the rRNA gene which is tandemly repeated in about 150 copies on chromosome XII. The high number of transcribed rRNA genes, the efficient recruitment of the transcription machinery and the dense packaging of elongating Pol I molecules on the gene ensure that enough rRNA is generated. Specific features of Pol I and of associated factors confer promoter selectivity and both elongation and termination competence. Many excellent reviews exist about the state of research about function and regulation of Pol I and how Pol I initiation complexes are assembled. In this report we focus on the Pol I specific lobe binding subunits which support efficient, error-free, and correctly terminated rRNA synthesis.
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Affiliation(s)
- Katrin Schwank
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Catharina Schmid
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Tobias Fremter
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Christoph Engel
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Philipp Milkereit
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Joachim Griesenbeck
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Herbert Tschochner
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
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5
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Sasaki M, Kobayashi T. Regulatory processes that maintain or alter ribosomal DNA stability during the repair of programmed DNA double-strand breaks. Genes Genet Syst 2023; 98:103-119. [PMID: 35922917 DOI: 10.1266/ggs.22-00046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Organisms have evolved elaborate mechanisms that maintain genome stability. Deficiencies in these mechanisms result in changes to the nucleotide sequence as well as copy number and structural variations in the genome. Genome instability has been implicated in numerous human diseases. However, genomic alterations can also be beneficial as they are an essential part of the evolutionary process. Organisms sometimes program genomic changes that drive genetic and phenotypic diversity. Therefore, genome alterations can have both positive and negative impacts on cellular growth and functions, which underscores the need to control the processes that restrict or induce such changes to the genome. The ribosomal RNA gene (rDNA) is highly abundant in eukaryotic genomes, forming a cluster where numerous rDNA copies are tandemly arrayed. Budding yeast can alter the stability of its rDNA cluster by changing the rDNA copy number within the cluster or by producing extrachromosomal rDNA circles. Here, we review the mechanisms that regulate the stability of the budding yeast rDNA cluster during repair of DNA double-strand breaks that are formed in response to programmed DNA replication fork arrest.
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Affiliation(s)
- Mariko Sasaki
- Laboratory of Genome Regeneration, Institute for Quantitative Biosciences (IQB), The University of Tokyo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | - Takehiko Kobayashi
- Laboratory of Genome Regeneration, Institute for Quantitative Biosciences (IQB), The University of Tokyo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
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6
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Huang Y, Liu Y, Guo X, Fan C, Yi C, Shi Q, Su H, Liu C, Yuan J, Liu D, Yang W, Han F. New insights on the evolution of nucleolar dominance in newly resynthesized hexaploid wheat Triticum zhukovskyi. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1298-1315. [PMID: 37246611 DOI: 10.1111/tpj.16320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/11/2023] [Accepted: 05/23/2023] [Indexed: 05/30/2023]
Abstract
Nucleolar dominance (ND) is a widespread epigenetic phenomenon in hybridizations where nucleolus transcription fails at the nucleolus organizer region (NOR). However, the dynamics of NORs during the formation of Triticum zhukovskyi (GGAu Au Am Am ), another evolutionary branch of allohexaploid wheat, remains poorly understood. Here, we elucidated genetic and epigenetic changes occurring at the NOR loci within the Am , G, and D subgenomes during allopolyploidization by synthesizing hexaploid wheat GGAu Au Am Am and GGAu Au DD. In T. zhukovskyi, Au genome NORs from T. timopheevii (GGAu Au ) were lost, while the second incoming NORs from T. monococcum (Am Am ) were retained. Analysis of the synthesized T. zhukovskyi revealed that rRNA genes from the Am genome were silenced in F1 hybrids (GAu Am ) and remained inactive after genome doubling and subsequent self-pollinations. We observed increased DNA methylation accompanying the inactivation of NORs in the Am genome and found that silencing of NORs in the S1 generation could be reversed by a cytidine methylase inhibitor. Our findings provide insights into the ND process during the evolutionary period of T. zhukovskyi and highlight that inactive rDNA units may serve as a 'first reserve' in the form of R-loops, contributing to the successful evolution of T. zhukovskyi.
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Affiliation(s)
- Yuhong Huang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xianrui Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chaolan Fan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Congyang Yi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qinghua Shi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Handong Su
- Huazhong Agricultural University, Hubei, 430070, China
| | - Chang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jing Yuan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dengcai Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wuyun Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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7
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Non-Coding, RNAPII-Dependent Transcription at the Promoters of rRNA Genes Regulates Their Chromatin State in S. cerevisiae. Noncoding RNA 2021; 7:ncrna7030041. [PMID: 34287362 PMCID: PMC8293398 DOI: 10.3390/ncrna7030041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/01/2021] [Accepted: 07/07/2021] [Indexed: 12/22/2022] Open
Abstract
Pervasive transcription is widespread in eukaryotes, generating large families of non-coding RNAs. Such pervasive transcription is a key player in the regulatory pathways controlling chromatin state and gene expression. Here, we describe long non-coding RNAs generated from the ribosomal RNA gene promoter called UPStream-initiating transcripts (UPS). In yeast, rDNA genes are organized in tandem repeats in at least two different chromatin states, either transcribed and largely depleted of nucleosomes (open) or assembled in regular arrays of nucleosomes (closed). The production of UPS transcripts by RNA Polymerase II from endogenous rDNA genes was initially documented in mutants defective for rRNA production by RNA polymerase I. We show here that UPS are produced in wild-type cells from closed rDNA genes but are hidden within the enormous production of rRNA. UPS levels are increased when rDNA chromatin states are modified at high temperatures or entering/leaving quiescence. We discuss their role in the regulation of rDNA chromatin states and rRNA production.
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8
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Egidi A, Di Felice F, Camilloni G. Saccharomyces cerevisiae rDNA as super-hub: the region where replication, transcription and recombination meet. Cell Mol Life Sci 2020; 77:4787-4798. [PMID: 32476055 PMCID: PMC11104796 DOI: 10.1007/s00018-020-03562-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 05/04/2020] [Accepted: 05/25/2020] [Indexed: 11/29/2022]
Abstract
Saccharomyces cerevisiae ribosomal DNA, the repeated region where rRNAs are synthesized by about 150 encoding units, hosts all the protein machineries responsible for the main DNA transactions such as replication, transcription and recombination. This and its repetitive nature make rDNA a unique and complex genetic locus compared to any other. All the different molecular machineries acting in this locus need to be accurately and finely controlled and coordinated and for this reason rDNA is one of the most impressive examples of highly complex molecular regulated loci. The region in which the large molecular complexes involved in rDNA activity and/or regulation are recruited is extremely small: that is, the 2.5 kb long intergenic spacer, interrupting each 35S RNA coding unit from the next. All S. cerevisiae RNA polymerases (I, II and III) transcribing the different genetic rDNA elements are recruited here; a sequence responsible for each rDNA unit replication, which needs its molecular apparatus, also localizes here; moreover, it is noteworthy that the rDNA replication proceeds almost unidirectionally because each replication fork is stopped in the so-called replication fork barrier. These localized fork blocking events induce, with a given frequency, the homologous recombination process by which cells maintain a high identity among the rDNA repeated units. Here, we describe the different processes involving the rDNA locus, how they influence each other and how these mutual interferences are highly regulated and coordinated. We propose that an rDNA conformation as a super-hub could help in optimizing the micro-environment for all basic DNA transactions.
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Affiliation(s)
- Alessandra Egidi
- Dipartimento di Biologia e Biotecnologie, Università di Roma, Sapienza, Rome, Italy
| | - Francesca Di Felice
- Dipartimento di Biologia e Biotecnologie, Università di Roma, Sapienza, Rome, Italy
| | - Giorgio Camilloni
- Dipartimento di Biologia e Biotecnologie, Università di Roma, Sapienza, Rome, Italy.
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9
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Dauban L, Kamgoué A, Wang R, Léger-Silvestre I, Beckouët F, Cantaloube S, Gadal O. Quantification of the dynamic behaviour of ribosomal DNA genes and nucleolus during yeast Saccharomyces cerevisiae cell cycle. J Struct Biol 2019; 208:152-164. [PMID: 31449968 DOI: 10.1016/j.jsb.2019.08.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 11/19/2022]
Abstract
Spatial organisation of chromosomes is a determinant of genome stability and is required for proper mitotic segregation. However, visualization of individual chromatids in living cells and quantification of their geometry, remains technically challenging. Here, we used live cell imaging to quantitate the three-dimensional conformation of yeast Saccharomyces cerevisiae ribosomal DNA (rDNA). rDNA is confined within the nucleolus and is composed of about 200 copies representing about 10% of the yeast genome. To fluorescently label rDNA in living cells, we generated a set of nucleolar proteins fused to GFP or made use of a tagged rDNA, in which lacO repetitions were inserted in each repeat unit. We could show that nucleolus is not modified in appearance, shape or size during interphase while rDNA is highly reorganized. Computationally tracing 3D rDNA paths allowed us to quantitatively assess rDNA size, shape and geometry. During interphase, rDNA was progressively reorganized from a zig-zag segmented line of small size (5,5 µm) to a long, homogeneous, line-like structure of 8,7 µm in metaphase. Most importantly, whatever the cell-cycle stage considered, rDNA fibre could be decomposed in subdomains, as previously suggested for 3D chromatin organisation. Finally, we could determine that spatial reorganisation of these subdomains and establishment of rDNA mitotic organisation is under the control of the cohesin complex.
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Affiliation(s)
- Lise Dauban
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Alain Kamgoué
- Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Renjie Wang
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Isabelle Léger-Silvestre
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Frédéric Beckouët
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Sylvain Cantaloube
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Olivier Gadal
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
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10
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Dynamic colocalization of 2 simultaneously active VSG expression sites within a single expression-site body in Trypanosoma brucei. Proc Natl Acad Sci U S A 2019; 116:16561-16570. [PMID: 31358644 PMCID: PMC6697882 DOI: 10.1073/pnas.1905552116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The African trypanosome Trypanosoma brucei expresses a single variant surface glycoprotein (VSG) gene from one of multiple VSG expression sites (ESs) in a stringent monoallelic fashion. The counting mechanism behind this restriction is poorly understood. Unusually for a eukaryote, the active ES is transcribed by RNA polymerase I (Pol I) within a unique Pol I body called the expression-site body (ESB). We have demonstrated the importance of the ESB in restricting the singular expression of VSG. We have generated double-expresser trypanosomes, which simultaneously express 2 ESs at the same time in an unstable dynamic fashion. These cells predominantly contain 1 ESB, and, surprisingly, simultaneous transcription of the 2 ESs is observed only when they are both colocalized within it. Monoallelic exclusion ensures that the African trypanosome Trypanosoma brucei exclusively expresses only 1 of thousands of different variant surface glycoprotein (VSG) coat genes. The active VSG is transcribed from 1 of 15 polycistronic bloodstream-form VSG expression sites (ESs), which are controlled in a mutually exclusive fashion. Unusually, T. brucei uses RNA polymerase I (Pol I) to transcribe the active ES, which is unprecedented among eukaryotes. This active ES is located within a unique extranucleolar Pol I body called the expression-site body (ESB). A stringent restriction mechanism prevents T. brucei from expressing multiple ESs at the same time, although how this is mediated is unclear. By using drug-selection pressure, we generated VSG double-expresser T. brucei lines, which have disrupted monoallelic exclusion, and simultaneously express 2 ESs in a dynamic fashion. The 2 unstably active ESs appear epigenetically similar to fully active ESs as determined by using chromatin immunoprecipitation for multiple epigenetic marks (histones H3 and H1, TDP1, and DNA base J). We find that the double-expresser cells, similar to wild-type single-expresser cells, predominantly contain 1 subnuclear ESB, as determined using Pol I or the ESB marker VEX1. Strikingly, simultaneous transcription of the 2 dynamically transcribed ESs is normally observed only when the 2 ESs are both located within this single ESB. This colocalization is reversible in the absence of drug selection. This discovery that simultaneously active ESs dynamically share a single ESB demonstrates the importance of this unique subnuclear body in restricting the monoallelic expression of VSG.
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11
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Genome Organization in and around the Nucleolus. Cells 2019; 8:cells8060579. [PMID: 31212844 PMCID: PMC6628108 DOI: 10.3390/cells8060579] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/09/2019] [Accepted: 06/11/2019] [Indexed: 12/17/2022] Open
Abstract
The nucleolus is the largest substructure in the nucleus, where ribosome biogenesis takes place, and forms around the nucleolar organizer regions (NORs) that comprise ribosomal RNA (rRNA) genes. Each cell contains hundreds of rRNA genes, which are organized in three distinct chromatin and transcriptional states—silent, inactive and active. Increasing evidence indicates that the role of the nucleolus and rRNA genes goes beyond the control of ribosome biogenesis. Recent results highlighted the nucleolus as a compartment for the location and regulation of repressive genomic domains and, together with the nuclear lamina, represents the hub for the organization of the inactive heterochromatin. In this review, we aim to describe the crosstalk between the nucleolus and the rest of the genome and how distinct rRNA gene chromatin states affect nucleolus structure and are implicated in genome stability, genome architecture, and cell fate decision.
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12
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How do cells count multi-copy genes?: "Musical Chair" model for preserving the number of rDNA copies. Curr Genet 2019; 65:883-885. [PMID: 30904990 DOI: 10.1007/s00294-019-00956-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 03/14/2019] [Accepted: 03/15/2019] [Indexed: 01/20/2023]
Abstract
To supply abundant ribosomes, multiple copies of ribosomal RNA genes (rDNA) are conserved from bacterial to human cells. In eukaryotic genomes, clusters of tandemly repeated rDNA units are present, and their number is stably maintained. Due to high level of transcription of rRNA genes, the repetitive structure is prone to rearrangement. In budding yeast, rDNA homeostasis can compensate for this by the regulation of recombination events that will change the copy number. The histone deacetylase Sir2 plays a key role in rDNA copy maintenance and its expression level determines a state of "maintenance" or "amplification" of rDNA copy number. We recently showed that Upstream Activating Factors (UAF) for RNA polymerase I act as a RNA polymerase II repressor of SIR2 transcription in response to rDNA copy loss. Furthermore, the amount of UAF, which is limited in the cell, determines the stable copy number of rDNA and is a molecular switch for rDNA recovery. In this mini-review, we propose a "Musical Chair" model for rDNA copy counting as mediated by UAF and Sir2. The model describes how a straightforward molecular mechanism can account for the "cellular memory" of the proper rDNA copy number.
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13
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Iida T, Kobayashi T. RNA Polymerase I Activators Count and Adjust Ribosomal RNA Gene Copy Number. Mol Cell 2019; 73:645-654.e13. [PMID: 30612878 DOI: 10.1016/j.molcel.2018.11.029] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/18/2018] [Accepted: 11/19/2018] [Indexed: 01/08/2023]
Abstract
Ribosome is the most abundant RNA-protein complex in a cell, and many copies of the ribosomal RNA gene (rDNA) have to be maintained. However, arrays of tandemly repeated rDNA genes can lose the copies by intra-repeat recombination. Loss of the rDNA copies of Saccharomyces cerevisiae is counteracted by gene amplification whereby the number of rDNA repeats stabilizes around 150 copies, suggesting the presence of a monitoring mechanism that counts and adjusts the number. Here, we report that, in response to rDNA copy loss, the upstream activating factor (UAF) for RNA polymerase I that transcribes the rDNA is released and directly binds to a RNA polymerase II-transcribed gene, SIR2, whose gene products silence rDNA recombination, to repress. We show that the amount of UAF determines the rDNA copy number that is stably maintained. UAF ensures rDNA production not only by rDNA transcription activation but also by its copy-number maintenance.
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Affiliation(s)
- Tetsushi Iida
- Laboratory of Genome Regeneration, Research Center for Biological Visualization, The Institute for Quantitative Biosciences (IQB), 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
| | - Takehiko Kobayashi
- Laboratory of Genome Regeneration, Research Center for Biological Visualization, The Institute for Quantitative Biosciences (IQB), 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; Collaborative Research Institute for Innovative Microbiology, the University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
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14
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Roscini L, Tristezza M, Corte L, Colabella C, Perrotta C, Rampino P, Robert V, Vu D, Cardinali G, Grieco F. Early Ongoing Speciation of Ogataea uvarum Sp. Nov. Within the Grape Ecosystem Revealed by the Internal Variability Among the rDNA Operon Repeats. Front Microbiol 2018; 9:1687. [PMID: 30123190 PMCID: PMC6085423 DOI: 10.3389/fmicb.2018.01687] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/06/2018] [Indexed: 11/13/2022] Open
Abstract
A yeast strain was isolated during a study on vineyard-associated yeast strains from Apulia in Southern Italy. ITS and LSU D1/D2 rDNA sequences showed this strain not to belong to any known species and was described as the type strain of Ogataea uvarum sp. nov., a close relative of O. philodendri. Several secondary peaks appeared in the sequences, suggesting internal heterogeneity among the copies of the rDNA. This hypothesis was tested by sequencing single clones of the marker region. The analyses showed different levels of variability throughout the operon with differences between the rRNA encoding genes and the internally transcribed regions. O. uvarum and O. philodendri share high frequency variants, i.e., variants frequently found in many clones, whereas there is a large variability of the low frequency polymorphisms, suggesting that the mechanism of homogenization is more active with the former than with the latter type of variation. These findings indicate that low frequency variants are detected in Sanger sequencing as secondary peaks whereas in Next Generation Sequencing (NGS) of metagenomics DNA would lead to an overestimate of the alpha diversity. For the first time in our knowledge, this investigation shed light on the variation of the copy number of the rDNA cistron during the yeast speciation process. These polymorphisms can be used to investigate on the processes occurring in these taxonomic markers during the separation of fungal species, it being a genetic process highly frequent in the complex microbial ecosystem existing in grape, must and wine.
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Affiliation(s)
- Luca Roscini
- Department of Pharmaceutical Sciences – Microbiology, University of Perugia, Perugia, Italy
| | - Mariana Tristezza
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Lecce, Italy
| | - Laura Corte
- Department of Pharmaceutical Sciences – Microbiology, University of Perugia, Perugia, Italy
| | - Claudia Colabella
- Department of Pharmaceutical Sciences – Microbiology, University of Perugia, Perugia, Italy
| | - Carla Perrotta
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Patrizia Rampino
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Vincent Robert
- Bioinformatics Unit, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Duong Vu
- Bioinformatics Unit, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences – Microbiology, University of Perugia, Perugia, Italy
- Centre of Excellence on Nanostructured Innovative Materials (CEMIN), Department of Chemistry Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Francesco Grieco
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Lecce, Italy
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15
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Borowska-Zuchowska N, Hasterok R. Epigenetics of the preferential silencing of Brachypodium stacei-originated 35S rDNA loci in the allotetraploid grass Brachypodium hybridum. Sci Rep 2017; 7:5260. [PMID: 28706212 PMCID: PMC5509716 DOI: 10.1038/s41598-017-05413-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 05/30/2017] [Indexed: 01/16/2023] Open
Abstract
Nucleolar dominance (ND), initially described as ‘differential amphiplasty’, is a phenomenon observed in some plant and animal allopolyploids and hybrids in which the selective suppression of the activity of 35S rRNA gene loci that have been inherited from one of the two or more ancestral genomes occurs. Although more than 80 years have passed since the discovery of ND, there is still a significant lack in our understanding of the mechanisms that determine this phenomenon. Here, we aimed to investigate the epigenetic status of 35S rRNA gene loci in the monocotyledonous Brachypodium hybridum, which is an allotetraploid that has resulted from a cross between B. distachyon and B. stacei. We revealed that the repressed B. stacei-inherited rDNA loci are characterised by a high level of DNA methylation. The global hypomethylation of B. hybridum nuclear DNA induced by 5-azacytidine, however, seems to be insufficient for the transcriptional reactivation of these loci, which indicates that factors other than DNA methylation are behind the suppression of B. stacei-originated loci. We also showed that the transcriptionally active and silenced fractions of rRNA genes that had been inherited from B. distachyon occupy different domains within the chromocentres adjacent to the nucleolus, depending on their epigenetic status.
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Affiliation(s)
- Natalia Borowska-Zuchowska
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, 28 Jagiellonska Street, 40-032, Katowice, Poland.
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, 28 Jagiellonska Street, 40-032, Katowice, Poland
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16
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Derenzini M, Pasquinelli G, O'Donohue MF, Ploton D, Thiry M. Structural and Functional Organization of Ribosomal Genes within the Mammalian Cell Nucleolus. J Histochem Cytochem 2016; 54:131-45. [PMID: 16204224 DOI: 10.1369/jhc.5r6780.2005] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Data on the in situ structural–functional organization of ribosomal genes in the mammalian cell nucleolus are reviewed here. Major findings on chromatin structure in situ come from investigations carried out using the Feulgen-like osmium ammine reaction as a highly specific electron-opaque DNA tracer. Intranucleolar chromatin shows three different levels of organization: compact clumps, fibers ranging from 11 to 30 nm, and loose agglomerates of extended DNA filaments. Both clumps and fibers of chromatin exhibit a nucleosomal organization that is lacking in the loose agglomerates of extended DNA filaments. In fact, these filaments constantly show a thickness of 2–3 nm, the same as a DNA doublehelix molecule. The loose agglomerates of DNA filaments are located in the fibrillar centers, the interphase counterpart of metaphase NORs, therefore being constituted by ribosomal DNA. The extended, non-nucleosomal configuration of this rDNA has been shown to be independent of transcriptional activity and characterizes ribosome genes that are either transcribed or transcriptionally silent. Data reviewed are consistent with a model of control for ribosome gene activity that is not mediated by changes in chromatin structure. The presence of rDNA in mammalian cells always structurally ready for transcription might facilitate a more rapid adjustment of the ribosome production in response to the metabolic needs of the cell.
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Affiliation(s)
- Massimo Derenzini
- Dipartimento di Patologia Sperimentale, Via S. Giacomo 14, 40126 Bologna, Italy.
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17
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Wang D, Mansisidor A, Prabhakar G, Hochwagen A. Condensin and Hmo1 Mediate a Starvation-Induced Transcriptional Position Effect within the Ribosomal DNA Array. Cell Rep 2016; 14:1010-1017. [PMID: 26832415 DOI: 10.1016/j.celrep.2016.01.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 10/30/2015] [Accepted: 12/28/2015] [Indexed: 02/06/2023] Open
Abstract
Repetitive DNA arrays are important structural features of eukaryotic genomes that are often heterochromatinized to suppress repeat instability. It is unclear, however, whether all repeats within an array are equally subject to heterochromatin formation and gene silencing. Here, we show that in starving Saccharomyces cerevisiae, silencing of reporter genes within the ribosomal DNA (rDNA) array is less pronounced in outer repeats compared with inner repeats. This position effect is linked to the starvation-induced contraction of the nucleolus. We show that the chromatin regulators condensin and Hmo1 redistribute within the rDNA upon starvation; that Hmo1, like condensin, is required for nucleolar contraction; and that the position effect partially depends on both proteins. Starvation-induced nucleolar contraction and differential desilencing of the outer rDNA repeats may provide a mechanism to activate rDNA-encoded RNAPII transcription units without causing general rDNA instability.
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Affiliation(s)
- Danni Wang
- Department of Biology, New York University, New York, NY 10003, USA
| | | | | | - Andreas Hochwagen
- Department of Biology, New York University, New York, NY 10003, USA.
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18
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Teschler S, Gotthardt J, Dammann G, Dammann RH. Aberrant DNA Methylation of rDNA and PRIMA1 in Borderline Personality Disorder. Int J Mol Sci 2016; 17:ijms17010067. [PMID: 26742039 PMCID: PMC4730312 DOI: 10.3390/ijms17010067] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/28/2015] [Accepted: 12/29/2015] [Indexed: 12/17/2022] Open
Abstract
Borderline personality disorder (BPD) is a serious psychic disease with a high risk for suicide. DNA methylation is a hallmark for aberrant epigenetic regulation and could be involved in the etiology of BPD. Previously, it has been reported that increased DNA methylation of neuropsychiatric genes is found in the blood of patients with BPD compared to healthy controls. Here, we analyzed DNA methylation patterns of the ribosomal RNA gene (rDNA promoter region and 5′-external transcribed spacer/5′ETS) and the promoter of the proline rich membrane anchor 1 gene (PRIMA1) in peripheral blood samples of 24 female patients (mean age (33 ± 11) years) diagnosed with DSM-IV BPD and in 11 female controls (mean age (32 ± 7) years). A significant aberrant methylation of rDNA and PRIMA1 was revealed for BPD patients using pyrosequencing. For the promoter of PRIMA1, the average methylation of six CpG sites was 1.6-fold higher in BPD patients compared to controls. In contrast, the methylation levels of the rDNA promoter region and the 5′ETS were significantly lower (0.9-fold) in patients with BPD compared to controls. Thus, for nine CpGs located in the rDNA promoter region and for four CpGs at the 5′ETS decreased methylation was found in peripheral blood of patients compared to controls. Our results suggest that aberrant methylation of rDNA and PRIMA1 is associated with the pathogenesis of BPD.
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Affiliation(s)
- Stefanie Teschler
- Institute for Genetics, Justus-Liebig-University Giessen, D-35392 Giessen, Germany.
| | - Julia Gotthardt
- Institute for Genetics, Justus-Liebig-University Giessen, D-35392 Giessen, Germany.
| | - Gerhard Dammann
- Psychiatric Hospital, Psychiatric Services of Thurgovia, CH-8596 Münsterlingen, Switzerland and Department of Psychiatry, Paracelsus Medical University, A-5020 Salzburg, Austria.
| | - Reinhard H Dammann
- Institute for Genetics, Justus-Liebig-University Giessen, D-35392 Giessen, Germany.
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19
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Charton R, Guintini L, Peyresaubes F, Conconi A. Repair of UV induced DNA lesions in ribosomal gene chromatin and the role of "Odd" RNA polymerases (I and III). DNA Repair (Amst) 2015; 36:49-58. [PMID: 26411875 DOI: 10.1016/j.dnarep.2015.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In fast growing eukaryotic cells, a subset of rRNA genes are transcribed at very high rates by RNA polymerase I (RNAPI). Nuclease digestion-assays and psoralen crosslinking have shown that they are open; that is, largely devoid of nucleosomes. In the yeast Saccharomyces cerevisae, nucleotide excision repair (NER) and photolyase remove UV photoproducts faster from open rRNA genes than from closed and nucleosome-loaded inactive rRNA genes. After UV irradiation, rRNA transcription declines because RNAPI halt at UV photoproducts and are then displaced from the transcribed strand. When the DNA lesion is quickly recognized by NER, it is the sub-pathway transcription-coupled TC-NER that removes the UV photoproduct. If dislodged RNAPI are replaced by nucleosomes before NER recognizes the lesion, then it is the sub-pathway global genome GG-NER that removes the UV photoproducts from the transcribed strand. Also, GG-NER maneuvers in the non-transcribed strand of open genes and in both strands of closed rRNA genes. After repair, transcription resumes and elongating RNAPI reopen the rRNA gene. In higher eukaryotes, NER in rRNA genes is inefficient and there is no evidence for TC-NER. Moreover, TC-NER does not occur in RNA polymerase III transcribed genes of both, yeast and human fibroblast.
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Affiliation(s)
- Romain Charton
- Département de Microbiologie et Infectiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Laetitia Guintini
- Département de Microbiologie et Infectiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - François Peyresaubes
- Département de Microbiologie et Infectiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Antonio Conconi
- Département de Microbiologie et Infectiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
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20
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Cahyani I, Cridge AG, Engelke DR, Ganley ARD, O'Sullivan JM. A sequence-specific interaction between the Saccharomyces cerevisiae rRNA gene repeats and a locus encoding an RNA polymerase I subunit affects ribosomal DNA stability. Mol Cell Biol 2015; 35:544-54. [PMID: 25421713 PMCID: PMC4285424 DOI: 10.1128/mcb.01249-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 11/08/2014] [Accepted: 11/16/2014] [Indexed: 11/20/2022] Open
Abstract
The spatial organization of eukaryotic genomes is linked to their functions. However, how individual features of the global spatial structure contribute to nuclear function remains largely unknown. We previously identified a high-frequency interchromosomal interaction within the Saccharomyces cerevisiae genome that occurs between the intergenic spacer of the ribosomal DNA (rDNA) repeats and the intergenic sequence between the locus encoding the second largest RNA polymerase I subunit and a lysine tRNA gene [i.e., RPA135-tK(CUU)P]. Here, we used quantitative chromosome conformation capture in combination with replacement mapping to identify a 75-bp sequence within the RPA135-tK(CUU)P intergenic region that is involved in the interaction. We demonstrate that the RPA135-IGS1 interaction is dependent on the rDNA copy number and the Msn2 protein. Surprisingly, we found that the interaction does not govern RPA135 transcription. Instead, replacement of a 605-bp region within the RPA135-tK(CUU)P intergenic region results in a reduction in the RPA135-IGS1 interaction level and fluctuations in rDNA copy number. We conclude that the chromosomal interaction that occurs between the RPA135-tK(CUU)P and rDNA IGS1 loci stabilizes rDNA repeat number and contributes to the maintenance of nucleolar stability. Our results provide evidence that the DNA loci involved in chromosomal interactions are composite elements, sections of which function in stabilizing the interaction or mediating a functional outcome.
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Affiliation(s)
- Inswasti Cahyani
- The Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - Andrew G Cridge
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - David R Engelke
- Department of Biological Chemistry, The University of Michigan, Ann Arbor, Michigan, USA
| | - Austen R D Ganley
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
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21
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Montiel EE, Cabrero J, Ruiz-Estévez M, Burke WD, Eickbush TH, Camacho JPM, López-León MD. Preferential occupancy of R2 retroelements on the B chromosomes of the grasshopper Eyprepocnemis plorans. PLoS One 2014; 9:e91820. [PMID: 24632855 PMCID: PMC3954772 DOI: 10.1371/journal.pone.0091820] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 02/14/2014] [Indexed: 02/02/2023] Open
Abstract
R2 non-LTR retrotransposons exclusively insert into the 28S rRNA genes of their host, and are expressed by co-transcription with the rDNA unit. The grasshopper Eyprepocnemis plorans contains transcribed rDNA clusters on most of its A chromosomes, as well as non-transcribed rDNA clusters on the parasitic B chromosomes found in many populations. Here the structure of the E. plorans R2 element, its abundance relative to the number of rDNA units and its retrotransposition activity were determined. Animals screened from five populations contained on average over 12,000 rDNA units on their A chromosomes, but surprisingly only about 100 R2 elements. Monitoring the patterns of R2 insertions in individuals from these populations revealed only low levels of retrotransposition. The low rates of R2 insertion observed in E. plorans differ from the high levels of R2 insertion previously observed in insect species that have many fewer rDNA units. It is proposed that high levels of R2 are strongly selected against in E. plorans, because the rDNA transcription machinery in this species is unable to differentiate between R2-inserted and uninserted units. The B chromosomes of E. plorans contain an additional 7,000 to 15,000 rDNA units, but in contrast to the A chromosomes, from 150 to over 1,500 R2 elements. The higher concentration of R2 in the inactive B chromosomes rDNA clusters suggests these chromosomes can act as a sink for R2 insertions thus further reducing the level of insertions on the A chromosomes. These studies suggest an interesting evolutionary relationship between the parasitic B chromosomes and R2 elements.
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Affiliation(s)
- Eugenia E. Montiel
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Josefa Cabrero
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Mercedes Ruiz-Estévez
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - William D. Burke
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Thomas H. Eickbush
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Juan Pedro M. Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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22
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Derenzini M, Olins AL, Olins DE. Chromatin structure in situ: the contribution of DNA ultrastructural cytochemistry. Eur J Histochem 2014; 58:2307. [PMID: 24704998 PMCID: PMC3980211 DOI: 10.4081/ejh.2014.2307] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 10/24/2013] [Accepted: 10/30/2013] [Indexed: 11/23/2022] Open
Abstract
Ultrastructural studies conducted in situ using conventional transmission electron microscopy have had relatively little impact on defining the structural organization of chromatin. This is due to the fact that in routine transmission electron microscopy, together with the deoxyribonucleoprotein, many different intermingled substances are contrasted, masking the ultrastructure of chromatin. By selective staining of DNA in thin sections, using the Feulgen-like osmium-ammine reaction, these drawbacks have been overcome and worthwhile data have been obtained both on the gross morphology and the ultrastructural-functional organization of chromatin in situ. In the present study these results are reviewed and discussed in light of recent achievements in both interphase nuclear chromatin compartmentalization in interphase nuclei and in the structural organization of chromatin fibers in transcriptionally active and inactive chromatin.
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23
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Srikumar T, Lewicki MC, Costanzo M, Tkach JM, van Bakel H, Tsui K, Johnson ES, Brown GW, Andrews BJ, Boone C, Giaever G, Nislow C, Raught B. Global analysis of SUMO chain function reveals multiple roles in chromatin regulation. ACTA ACUST UNITED AC 2013; 201:145-63. [PMID: 23547032 PMCID: PMC3613684 DOI: 10.1083/jcb.201210019] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Multiple large-scale analyses in yeast implicate SUMO chain function in the
maintenance of higher-order chromatin structure and transcriptional repression
of environmental stress response genes. Like ubiquitin, the small ubiquitin-related modifier (SUMO) proteins can form
oligomeric “chains,” but the biological functions of these
superstructures are not well understood. Here, we created mutant yeast strains
unable to synthesize SUMO chains (smt3allR) and
subjected them to high-content microscopic screening, synthetic genetic array
(SGA) analysis, and high-density transcript profiling to perform the first
global analysis of SUMO chain function. This comprehensive assessment identified
144 proteins with altered localization or intensity in
smt3allR cells, 149 synthetic genetic
interactions, and 225 mRNA transcripts (primarily consisting of stress- and
nutrient-response genes) that displayed a >1.5-fold increase in
expression levels. This information-rich resource strongly implicates SUMO
chains in the regulation of chromatin. Indeed, using several different
approaches, we demonstrate that SUMO chains are required for the maintenance of
normal higher-order chromatin structure and transcriptional repression of
environmental stress response genes in budding yeast.
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Affiliation(s)
- Tharan Srikumar
- Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
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24
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Rpd3- and spt16-mediated nucleosome assembly and transcriptional regulation on yeast ribosomal DNA genes. Mol Cell Biol 2013; 33:2748-59. [PMID: 23689130 DOI: 10.1128/mcb.00112-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ribosomal DNA (rDNA) genes in eukaryotes are organized into multicopy tandem arrays and transcribed by RNA polymerase I. During cell proliferation, ∼50% of these genes are active and have a relatively open chromatin structure characterized by elevated accessibility to psoralen cross-linking. In Saccharomyces cerevisiae, transcription of rDNA genes becomes repressed and chromatin structure closes when cells enter the diauxic shift and growth dramatically slows. In this study, we found that nucleosomes are massively depleted from the active rDNA genes during log phase and reassembled during the diauxic shift, largely accounting for the differences in psoralen accessibility between active and inactive genes. The Rpd3L histone deacetylase complex was required for diauxic shift-induced H4 and H2B deposition onto rDNA genes, suggesting involvement in assembly or stabilization of the entire nucleosome. The Spt16 subunit of FACT, however, was specifically required for H2B deposition, suggesting specificity for the H2A/H2B dimer. Miller chromatin spreads were used for electron microscopic visualization of rDNA genes in an spt16 mutant, which was found to be deficient in the assembly of normal nucleosomes on inactive genes and the disruption of nucleosomes on active genes, consistent with an inability to fully reactivate polymerase I (Pol I) transcription when cells exit stationary phase.
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25
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Narayanan MS, Rudenko G. TDP1 is an HMG chromatin protein facilitating RNA polymerase I transcription in African trypanosomes. Nucleic Acids Res 2013; 41:2981-92. [PMID: 23361461 PMCID: PMC3597664 DOI: 10.1093/nar/gks1469] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Unusually for a eukaryote, Trypanosoma brucei transcribes its variant surface glycoprotein (VSG) gene expression sites (ESs) in a monoallelic fashion using RNA polymerase I (Pol I). It is still unclear how ES transcription is controlled in T. brucei. Here, we show that the TDP1 architectural chromatin protein is an essential high mobility group box (HMGB) protein facilitating Pol I transcription in T. brucei. TDP1 is specifically enriched at the active compared with silent VSG ES and immediately downstream of ribosomal DNA promoters and is abundant in the nucleolus and the expression site body subnuclear compartments. Distribution of TDP1 at Pol I-transcribed loci is inversely correlated with histones. Depletion of TDP1 results in up to 40–90% reduction in VSG and rRNA transcripts and a concomitant increase in histones H3, H2A and H1 at these Pol I transcription units. TDP1 shares features with the Saccharomyces cerevisiae HMGB protein Hmo1, but it is the first architectural chromatin protein facilitating Pol I-mediated transcription of both protein coding genes as well as rRNA. These results show that TDP1 has a mutually exclusive relationship with histones on actively transcribed Pol I transcription units, providing insight into how Pol I transcription is controlled.
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Affiliation(s)
- Mani Shankar Narayanan
- Division of Cell and Molecular Biology, Imperial College London, South Kensington, London SW7 2AZ, UK
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26
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A population genetic model for the maintenance of R2 retrotransposons in rRNA gene loci. PLoS Genet 2013; 9:e1003179. [PMID: 23326244 PMCID: PMC3542110 DOI: 10.1371/journal.pgen.1003179] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 11/02/2012] [Indexed: 01/03/2023] Open
Abstract
R2 retrotransposable elements exclusively insert into the tandemly repeated rRNA genes, the rDNA loci, of their animal hosts. R2 elements form stable long-term associations with their host, in which all individuals in a population contain many potentially active copies, but only a fraction of these individuals show active R2 retrotransposition. Previous studies have found that R2 RNA transcripts are processed from a 28S co-transcript and that the likelihood of R2-inserted units being transcribed is dependent upon their distribution within the rDNA locus. Here we analyze the rDNA locus and R2 elements from nearly 100 R2-active and R2-inactive individuals from natural populations of Drosophila simulans. Along with previous findings concerning the structure and expression of the rDNA loci, these data were incorporated into computer simulations to model the crossover events that give rise to the concerted evolution of the rRNA genes. The simulations that best reproduce the population data assume that only about 40 rDNA units out of the over 200 total units are actively transcribed and that these transcribed units are clustered in a single region of the locus. In the model, the host establishes this transcription domain at each generation in the region with the fewest R2 insertions. Only if the host cannot avoid R2 insertions within this 40-unit domain are R2 elements active in that generation. The simulations also require that most crossover events in the locus occur in the transcription domain in order to explain the empirical observation that R2 elements are seldom duplicated by crossover events. Thus the key to the long-term stability of R2 elements is the stochastic nature of the crossover events within the rDNA locus, and the inevitable expansions and contractions that introduce and remove R2-inserted units from the transcriptionally active domain. Selfish transposable elements survive in eukaryotic genomes despite the elaborate mechanisms developed by the hosts to limit their activity. One accessible system that simplifies the complex interactions between element and host involves the R2 elements, which exclusively insert in the tandemly arranged rRNA genes. R2 exhibits remarkable stability in animal lineages even though each insertion inactivates one rRNA gene. Here we determine the size of the rDNA locus and R2 number in natural isolates of Drosophila simulans. Combined with previous data concerning the expression and regulation of R2, we develop a detailed population genetic model for rRNA gene and R2 evolution that duplicates all properties of the rRNA loci in natural populations. Critical components of the model are that only a contiguous 40 unit array of rRNA gene units are needed for transcription, that R2 elements are active only when present in this transcription domain, and that most of the crossovers in the rDNA loci occur in this domain. These results suggest that the key to the long-term survival of R2 is the redistribution of rDNA units in the locus brought about by the crossovers that maintain sequence identity in all rDNA units.
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27
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Epigenetic control of RNA polymerase I transcription in mammalian cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:393-404. [PMID: 23063748 DOI: 10.1016/j.bbagrm.2012.10.004] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 10/04/2012] [Accepted: 10/06/2012] [Indexed: 11/22/2022]
Abstract
rRNA synthesis is regulated by genetic and epigenetic mechanisms. Epigenetic states are metastable, changing in response to appropriate signals, thereby modulating transcription in vivo. The establishment, maintenance and reversal of epigenetic features are fundamental for the cell's ability to 'remember' past events, to adapt to environmental changes or developmental cues and to propagate this information to the progeny. As packaging into chromatin is critical for the stability and integrity of repetitive DNA, keeping a fraction of rRNA genes in a metastable heterochromatic conformation prevents aberrant exchanges between repeats, thus safeguarding nucleolar structure and rDNA stability. In this review, we will focus on the nature of the molecular signatures that characterize a given epigenetic state of rDNA in mammalian cells, including noncoding RNA, DNA methylation and histone modifications, and the mechanisms by which they are established and maintained. This article is part of a Special Issue entitled: Transcription by Odd Pols.
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Chromatin structure of ribosomal RNA genes in dipterans and its relationship to the location of nucleolar organizers. PLoS One 2012; 7:e44006. [PMID: 22952852 PMCID: PMC3431366 DOI: 10.1371/journal.pone.0044006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 07/27/2012] [Indexed: 01/12/2023] Open
Abstract
Nucleoli, nuclear organelles in which ribosomal RNA is synthesized and processed, emerge from nucleolar organizers (NORs) located in distinct chromosomal regions. In polytene nuclei of dipterans, nucleoli of some species can be observed under light microscopy exhibiting distinctive morphology: Drosophila and chironomid species display well-formed nucleoli in contrast to the fragmented and dispersed nucleoli seen in sciarid flies. The available data show no apparent relationship between nucleolar morphology and location of NORs in Diptera. The regulation of rRNA transcription involves controlling both the transcription rate per gene as well as the proportion of rRNA genes adopting a proper chromatin structure for transcription, since active and inactive rRNA gene copies coexist in NORs. Transcription units organized in nucleosomes and those lacking canonical nucleosomes can be analyzed by the method termed psoralen gel retarding assay (PGRA), allowing inferences on the ratio of active to inactive rRNA gene copies. In this work, possible connections between chromosomal location of NORs and proportion of active rRNA genes were studied in Drosophila melanogaster, and in chironomid and sciarid species. The data suggested a link between location of NORs and proportion of active rRNA genes since the copy number showing nucleosomal organization predominates when NORs are located in the pericentric heterochromatin. The results presented in this work are in agreement with previous data on the chromatin structure of rRNA genes from distantly related eukaryotes, as assessed by the PGRA.
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Wittner M, Hamperl S, Stöckl U, Seufert W, Tschochner H, Milkereit P, Griesenbeck J. Establishment and Maintenance of Alternative Chromatin States at a Multicopy Gene Locus. Cell 2011; 145:543-54. [DOI: 10.1016/j.cell.2011.03.051] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 01/17/2011] [Accepted: 03/18/2011] [Indexed: 11/15/2022]
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Abstract
The African trypanosome Trypanosoma brucei is a unicellular parasite which causes African sleeping sickness. Transcription in African trypanosomes displays some unusual features, as most of the trypanosome genome is transcribed as extensive polycistronic RNA Pol II (polymerase II) transcription units that are not transcriptionally regulated. In addition, RNA Pol I is used for transcription of a small subset of protein coding genes in addition to the rDNA (ribosomal DNA). These Pol I-transcribed protein coding genes include the VSG (variant surface glycoprotein) genes. Although a single trypanosome has many hundreds of VSG genes, the active VSG is transcribed in a strictly monoalleleic fashion from one of approx. 15 telomeric VSG ESs (expression sites). Originally, it was thought that chromatin was not involved in the transcriptional control of ESs; however, this view is now being re-evaluated. It has since been shown that the active ES is depleted of nucleosomes compared with silent ESs. In addition, a number of proteins involved in chromatin remodelling or histone modification and which play a role in ES silencing {including TbISWI [T. brucei ISWI (imitation-switch protein)] and DOT1B} have recently been identified. Lastly, the telomere-binding protein TbRAP1 (T. brucei RAP1) has been shown to establish a repressive gradient extending from the ES telomere end up to the ES promoter. We still need to determine which epigenetic factors are involved in ‘marking’ the active ES as part of the counting mechanism of monoallelic exclusion. The challenge will come in determining how these multiple regulatory layers contribute to ES control.
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Tan RZ, van Oudenaarden A. Transcript counting in single cells reveals dynamics of rDNA transcription. Mol Syst Biol 2010; 6:358. [PMID: 20393578 PMCID: PMC2872610 DOI: 10.1038/msb.2010.14] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Accepted: 02/09/2010] [Indexed: 11/09/2022] Open
Abstract
Fluorescence in-situ hybridization (FISH) technique allows the detection of single RNA molecules in individual yeast cells. We use this method complemented with theoretical modeling to determine the rate of switching from OFF to ON (activation rate) and the average number of RNA molecules produced during each transcriptional burst (burst size). Switching of the rDNA repeats between the inactive non-transcribing state and the active transcribing state occurs rapidly. On average, it takes an inactive repeat 8 2 min to transit to the active state. As cell density increases, mean rRNA transcriptional activity decreases. This is due to the decreases in burst size. The activation rate remains constant. In the rpd3 strain, activation rate doubles and the burst size is half that of wild-type cells in log-phase. This effect of Rpd3 on activation rate is independent of cell density. As the cell density increases, the burst size of the rpd3 strain becomes similar to that of wild-type cells.
Most eukaryotes contain many tandem repeats of ribosomal RNA genes of which only a subset is transcribed at any given time. Current biochemical methods allow for the determination of the fraction of transcribing repeats (ON) versus non-transcribing repeats (OFF) but do not provide any dynamical information and obscure any transcription activity at the single-cell level. Here, we use a fluorescence in situ hybridization (FISH) technique that allows the detection of single-RNA molecules in individual yeast cells. We use this method complemented with theoretical modeling to determine the rate of switching from OFF to ON (activation rate) and the average number of RNA molecules produced during each transcriptional burst (burst size). We explore how these two variables change in mutants and different growth conditions, and show that this method resolves changes in these two variables even when the average rDNA expression is unaltered. These phenotypic changes could not have been detected by traditional biochemical assays.
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Affiliation(s)
- Rui Zhen Tan
- Harvard University Graduate Biophysics Program, Harvard Medical School, Boston, MA, USA
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Active VSG expression sites in Trypanosoma brucei are depleted of nucleosomes. EUKARYOTIC CELL 2009; 9:136-47. [PMID: 19915073 DOI: 10.1128/ec.00281-09] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
African trypanosomes regulate transcription differently from other eukaryotes. Most of the trypanosome genome is constitutively transcribed by RNA polymerase II (Pol II) as large polycistronic transcription units while the genes encoding the major surface proteins are transcribed by RNA polymerase I (Pol I). In bloodstream form Trypanosoma brucei, the gene encoding the variant surface glycoprotein (VSG) coat is expressed in a monoallelic fashion from one of about 15 VSG bloodstream form expression sites (BESs). Little is known about the chromatin structure of the trypanosome genome, and the chromatin state of active versus silent VSG BESs remains controversial. Here, we determined histone H3 occupancy within the genome of T. brucei, focusing on active versus silent VSG BESs in the bloodstream form. We found that histone H3 was most enriched in the nontranscribed 50-bp and 177-bp repeats and relatively depleted in Pol I, II, and III transcription units, with particular depletion over promoter regions. Using two isogenic T. brucei lines containing marker genes in different VSG BESs, we determined that histone H3 is 11- to 40-fold depleted from active VSG BESs compared with silent VSG BESs. Quantitative PCR analysis of fractionated micrococcal nuclease-digested chromatin revealed that the active VSG BES is depleted of nucleosomes. Therefore, in contrast to earlier views, nucleosome positioning appears to be involved in the monoalleleic control of VSG BESs in T. brucei. This may provide a level of epigenetic regulation enabling bloodstream form trypanosomes to efficiently pass on the transcriptional state of active and silent BESs to daughter cells.
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Tremblay M, Toussaint M, D'Amours A, Conconi A. Nucleotide excision repair and photolyase repair of UV photoproducts in nucleosomes: assessing the existence of nucleosome and non-nucleosome rDNA chromatin in vivo. Biochem Cell Biol 2009; 87:337-46. [PMID: 19234545 DOI: 10.1139/o08-128] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The genome is organized into nuclear domains, which create microenvironments that favor distinct chromatin structures and functions (e.g., highly repetitive sequences, centromeres, telomeres, noncoding sequences, inactive genes, RNA polymerase II and III transcribed genes, and the nucleolus). Correlations have been drawn between gene silencing and proximity to a heterochromatic compartment. At the other end of the scale are ribosomal genes, which are transcribed at a very high rate by RNA polymerase I (~60% of total transcription), have a loose chromatin structure, and are clustered in the nucleolus. The rDNA sequences have 2 distinct structures: active rRNA genes, which have no nucleosomes; and inactive rRNA genes, which have nucleosomes. Like DNA transcription and replication, DNA repair is modulated by the structure of chromatin, and the kinetics of DNA repair vary among the nuclear domains. Although research on DNA repair in all chromosomal contexts is important to understand the mechanisms of genome maintenance, this review focuses on nucleotide excision repair and photolyase repair of UV photoproducts in the first-order packing of DNA in chromatin: the nucleosome. In addition, it summarizes the studies that have demonstrated the existence of the 2 rDNA chromatins, and the way this feature of the rDNA locus allows for direct comparison of DNA repair in 2 very different structures: nucleosome and non-nucleosome DNA.
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Affiliation(s)
- Maxime Tremblay
- Departement de Microbiologie et Infectiologie, Faculte de Medecine, Universite de Sherbrooke, Sherbrooke, QCJ1H5N4, Canada
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O'Sullivan JM, Sontam DM, Grierson R, Jones B. Repeated elements coordinate the spatial organization of the yeast genome. Yeast 2009; 26:125-38. [PMID: 19235779 DOI: 10.1002/yea.1657] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The spatial organization of the chromosomes is crucial for gene expression and development. Inter- and intrachromosomal interactions form a crucial part of this epigenomic regulatory system. Here we use circular chromosome conformation capture-on-chip (4C) to identify interactions between repetitive and non-repetitive loci within the yeast genome. The interacting regions occur in non-randomly distributed clusters. Furthermore, the SIR2 histone deacetylase has opposing roles in the organization of the inter- or intrachromosomal interactions. These data establish a dynamic domain model for yeast genome organization. Moreover, they point to the repeated elements playing a central role in the dynamic organization of genome architecture.
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Affiliation(s)
- J M O'Sullivan
- Institute of Molecular Biosciences, Massey University, Albany, New Zealand.
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35
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Zhou J, Eickbush TH. The pattern of R2 retrotransposon activity in natural populations of Drosophila simulans reflects the dynamic nature of the rDNA locus. PLoS Genet 2009; 5:e1000386. [PMID: 19229317 PMCID: PMC2637433 DOI: 10.1371/journal.pgen.1000386] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Accepted: 01/20/2009] [Indexed: 11/18/2022] Open
Abstract
The pattern and frequency of insertions that enable transposable elements to remain active in a population are poorly understood. The retrotransposable element R2 exclusively inserts into the 28S rRNA genes where it establishes long-term, stable relationships with its animal hosts. Previous studies with laboratory stocks of Drosophila simulans have suggested that control over R2 retrotransposition resides within the rDNA loci. In this report, we sampled 180 rDNA loci of animals collected from two natural populations of D. simulans. The two populations were found to have similar patterns of R2 activity. About half of the rDNA loci supported no or very low levels of R2 transcripts with no evidence of R2 retrotransposition. The remaining half of the rDNA loci had levels of R2 transcripts that varied in a continuous manner over almost a 100-fold range and did support new retrotransposition events. Structural analysis of the rDNA loci in 18 lines that spanned the range of R2 transcript levels in these populations revealed that R2 number and rDNA locus size varied 2-fold; however, R2 activity was not readily correlated with either of these parameters. Instead R2 activity was best correlated with the distribution of elements within the rDNA locus. Loci with no activity had larger contiguous blocks of rDNA units free of R2-insertions. These data suggest a model in which frequent recombination within the rDNA locus continually redistributes R2-inserted units resulting in changing levels of R2 activity within individual loci and persistent R2 activity within the population.
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Affiliation(s)
- Jun Zhou
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Thomas H. Eickbush
- Department of Biology, University of Rochester, Rochester, New York, United States of America
- * E-mail:
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Birch JL, Tan BCM, Panov KI, Panova TB, Andersen JS, Owen-Hughes TA, Russell J, Lee SC, Zomerdijk JCBM. FACT facilitates chromatin transcription by RNA polymerases I and III. EMBO J 2009; 28:854-65. [PMID: 19214185 PMCID: PMC2647773 DOI: 10.1038/emboj.2009.33] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Accepted: 01/21/2009] [Indexed: 01/23/2023] Open
Abstract
Efficient transcription elongation from a chromatin template requires RNA polymerases (Pols) to negotiate nucleosomes. Our biochemical analyses demonstrate that RNA Pol I can transcribe through nucleosome templates and that this requires structural rearrangement of the nucleosomal core particle. The subunits of the histone chaperone FACT (facilitates chromatin transcription), SSRP1 and Spt16, co-purify and co-immunoprecipitate with mammalian Pol I complexes. In cells, SSRP1 is detectable at the rRNA gene repeats. Crucially, siRNA-mediated repression of FACT subunit expression in cells results in a significant reduction in 47S pre-rRNA levels, whereas synthesis of the first 40 nt of the rRNA is not affected, implying that FACT is important for Pol I transcription elongation through chromatin. FACT also associates with RNA Pol III complexes, is present at the chromatin of genes transcribed by Pol III and facilitates their transcription in cells. Our findings indicate that, beyond the established role in Pol II transcription, FACT has physiological functions in chromatin transcription by all three nuclear RNA Pols. Our data also imply that local chromatin dynamics influence transcription of the active rRNA genes by Pol I and of Pol III-transcribed genes.
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Affiliation(s)
- Joanna L Birch
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, UK
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37
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Tremblay M, Teng Y, Paquette M, Waters R, Conconi A. Complementary roles of yeast Rad4p and Rad34p in nucleotide excision repair of active and inactive rRNA gene chromatin. Mol Cell Biol 2008; 28:7504-13. [PMID: 18936173 PMCID: PMC2593431 DOI: 10.1128/mcb.00137-08] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2008] [Revised: 02/26/2008] [Accepted: 10/08/2008] [Indexed: 02/03/2023] Open
Abstract
Nucleotide excision repair (NER) removes a plethora of DNA lesions. It is performed by a large multisubunit protein complex that finds and repairs damaged DNA in different chromatin contexts and nuclear domains. The nucleolus is the most transcriptionally active domain, and in yeast, transcription-coupled NER occurs in RNA polymerase I-transcribed genes (rDNA). Here we have analyzed the roles of two members of the xeroderma pigmentosum group C family of proteins, Rad4p and Rad34p, during NER in the active and inactive rDNA. We report that Rad4p is essential for repair in the intergenic spacer, the inactive rDNA coding region, and for strand-specific repair at the transcription initiation site, whereas Rad34p is not. Rad34p is necessary for transcription-coupled NER that starts about 40 nucleotides downstream of the transcription initiation site of the active rDNA, whereas Rad4p is not. Thus, although Rad4p and Rad34p share sequence homology, their roles in NER in the rDNA locus are almost entirely distinct and complementary. These results provide evidences that transcription-coupled NER and global genome NER participate in the removal of UV-induced DNA lesions from the transcribed strand of active rDNA. Furthermore, nonnucleosome rDNA is repaired faster than nucleosome rDNA, indicating that an open chromatin structure facilitates NER in vivo.
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Affiliation(s)
- Maxime Tremblay
- Département de Microbiologie et Infectiologie, Faculté de Médecine, Poste 7446, Université de Sherbrooke, 3001 12th Ave. Nord, Sherbrooke, QC J1H 5N4, Canada
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38
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Abstract
Transcription of the major ribosomal RNAs by Pol I (RNA polymerase I) is a key determinant of ribosome biogenesis, driving cell growth and proliferation in eukaryotes. Hundreds of copies of rRNA genes are present in each cell, and there is evidence that the cellular control of Pol I transcription involves adjustments to the number of rRNA genes actively engaged in transcription, as well as to the rate of transcription from each active gene. Chromatin structure is inextricably linked to rRNA gene activity, and the present review highlights recent advances in this area.
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39
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Role of recombination in the long-term retention of transposable elements in rRNA gene loci. Genetics 2008; 180:1617-26. [PMID: 18791229 DOI: 10.1534/genetics.108.093716] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Multiple theoretical studies have focused on the concerted evolution of the tandemly repeated rRNA genes of eukaryotes; however, these studies did not consider the transposable elements that interrupt the rRNA genes in many organisms. For example, in insects, R1 and R2 have been stable components of the rDNA locus for hundreds of millions of years, suggesting either that they have minimal effects on fitness or that they are unable to be eliminated. We constructed a simulation model of recombination and retrotransposition within the rDNA locus that addresses the population dynamics and fitness consequences associated with R1 and R2 insertions. The simulations suggest that even without R1 and R2 retrotransposition the frequent sister chromatid exchanges postulated from various empirical studies will, in combination with selection, generate rDNA loci that are much larger than those needed for transcription. These large loci enable the host to tolerate high levels of R1 and R2 insertions with little fitness consequences. Changes in retrotransposition rates are likely to be accommodated by adjustments in sister chromatid exchange (SCE) rate, rather than by direct selection on the number of uninserted rDNA units. These simulations suggest that the rDNA locus serves as an ideal niche for the long-term survival of transposable elements.
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40
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Pnc1p-mediated nicotinamide clearance modifies the epigenetic properties of rDNA silencing in Saccharomyces cerevisiae. Genetics 2008; 180:797-810. [PMID: 18780747 DOI: 10.1534/genetics.108.091090] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The histone deacetylase activity of Sir2p is dependent on NAD(+) and inhibited by nicotinamide (NAM). As a result, Sir2p-regulated processes in Saccharomyces cerevisiae such as silencing and replicative aging are susceptible to alterations in cellular NAD(+) and NAM levels. We have determined that high concentrations of NAM in the growth medium elevate the intracellular NAD(+) concentration through a mechanism that is partially dependent on NPT1, an important gene in the Preiss-Handler NAD(+) salvage pathway. Overexpression of the nicotinamidase, Pnc1p, prevents inhibition of Sir2p by the excess NAM while maintaining the elevated NAD(+) concentration. This growth condition alters the epigenetics of rDNA silencing, such that repression of a URA3 reporter gene located at the rDNA induces growth on media that either lacks uracil or contains 5-fluoroorotic acid (5-FOA), an unusual dual phenotype that is reminiscent of telomeric silencing (TPE) of URA3. Despite the similarities to TPE, the modified rDNA silencing phenotype does not require the SIR complex. Instead, it retains key characteristics of typical rDNA silencing, including RENT and Pol I dependence, as well as a requirement for the Preiss-Handler NAD(+) salvage pathway. Exogenous nicotinamide can therefore have negative or positive impacts on rDNA silencing, depending on the PNC1 expression level.
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41
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Transcription of multiple yeast ribosomal DNA genes requires targeting of UAF to the promoter by Uaf30. Mol Cell Biol 2008; 28:6709-19. [PMID: 18765638 DOI: 10.1128/mcb.00703-08] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Upstream activating factor (UAF) is a multisubunit complex that functions in the activation of ribosomal DNA (rDNA) transcription by RNA polymerase I (Pol I). Cells lacking the Uaf30 subunit of UAF reduce the rRNA synthesis rate by approximately 70% compared to wild-type cells and produce rRNA using both Pol I and Pol II. Miller chromatin spreads demonstrated that even though there is an overall reduction in rRNA synthesis in uaf30 mutants, the active rDNA genes in such strains are overloaded with polymerases. This phenotype was specific to defects in Uaf30, as mutations in other UAF subunits resulted in a complete absence of rDNA genes with high or even modest Pol densities. The lack of Uaf30 prevented UAF from efficiently binding to the rDNA promoter in vivo, leading to an inability to activate a large number of rDNA genes. The relatively few genes that did become activated were highly transcribed, apparently to compensate for the reduced rRNA synthesis capacity. The results show that Uaf30p is a key targeting factor for the UAF complex that facilitates activation of a large proportion of rDNA genes in the tandem array.
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42
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Yeast linker histone Hho1p is required for efficient RNA polymerase I processivity and transcriptional silencing at the ribosomal DNA. Proc Natl Acad Sci U S A 2008; 105:11703-8. [PMID: 18687885 DOI: 10.1073/pnas.0709403105] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nucleosome core particles in eukaryotes are linked by a stretch of DNA that is usually associated with a linker histone. Here, we show in yeast, that the presence of yeast linker histone Hho1p represses expression of a pol II transcribed gene (MET15) embedded in the rDNA. In vivo deletions of Hho1p sequences showed that the second globular domain is sufficient for that repression, whereas the presence of the N terminus is required for its derepression. In contrast, a run-on assay confirmed by a ChIP experiment showed that Hho1p is required for maximal pol I processivity during rDNA transcription. Psoralen accessibility experiments indicated that Hho1p is necessary for normal rDNA compaction. DNA array expression analysis comparing RNA transcripts in wild-type and hho1 strains before and after a heat-shock showed that Hho1p is necessary to achieve wild-type mRNA levels of transcripts that encode ribosomal components. Taken together, our results suggest that Hho1p is involved in rDNA compaction, and like core histones, is required for efficient rDNA transcription by pol I.
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43
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Epigenetic regulation of retrotransposons within the nucleolus of Drosophila. Mol Cell Biol 2008; 28:6452-61. [PMID: 18678644 DOI: 10.1128/mcb.01015-08] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
R2 retrotransposable elements exclusively insert into a conserved region of the tandemly organized 28S rRNA genes. Despite inactivating a subset of these genes, R2 elements have persisted in the ribosomal DNA (rDNA) loci of insects for hundreds of millions of years. Controlling R2 proliferation was addressed in this study using lines of Drosophila simulans previously shown to have either active or inactive R2 retrotransposition. Lines with active retrotransposition were shown to have high R2 transcript levels, which nuclear run-on transcription experiments revealed were due to increased transcription of R2-inserted genes. Crosses between R2 active and inactive lines indicated that an important component of this transcriptional control is linked to or near the rDNA locus, with the R2 transcription level of the inactive parent being dominant. Pulsed-field gel analysis suggested that the R2 active and inactive states were determined by R2 distribution within the locus. Molecular and cytological analyses further suggested that the entire rDNA locus from the active line can be silenced in favor of the locus from the inactive line. This silencing of entire rDNA loci represents an example of the large-scale epigenetic control of transposable elements and shares features with the nucleolar dominance frequently seen in interspecies hybrids.
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44
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French SL, Osheim YN, Schneider DA, Sikes ML, Fernandez CF, Copela LA, Misra VA, Nomura M, Wolin SL, Beyer AL. Visual analysis of the yeast 5S rRNA gene transcriptome: regulation and role of La protein. Mol Cell Biol 2008; 28:4576-87. [PMID: 18474615 PMCID: PMC2447126 DOI: 10.1128/mcb.00127-08] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Revised: 03/04/2008] [Accepted: 05/02/2008] [Indexed: 01/15/2023] Open
Abstract
5S rRNA genes from Saccharomyces cerevisiae were examined by Miller chromatin spreading, representing the first quantitative analysis of RNA polymerase III genes in situ by electron microscopy. These very short genes, approximately 132 nucleotides (nt), were engaged by one to three RNA polymerases. Analysis in different growth conditions and in strains with a fourfold range in gene copy number revealed regulation at two levels: number of active genes and polymerase loading per gene. Repressive growth conditions (presence of rapamycin or postexponential growth) led first to fewer active genes, followed by lower polymerase loading per active gene. The polymerase III elongation rate was estimated to be in the range of 60 to 75 nt/s, with a reinitiation interval of approximately 1.2 s. The yeast La protein, Lhp1, was associated with 5S genes. Its absence had no discernible effect on the amount or size of 5S RNA produced yet resulted in more polymerases per gene on average, consistent with a non-rate-limiting role for Lhp1 in a process such as polymerase release/recycling upon transcription termination.
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Affiliation(s)
- Sarah L French
- Department of Microbiology, University of Virginia Health System, Charlottesville, Virginia 22908-0734, USA
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45
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Vasiljeva L, Kim M, Terzi N, Soares LM, Buratowski S. Transcription termination and RNA degradation contribute to silencing of RNA polymerase II transcription within heterochromatin. Mol Cell 2008; 29:313-23. [PMID: 18280237 DOI: 10.1016/j.molcel.2008.01.011] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Revised: 12/12/2007] [Accepted: 01/30/2008] [Indexed: 01/19/2023]
Abstract
Within the heterochromatin of budding yeast, RNA polymerase II (RNAPII) transcription is repressed by the Sir2 deacetylase. Although heterochromatic silencing is generally thought to be due to limited accessibility of the underlying DNA, there are several reports of RNAPII and basal transcription factors within silenced regions. Analysis of the rDNA array revealed cryptic RNAPII transcription within the "nontranscribed" spacer region. These transcripts are terminated by the Nrd1/Sen1 complex and degraded by the exosome. Mutations in this pathway lead to decreased silencing and dramatic chromatin changes in the rDNA locus. Interestingly, Nrd1 mutants also show higher levels of rDNA recombination, suggesting that the cryptic RNAPII transcription might have a physiological role in regulating rDNA copy number. The Nrd1/Sen1/exosome pathway also contributes to silencing at telomeric loci. These results suggest that silencing of heterochromatic genes in Saccharomyces cerevisiae occurs at both transcriptional and posttranscriptional levels.
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Affiliation(s)
- Lidia Vasiljeva
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
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46
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Abstract
In the fission yeast Schizosaccharomyces pombe, the RNAi pathway plays an important role in the formation and maintenance of heterochromatin. Heterochromatin, or silent chromatin, is an epigenetically inherited attribute of eukaryotic chromosomes which is required for gene regulation, chromosome segregation and maintenance of genome stability. In S. pombe, heterochromatin forms on related repetitive DNA sequences at specific loci. These repetitive sequences, in concert with the RNAi machinery, are thought to attract several proteins including chromatin-modifying enzymes which act to promote heterochromatin formation. The purification of complexes participating in heterochromatin formation has allowed us to begin to analyse in detail the processes involved. In the future this will help us to understand how the RNAi machinery acts to induce the chromatin modifications which lead to heterochromatin assembly in fission yeast.
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Affiliation(s)
- Sharon A White
- Welcome Trust Centre for Cell Biology, Institute of Cell Biology, The University of Edinburgh, Edinburgh, EH9 3JR Scotland, UK.
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47
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Wang BD, Strunnikov A. Transcriptional homogenization of rDNA repeats in the episome-based nucleolus induces genome-wide changes in the chromosomal distribution of condensin. Plasmid 2007; 59:45-53. [PMID: 18023874 DOI: 10.1016/j.plasmid.2007.09.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Revised: 09/27/2007] [Accepted: 09/27/2007] [Indexed: 11/17/2022]
Abstract
Condensin activity establishes and maintains mitotic chromosome condensation, however the mechanisms of condensin recognition of specific chromosomal sites remain unknown. rDNA is the chief condensin binding locus in Saccharomyces cerevisiae, and the level of nucleolar transcription is one of the key factors determining condensin loading to the nucleolar organizer. A new aspect of this transcriptional control is demonstrated in cells with a diffuse (episomal) nucleolar organizer, where active transcription excludes condensin from the transcribed regions of rDNA. Genome-wide ChIP-chip analysis showed that these cells acquire an altered and a more robust pattern of chromosomal condensin distribution, with increased enrichment of wild-type hotspots and with emergence of new sites, most notably in the subtelomeric regions. This genome-wide condensin relocalization induced by the increase in rDNA transcription and, possibly, nucleolar architecture uncovers a novel potential role of the nucleolus in the general chromosome organization.
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Affiliation(s)
- Bi-Dar Wang
- NIH, NICHD, Laboratory of Gene Regulation and Development, 18T Library Drive, Room 106, Bethesda, MD 20892, USA
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48
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Kasahara K, Ohtsuki K, Ki S, Aoyama K, Takahashi H, Kobayashi T, Shirahige K, Kokubo T. Assembly of regulatory factors on rRNA and ribosomal protein genes in Saccharomyces cerevisiae. Mol Cell Biol 2007; 27:6686-705. [PMID: 17646381 PMCID: PMC2099245 DOI: 10.1128/mcb.00876-07] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HMO1 is a high-mobility group B protein that plays a role in transcription of genes encoding rRNA and ribosomal proteins (RPGs) in Saccharomyces cerevisiae. This study uses genome-wide chromatin immunoprecipitation to study the roles of HMO1, FHL1, and RAP1 in transcription of these genes as well as other RNA polymerase II-transcribed genes in yeast. The results show that HMO1 associates with the 35S rRNA gene in an RNA polymerase I-dependent manner and that RPG promoters (138 in total) can be classified into several distinct groups based on HMO1 abundance at the promoter and the HMO1 dependence of FHL1 and/or RAP1 binding to the promoter. FHL1, a key regulator of RPGs, binds to most of the HMO1-enriched and transcriptionally HMO1-dependent RPG promoters in an HMO1-dependent manner, whereas it binds to HMO1-limited RPG promoters in an HMO1-independent manner, irrespective of whether they are transcribed in an HMO1-dependent manner. Reporter gene assays indicate that these functional properties are determined by the promoter sequence.
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Affiliation(s)
- Koji Kasahara
- Division of Molecular and Cellular Biology, Science of Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, Yokohama, Kanagawa, Japan
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49
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Sanz C, Gorab E, Ruiz MF, Sogo JM, Díez JL. Chromatin structure of ribosomal genes in Chironomus thummi (Diptera: Chironomidae): tissue specificity and behaviour under drug treatment. Chromosome Res 2007; 15:429-38. [PMID: 17487564 DOI: 10.1007/s10577-007-1134-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Revised: 03/02/2007] [Accepted: 03/02/2007] [Indexed: 12/27/2022]
Abstract
In eukaryotes the ribosomal gene population shows two different states in terms of chromatin structure. One subset is organized as nucleosomes (silent copies) while the other has a non-nucleosomal configuration (active copies). Insect cells are not the exception and this bimodal distribution of ribosomal chromatin also occurs in salivary gland cells, and cells of other larval tissues, of the midge Chironomus thummi. In run-on experiments on salivary glands cells we confirmed that transcribed rRNA genes show a non-nucleosomal configuration. The proportion of rRNA genes adopting an open, non-nucleosomal configuration was found to be tissue-dependent, suggesting that the population of unfolded ribosomal chromatin in C. thummi was established during cell differentiation. We propose that cell differentiation determines the fraction of non-nucleosomal rRNA gene copies and thus defines the range of possible rRNA synthesis rates in a particular cell type. In the salivary gland the fraction of unfolded chromatin was not significantly affected when transcription was repressed. However, transcription activation by pilocarpine led to a moderate increase in this fraction. These findings indicate that, in addition to a possible increase in the number of RNA-polymerases per transcribing rDNA unit, the proportion of transcribed ribosomal genes in differentiated cells can be modulated in response to an exceptional rRNA synthesis requirement.
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Affiliation(s)
- Cristina Sanz
- Departamento de Biología Celular y del Desarrollo, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
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50
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Kulaeva OI, Gaykalova D, Studitsky VM. Transcription through chromatin by RNA polymerase II: histone displacement and exchange. Mutat Res 2007; 618:116-29. [PMID: 17313961 PMCID: PMC1924643 DOI: 10.1016/j.mrfmmm.2006.05.040] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2006] [Accepted: 05/30/2006] [Indexed: 12/31/2022]
Abstract
The process of transcript elongation by RNA polymerase II (Pol II) involves transcription-dependent exchange and displacement of all core histones and is tightly controlled by numerous protein complexes modifying chromatin structure. These processes can contribute to regulation of transcription initiation and elongation, as well as the chromatin state. Recent data suggest that the histone octamer is displaced from DNA at a high rate of transcription, but can survive less frequent transcription that is accompanied only by partial loss of H2A/H2B histones. Here we propose that critical density of Pol II molecules could be required for displacement of the histone octamer and discuss mechanisms that are most likely involved in the processes of histone exchange.
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Affiliation(s)
- Olga I. Kulaeva
- Department of Pharmacology, UMDNJ, Robert Wood Johnson Medical School, 675 Hoes Lane, Room 405, Piscataway, NJ 08854, USA
| | - Daria Gaykalova
- Department of Pharmacology, UMDNJ, Robert Wood Johnson Medical School, 675 Hoes Lane, Room 405, Piscataway, NJ 08854, USA
| | - Vasily M. Studitsky
- Department of Pharmacology, UMDNJ, Robert Wood Johnson Medical School, 675 Hoes Lane, Room 405, Piscataway, NJ 08854, USA
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