1
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A stress-blinded Atf1 can fully assemble heterochromatin in a RNAi-independent minimal mat locus but impairs directionality of mat2/3 switching. iScience 2022; 25:104820. [PMID: 35992058 PMCID: PMC9389250 DOI: 10.1016/j.isci.2022.104820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/03/2022] [Accepted: 07/19/2022] [Indexed: 11/28/2022] Open
Abstract
The MAP kinase Sty1 phosphorylates and activates the transcription factor Atf1 in response to several stress conditions, which then shifts from a transcriptional repressor to an activator. Atf1 also participates in heterochromatin assembly at the mat locus, in combination with the RNA interference (RNAi) machinery. Here, we study the role of signal-dependent phosphorylation of Atf1 in heterochromatin establishment at mat, using different Atf1 phospho mutants. Although a hypo-phosphorylation Atf1 mutant, Atf1.10M, mediates heterochromatin assembly, the phosphomimic Atf1.10D is unable to maintain silencing. In a minimal mat locus, lacking the RNAi-recruiting cis elements and displaying intermediate silencing, Atf1.10M restores full heterochromatin and silencing. However, evolution experiments with this stress-blinded Atf1.10M show that it is unable to facilitate switching between the donor site mat3 and mat1. We propose that the unphosphorylated, inactive Atf1 contributes to proper heterochromatin assembly by recruiting repressive complexes, but its stress-dependent phosphorylation is required for recombination/switching to occur. The phosphorylation domain of Atf1 TF is required for heterochromatin assembly at mat Hypo-phosphorylated Atf1.10M mediates silencing by recruiting repressive complexes Stress-dependent phosphorylation of Atf1 is required for recombination and switching Atf1.10M is a heterochromatin assembly factor but impairs mat2/3 switching
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2
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Weiner AKM, Cerón-Romero MA, Yan Y, Katz LA. Phylogenomics of the Epigenetic Toolkit Reveals Punctate Retention of Genes across Eukaryotes. Genome Biol Evol 2021; 12:2196-2210. [PMID: 33049043 DOI: 10.1093/gbe/evaa198] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2020] [Indexed: 12/17/2022] Open
Abstract
Epigenetic processes in eukaryotes play important roles through regulation of gene expression, chromatin structure, and genome rearrangements. The roles of chromatin modification (e.g., DNA methylation and histone modification) and non-protein-coding RNAs have been well studied in animals and plants. With the exception of a few model organisms (e.g., Saccharomyces and Plasmodium), much less is known about epigenetic toolkits across the remainder of the eukaryotic tree of life. Even with limited data, previous work suggested the existence of an ancient epigenetic toolkit in the last eukaryotic common ancestor. We use PhyloToL, our taxon-rich phylogenomic pipeline, to detect homologs of epigenetic genes and evaluate their macroevolutionary patterns among eukaryotes. In addition to data from GenBank, we increase taxon sampling from understudied clades of SAR (Stramenopila, Alveolata, and Rhizaria) and Amoebozoa by adding new single-cell transcriptomes from ciliates, foraminifera, and testate amoebae. We focus on 118 gene families, 94 involved in chromatin modification and 24 involved in non-protein-coding RNA processes based on the epigenetics literature. Our results indicate 1) the presence of a large number of epigenetic gene families in the last eukaryotic common ancestor; 2) differential conservation among major eukaryotic clades, with a notable paucity of genes within Excavata; and 3) punctate distribution of epigenetic gene families between species consistent with rapid evolution leading to gene loss. Together these data demonstrate the power of taxon-rich phylogenomic studies for illuminating evolutionary patterns at scales of >1 billion years of evolution and suggest that macroevolutionary phenomena, such as genome conflict, have shaped the evolution of the eukaryotic epigenetic toolkit.
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Affiliation(s)
- Agnes K M Weiner
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
| | - Mario A Cerón-Romero
- Department of Biological Sciences, Smith College, Northampton, Massachusetts.,Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst
| | - Ying Yan
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts.,Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst
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3
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Shi S, Zhou Y, Lu Y, Sun H, Xue J, Wu Z, Lei M. Ccq1-Raf2 interaction mediates CLRC recruitment to establish heterochromatin at telomeres. Life Sci Alliance 2021; 4:4/11/e202101106. [PMID: 34493579 PMCID: PMC8424379 DOI: 10.26508/lsa.202101106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 12/01/2022] Open
Abstract
This study unveils a role of Ccq1–Raf2 interaction in CLRC recruitment to establish heterochromatin at telomeres, providing a positive feedback mechanism between shelterin and CLRC for subtelomeric heterochromatin assembly. Telomeres, highly ordered DNA-protein complexes at eukaryotic linear chromosome ends, are specialized heterochromatin loci conserved among eukaryotes. In Schizosaccharomyces pombe, the shelterin complex is important for subtelomeric heterochromatin establishment. Despite shelterin has been demonstrated to mediate the recruitment of the Snf2/histone deacetylase–containing repressor complex (SHREC) and the Clr4 methyltransferase complex (CLRC) to telomeres, the mechanism involved in telomeric heterochromatin assembly remains elusive due to the multiple functions of the shelterin complex. Here, we found that CLRC plays a dominant role in heterochromatin establishment at telomeres. In addition, we identified a series of amino acids in the shelterin subunit Ccq1 that are important for the specific interaction between Ccq1 and the CLRC subunit Raf2. Finally, we demonstrated that the Ccq1–Raf2 interaction is essential for the recruitment of CLRC to telomeres, that contributes to histone H3 lysine 9 methylation, nucleosome stability and the shelterin-chromatin association, promoting a positive feedback mechanism for the nucleation and spreading of heterochromatin at subtelomeres. Together, our findings provide a mechanistic understanding of subtelomeric heterochromatin assembly by shelterin-dependent CLRC recruitment to chromosomal ends.
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Affiliation(s)
- Shaohua Shi
- State Key Laboratory of Oncogenes and Related Genes, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Precision Medicine, Shanghai, China
| | - Yuanze Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yanjia Lu
- State Key Laboratory of Oncogenes and Related Genes, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Precision Medicine, Shanghai, China
| | - Hong Sun
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jing Xue
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Zhenfang Wu
- State Key Laboratory of Oncogenes and Related Genes, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China .,Shanghai Institute of Precision Medicine, Shanghai, China
| | - Ming Lei
- State Key Laboratory of Oncogenes and Related Genes, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China .,Shanghai Institute of Precision Medicine, Shanghai, China.,Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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4
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Raimondi C, Jagla B, Proux C, Waxin H, Gangloff S, Arcangioli B. Molecular signature of the imprintosome complex at the mating-type locus in fission yeast. MICROBIAL CELL 2018; 5:169-183. [PMID: 29610759 PMCID: PMC5878685 DOI: 10.15698/mic2018.04.623] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Genetic and molecular studies have indicated that an epigenetic imprint at mat1, the sexual locus of fission yeast, initiates mating type switching. The polar DNA replication of mat1 generates an imprint on the Watson strand. The process by which the imprint is formed and maintained through the cell cycle remains unclear. To understand better the mechanism of imprint formation and stability, we characterized the recruitment of early players of mating type switching at the mat1 region. We found that the switch activating protein 1 (Sap1) is preferentially recruited inside the mat1M allele on a sequence (SS13) that enhances the imprint. The lysine specific demethylases, Lsd1/2, that control the replication fork pause at MPS1 and the formation of the imprint are specifically drafted inside of mat1, regardless of the allele. The CENP-B homolog, Abp1, is highly enriched next to mat1 but it is not required in the process. Additionally, we established the computational signature of the imprint. Using this signature, we show that both sides of the imprinted molecule are bound by Lsd1/2 and Sap1, suggesting a nucleoprotein protective structure defined as imprintosome.
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Affiliation(s)
- Célia Raimondi
- Genomes and Genetics department, Genome Dynamics Unit, UMR 3525 CNRS, Institut Pasteur, 25-28 rue du docteur Roux, Paris, France. Sorbonne Universités, Université Pierre et Marie Curie, Institut de Formation Doctorale, 75252 Paris Cedex 05, France
| | - Bernd Jagla
- Center for Human Immunology, CRT & Hub de Bioinformatique et Biostatistiques, C3BI, Institut Pasteur, 25-28 rue du Docteur Roux, Paris, France
| | - Caroline Proux
- Genomes and Genetics department, Plate-forme Transcriptome & Epigenome, Biomics, Centre d'Innovation et Recherche Technologique (Citech), Institut Pasteur, 25-28 rue du Docteur Roux, Paris, France
| | - Hervé Waxin
- Enseignement, Institut Pasteur, 25-28 rue du Docteur Roux, Paris, France
| | - Serge Gangloff
- Genomes and Genetics department, Genome Dynamics Unit, UMR 3525 CNRS, Institut Pasteur, 25-28 rue du docteur Roux, Paris, France. Sorbonne Universités, Université Pierre et Marie Curie, Institut de Formation Doctorale, 75252 Paris Cedex 05, France
| | - Benoit Arcangioli
- Genomes and Genetics department, Genome Dynamics Unit, UMR 3525 CNRS, Institut Pasteur, 25-28 rue du docteur Roux, Paris, France. Sorbonne Universités, Université Pierre et Marie Curie, Institut de Formation Doctorale, 75252 Paris Cedex 05, France
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5
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Abstract
SUMMARY The involvement of RNA interference (RNAi) in heterochromatin formation has become clear largely through studies in the fission yeast Schizosaccharomyces pombe and plants like Arabidopsis thaliana. This article discusses how heterochromatic small interfering RNAs are produced and how the RNAi machinery participates in the formation and function of heterochromatin.
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Affiliation(s)
| | - Danesh Moazed
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115-5730
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6
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Matsuda A, Chikashige Y, Ding DQ, Ohtsuki C, Mori C, Asakawa H, Kimura H, Haraguchi T, Hiraoka Y. Highly condensed chromatins are formed adjacent to subtelomeric and decondensed silent chromatin in fission yeast. Nat Commun 2015; 6:7753. [PMID: 26205977 PMCID: PMC4525289 DOI: 10.1038/ncomms8753] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 06/08/2015] [Indexed: 11/09/2022] Open
Abstract
It is generally believed that silent chromatin is condensed and transcriptionally active chromatin is decondensed. However, little is known about the relationship between the condensation levels and gene expression. Here we report the condensation levels of interphase chromatin in the fission yeast Schizosaccharomyces pombe examined by super-resolution fluorescence microscopy. Unexpectedly, silent chromatin is less condensed than the euchromatin. Furthermore, the telomeric silent regions are flanked by highly condensed chromatin bodies, or 'knobs'. Knob regions span ∼50 kb of sequence devoid of methylated histones. Knob condensation is independent of HP1 homologue Swi6 and other gene silencing factors. Disruption of methylation at lysine 36 of histone H3 (H3K36) eliminates knob formation and gene repression at the subtelomeric and adjacent knob regions. Thus, epigenetic marks at H3K36 play crucial roles in the formation of a unique chromatin structure and in gene regulation at those regions in S. pombe.
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Affiliation(s)
- Atsushi Matsuda
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, 588-2, Iwaoka, Iwaoka-cho, Kobe 651-2492, Japan
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan
| | - Yuji Chikashige
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, 588-2, Iwaoka, Iwaoka-cho, Kobe 651-2492, Japan
| | - Da-Qiao Ding
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, 588-2, Iwaoka, Iwaoka-cho, Kobe 651-2492, Japan
| | - Chizuru Ohtsuki
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan
| | - Chie Mori
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, 588-2, Iwaoka, Iwaoka-cho, Kobe 651-2492, Japan
| | - Haruhiko Asakawa
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan
| | - Hiroshi Kimura
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B, Nagatsuda, Yokohama 226-8501, Japan
| | - Tokuko Haraguchi
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, 588-2, Iwaoka, Iwaoka-cho, Kobe 651-2492, Japan
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan
| | - Yasushi Hiraoka
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, 588-2, Iwaoka, Iwaoka-cho, Kobe 651-2492, Japan
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan
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7
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Abstract
Germ cell differentiation, the cellular process by which a diploid progenitor cell produces by meiotic divisions haploid cells, is conserved from the unicellular yeasts to mammals. Over the recent years, yeast germ cell differentiation process has proven to be a powerful biological system to identify and study several long noncoding RNAs (lncRNAs) that play a central role in regulating cellular differentiation by acting directly on chromatin. Remarkably, in the well-studied budding yeast Saccharomyces cerevisiae and fission yeast Schizosaccharomyces pombe, the lncRNA-based chromatin regulations of germ cell differentiation are quite different. In this review, we present an overview of these regulations by focusing on the mechanisms and their respective functions both in S. cerevisiae and in S. pombe. Part of these lncRNA-based chromatin regulations may be conserved in other eukaryotes and play critical roles either in the context of germ cell differentiation or, more generally, in the development of multicellular organisms.
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8
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Kunoh T, Habu T. Pcf1, a large subunit of CAF-1, required for maintenance of checkpoint kinase Cds1 activity. SPRINGERPLUS 2014; 3:30. [PMID: 24478943 PMCID: PMC3902073 DOI: 10.1186/2193-1801-3-30] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 01/14/2014] [Indexed: 01/30/2023]
Abstract
Highly conserved chromatin assembly factor 1 (CAF-1) is required for histone deposition onto newly synthesized DNA to maintain genome stability. This study shows that the fission yeast Pcf1, the large subunit in CAF-1, is crucial for maintaining checkpoint kinase Cds1. Chromatin recruitment of Cds1 is enhanced by Pcf1 overproduction but is attenuated by the Δpcf1 mutation. Mutation of acetylation sites in the histone H4 tail abrogates the chromatin recruitment of Pcf1, which resembles that of Cds1 as reported previously. The present results provide evidence that chromatin recruitment of Pcf1, moderated by Clr6-HDAC activity, is essential for inactivating Cds1.
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Affiliation(s)
- Tatsuki Kunoh
- Laboratory of Molecular Pharmacogenomics, School of Pharmaceutical Sciences, Kinki University, Higashiosaka, 577-8502 Japan
| | - Toshiyuki Habu
- Radiation Biology Center, Kyoto University, Kyoto, 606-8501 Japan
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9
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Sunder S, Greeson-Lott NT, Runge KW, Sanders SL. A new method to efficiently induce a site-specific double-strand break in the fission yeast Schizosaccharomyces pombe. Yeast 2012; 29:275-91. [PMID: 22674789 DOI: 10.1002/yea.2908] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 05/03/2012] [Indexed: 12/16/2022] Open
Abstract
Double-strand DNA breaks are a serious threat to cellular viability and yeast systems have proved invaluable in helping to understand how these potentially toxic lesions are sensed and repaired. An important method to study the processing of DNA breaks in the budding yeast Saccharomyces cerevisiae is to introduce a unique double-strand break into the genome by regulating the expression of the site-specific HO endonuclease with a galactose inducible promoter. Variations of the HO site-specific DSB assay have been adapted to many organisms, but the methodology has seen only limited use in the fission yeast Schizosaccharomyces pombe because of the lack of a promoter capable of inducing endonuclease expression on a relatively short time scale (~1 h). We have overcome this limitation by developing a new assay in which expression of the homing endonuclease I-PpoI is tightly regulated with a tetracycline-inducible promoter. We show that induction of the I-PpoI endonuclease produces rapid cutting of a defined cleavage site (> 80% after 1 h), efficient cell cycle arrest and significant accumulation of the checkpoint protein Crb2 at break-adjacent regions in a manner that is analogous to published findings with DSBs produced by an acute exposure to ionizing irradiation. This assay provides an important new tool for the fission yeast community and, because many aspects of mammalian chromatin organization have been well-conserved in Sz. pombe but not in S. cerevisiae, also offers an attractive system to decipher the role of chromatin structure in modulating the repair of double-stranded DNA breaks.
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Affiliation(s)
- Sham Sunder
- Department of Biochemistry and Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
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10
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Tarhan C, Sarikaya A. Does copper stress lead to spindle misposition-dependent cell cycle arrest? GENETICS AND MOLECULAR RESEARCH 2012; 11:3824-34. [DOI: 10.4238/2012.october.25.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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11
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Pluskal T, Hayashi T, Saitoh S, Fujisawa A, Yanagida M. Specific biomarkers for stochastic division patterns and starvation-induced quiescence under limited glucose levels in fission yeast. FEBS J 2011; 278:1299-315. [PMID: 21306563 PMCID: PMC3123465 DOI: 10.1111/j.1742-4658.2011.08050.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Glucose as a source of energy is centrally important to our understanding of life. We investigated the cell division–quiescence behavior of the fission yeast Schizosaccharomyces pombe under a wide range of glucose concentrations (0–111 mm). The mode of S. pombe cell division under a microfluidic perfusion system was surprisingly normal under highly diluted glucose concentrations (5.6 mm, 1/20 of the standard medium, within human blood sugar levels). Division became stochastic, accompanied by a curious division-timing inheritance, in 2.2–4.4 mm glucose. A critical transition from division to quiescence occurred within a narrow range of concentrations (2.2–1.7 mm). Under starvation (1.1 mm) conditions, cells were mostly quiescent and only a small population of cells divided. Under fasting (0 mm) conditions, division was immediately arrested with a short chronological lifespan (16 h). When cells were first glucose starved prior to fasting, they possessed a substantially extended lifespan (∼14 days). We employed a quantitative metabolomic approach for S. pombe cell extracts, and identified specific metabolites (e.g. biotin, trehalose, ergothioneine, S-adenosyl methionine and CDP-choline), which increased or decreased at different glucose concentrations, whereas nucleotide triphosphates, such as ATP, maintained high concentrations even under starvation. Under starvation, the level of S-adenosyl methionine increased sharply, accompanied by an increase in methylated amino acids and nucleotides. Under fasting, cells rapidly lost antioxidant and energy compounds, such as glutathione and ATP, but, in fasting cells after starvation, these and other metabolites ensuring longevity remained abundant. Glucose-starved cells became resistant to 40 mm H2O2 as a result of the accumulation of antioxidant compounds.
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Affiliation(s)
- Tomáš Pluskal
- Okinawa Institute of Science and Technology Promotion Corporation, Okinawa, Japan
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12
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Balance between distinct HP1 family proteins controls heterochromatin assembly in fission yeast. Mol Cell Biol 2008; 28:6973-88. [PMID: 18809570 DOI: 10.1128/mcb.00791-08] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Heterochromatin protein 1 (HP1) is a conserved chromosomal protein with important roles in chromatin packaging and gene silencing. In fission yeast, two HP1 family proteins, Swi6 and Chp2, are involved in transcriptional silencing at heterochromatic regions, but how they function and whether they act cooperatively or differentially in heterochromatin assembly remain elusive. Here, we show that both Swi6 and Chp2 are required for the assembly of fully repressive heterochromatin, in which they play distinct, nonoverlapping roles. Swi6 is expressed abundantly and plays a dose-dependent role in forming a repressive structure through its self-association property. In contrast, Chp2, expressed at a lower level, does not show a simple dose-dependent repressive activity. However, it contributes to the recruitment of chromatin-modulating factors Clr3 and Epe1 and possesses a novel ability to bind the chromatin-enriched nuclear subfraction that is closely linked with its silencing function. Finally, we demonstrate that a proper balance between Swi6 and Chp2 is critical for heterochromatin assembly. Our findings provide novel insight into the distinct and cooperative functions of multiple HP1 family proteins in the formation of higher-order chromatin structure.
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13
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Small RNA-directed heterochromatin formation in the context of development: what flies might learn from fission yeast. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2008; 1789:3-16. [PMID: 18789407 DOI: 10.1016/j.bbagrm.2008.08.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2008] [Revised: 08/03/2008] [Accepted: 08/07/2008] [Indexed: 11/21/2022]
Abstract
A link between the RNAi system and heterochromatin formation has been established in several model organisms including Schizosaccharomyces pombe and Arabidopsis thaliana. However, the data to support a role for small RNAs and the associated machinery in transcriptional gene silencing in animal systems is more tenuous. Using the S. pombe system as a model, we analyze the role of small RNA pathway components and associated small RNAs in regulating transposable elements and potentially directing heterochromatin formation at these elements in Drosophila melanogaster.
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14
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Zacharioudakis I, Gligoris T, Tzamarias D. A yeast catabolic enzyme controls transcriptional memory. Curr Biol 2007; 17:2041-6. [PMID: 17997309 DOI: 10.1016/j.cub.2007.10.044] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2007] [Revised: 10/05/2007] [Accepted: 10/15/2007] [Indexed: 10/22/2022]
Abstract
It has been postulated that chromatin modifications can persist through mitosis and meiosis, thereby securing memory of transcriptional states. Whether these chromatin marks can self-propagate in progeny independently of relevant trans-acting factors is an important question in phenomena related to epigenesis. "Adaptive cellular memory" displayed by yeast cells offers a convenient system to address this question. The yeast GAL genes are slowly activated by Gal4 when cells are first exposed to galactose, but their progeny, grown in glucose media, exhibit a fast activation mode upon re-exposure to this sugar. This "galactose memory" persists for several generations and was recently proposed to involve chromatin modifications and perinuclear topology of the GAL genes cluster. Here, we perform a heterokaryon assay demonstrating that this memory does not have a chromatin basis but is maintained by cytoplasmic factor(s) produced upon previous galactose induction. We show that Gal3, the cytoplasmic rate-limiting factor that releases the Gal4 activator, is dispensable for preserving galactose memory. Instead, the important memory determinant is a close Gal3 homolog, the highly expressed Gal1 galactokinase, the residual activity of which preserves memory in progeny cells by rapidly turning on the Gal4 activator upon cells' re-exposure to galactose.
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Affiliation(s)
- Ioannis Zacharioudakis
- Institute of Molecular Biology & Biotechnology-Foundation of Research and Technology, 71110 Heraklion, Crete, Greece
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15
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Moazed D, Bühler M, Buker SM, Colmenares SU, Gerace EL, Gerber SA, Hong EJE, Motamedi MR, Verdel A, Villén J, Gygi SP. Studies on the mechanism of RNAi-dependent heterochromatin assembly. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2007; 71:461-71. [PMID: 17381328 DOI: 10.1101/sqb.2006.71.044] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Assembly of heterochromatin at centromeric DNA regions in the fission yeast Schizosaccharomyces pombe involves an intimate interplay between chromatin modifying complexes and components of the RNAi pathway. The RNA-induced transcriptional silencing (RITS) complex, containing Chp1, Ago1, Tas3, and centromeric siRNAs, localizes to centromeric DNA repeats and is required for the assembly and maintenance of heterochromatin. RITS brings together two types of molecular recognition modules: a chromodomain protein, which binds to lysine 9 methylated histone H3 (H3K9), and Argonaute, which binds to specific sequences by siRNA-directed base-pairing interactions. The RNA-directed RNA polymerase complex (RDRC), composed of Rdp1, the Hrr1 helicase, and the Cid12 Poly(A) polymerase family member, synthesizes double-stranded RNA and creates the substrate for Dicer to generate siRNAs. RDRC physically associates with RITS, and both complexes localize to noncoding centromeric RNAs and centromeric DNA repeats, suggesting that recognition of nascent RNA transcripts may be involved in localization of these complexes to specific chromosome regions. In support of this possibility, tethering of the RITS complex to the transcript of the normally euchromatic ura4 (+) gene results in siRNA generation and RNAi- and heterochromatin-dependent silencing of the ura4 (+) gene. Finally, silencing of a subset of endogenous and transgene promoters within heterochromatic DNA domains occurs by RNAi-dependent degradation of nascent transcripts by a mechanism that we have termed co-transcriptional gene silencing (CTGS).
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Affiliation(s)
- D Moazed
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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16
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Gordon M, Holt DG, Panigrahi A, Wilhelm BT, Erdjument-Bromage H, Tempst P, Bähler J, Cairns BR. Genome-wide dynamics of SAPHIRE, an essential complex for gene activation and chromatin boundaries. Mol Cell Biol 2007; 27:4058-69. [PMID: 17371846 PMCID: PMC1900013 DOI: 10.1128/mcb.02044-06] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Revised: 12/19/2006] [Accepted: 03/09/2007] [Indexed: 11/20/2022] Open
Abstract
In this study, we characterize a four-protein nucleosome-binding complex from Schizosaccharomyces pombe, termed SAPHIRE, that includes two orthologs of human Lsd1, a histone demethylase. The SAPHIRE complex is essential for cell viability, whereas saphire mutants lacking key conserved catalytic residues are viable but thermosensitive, suggesting that SAPHIRE has both an important enzymatic function and an essential nonenzymatic function. SAPHIRE is present in (or adjacent to) particular heterochromatic loci and also in the transcription start site regions of many highly active polymerase II genes. However, ribosomal protein genes are notably SAPHIRE deficient. SAPHIRE promotes activation, as target genes are selectively attenuated in saphire mutants. Interestingly, saphire mutants display increased histone H3 lysine 4 dimethylation, a modification typically associated with euchromatin. SAPHIRE localization is dynamic, as activated genes rapidly acquire SAPHIRE. Furthermore, saphire mutants dramatically shift a heterochromatin-euchromatin boundary in Chr1, suggesting a novel role in boundary regulation.
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Affiliation(s)
- Matthew Gordon
- University of Utah, Huntsman Cancer Institute, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
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17
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Isaac S, Walfridsson J, Zohar T, Lazar D, Kahan T, Ekwall K, Cohen A. Interaction of Epe1 with the heterochromatin assembly pathway in Schizosaccharomyces pombe. Genetics 2007; 175:1549-60. [PMID: 17449867 PMCID: PMC1855143 DOI: 10.1534/genetics.106.068684] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Accepted: 01/05/2007] [Indexed: 11/18/2022] Open
Abstract
Epe1 is a JmjC domain protein that antagonizes heterochromatization in Schizosaccharomyces pombe. Related JmjC domain proteins catalyze a histone demethylation reaction that depends on Fe(II) and alpha-ketoglutarate. However, no detectable demethylase activity is associated with Epe1, and its JmjC domain lacks conservation of Fe(II)-binding residues. We report that Swi6 recruits Epe1 to heterochromatin and that overexpression of epe1+, like mutations in silencing genes or overexpression of swi6+, upregulates expression of certain genes. A significant overlap was observed between the lists of genes that are upregulated by overexpression of epe1+ and those that are upregulated by mutations in histone deacetylase genes. However, most of the common genes are not regulated by Clr4 histone methyltransferase. This suggests that Epe1 interacts with the heterochromatin assembly pathway at the stage of histone deacetylation. Mutational inactivation of Epe1 downregulates approximately 12% of S. pombe genes, and the list of these genes overlaps significantly with the lists of genes that are upregulated by mutations in silencing genes and genes that are hyperacetylated at their promoter regions in clr6-1 mutants. We propose that an interplay between the repressive HDACs activity and Epe1 helps to regulate gene expression in S. pombe.
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Affiliation(s)
- Sara Isaac
- Department of Molecular Biology, The Hebrew University-Hadassah Medical School, Jerusalem, Israel 91010
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18
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Lan F, Zaratiegui M, Villén J, Vaughn MW, Verdel A, Huarte M, Shi Y, Gygi SP, Moazed D, Martienssen RA, Shi Y. S. pombe LSD1 Homologs Regulate Heterochromatin Propagation and Euchromatic Gene Transcription. Mol Cell 2007; 26:89-101. [PMID: 17434129 DOI: 10.1016/j.molcel.2007.02.023] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2006] [Revised: 12/19/2006] [Accepted: 02/22/2007] [Indexed: 01/05/2023]
Abstract
LSD1 represses and activates transcription by demethylating histone H3K4me and H3K9me, respectively. Genetic ablation of the S. pombe homologs, splsd1 and splsd2, resulted in slow growth and lethality, respectively, underscoring their physiological importance. spLsd1 and spLsd2 form a stable protein complex, which exhibits demethylase activity toward methylated H3K9 in vitro. Both proteins were associated with the heterochromatin boundary regions and euchromatic gene promoters. Loss of spLsd1 resulted in increased H3K9 methylation accompanied by reduced euchromatic gene transcription and heterochromatin propagation. Removal of the H3K9 methylase Clr4 partially suppressed the slow growth phenotype of splsd1Delta. Conversely, catalytically inactivating point mutations in the splsd1 and splsd2 genes partially mimicked the growth and heterochromatin propagation phenotypes. Taken together, these findings suggest the importance of both enzymatic and nonenzymatic roles of spLsd1 in regulating heterochromatin propagation and euchromatic transcription and also suggest that misregulation of spLsd1/2 is likely to impact the epigenetic state of the cell.
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Affiliation(s)
- Fei Lan
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
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19
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20
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Martin DGE, Baetz K, Shi X, Walter KL, MacDonald VE, Wlodarski MJ, Gozani O, Hieter P, Howe L. The Yng1p plant homeodomain finger is a methyl-histone binding module that recognizes lysine 4-methylated histone H3. Mol Cell Biol 2006; 26:7871-9. [PMID: 16923967 PMCID: PMC1636756 DOI: 10.1128/mcb.00573-06] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The ING (inhibitor of growth) protein family includes a group of homologous nuclear proteins that share a highly conserved plant homeodomain (PHD) finger domain at their carboxyl termini. Members of this family are found in multiprotein complexes that posttranslationally modify histones, suggesting that these proteins serve a general role in permitting various enzymatic activities to interact with nucleosomes. There are three members of the ING family in Saccharomyces cerevisiae: Yng1p, Yng2p, and Pho23p. Yng1p is a component of the NuA3 histone acetyltransferase complex and is required for the interaction of NuA3 with chromatin. To gain insight into the function of the ING proteins, we made use of a genetic strategy to identify genes required for the binding of Yng1p to histones. Using the toxicity of YNG1 overexpression as a tool, we showed that Yng1p interacts with the amino-terminal tail of histone H3 and that this interaction can be disrupted by loss of lysine 4 methylation within this tail. Additionally, we mapped the region of Yng1p required for overexpression of toxicity to the PHD finger, showed that this region capable of binding lysine 4-methylated histone H3 in vitro, and demonstrated that mutations of the PHD finger that abolish binding in vitro are no longer toxic in vivo. These results identify a novel function for the Yng1p PHD finger in promoting stabilization of the NuA3 complex at chromatin through recognition of histone H3 lysine 4 methylation.
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Affiliation(s)
- David G E Martin
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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21
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Bühler M, Verdel A, Moazed D. Tethering RITS to a nascent transcript initiates RNAi- and heterochromatin-dependent gene silencing. Cell 2006; 125:873-86. [PMID: 16751098 DOI: 10.1016/j.cell.2006.04.025] [Citation(s) in RCA: 302] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2005] [Revised: 02/24/2006] [Accepted: 04/20/2006] [Indexed: 11/27/2022]
Abstract
In the fission yeast Schizosaccharomyces pombe, the RNA-Induced Transcriptional Silencing (RITS) complex has been proposed to target the chromosome via siRNA-dependent base-pairing interactions to initiate heterochromatin formation. Here we show that tethering of the RITS subunit, Tas3, to the RNA transcript of the normally active ura4+ gene silences ura4+ expression. This silencing depends on a functional RNAi pathway, requires the heterochromatin proteins, Swi6/HP1, Clr4/Suv39h, and Sir2, and is accompanied by the generation of ura4+ siRNAs, histone H3-lysine 9 methylation, and Swi6 binding. Furthermore, the ability of the newly generated ura4+ siRNAs to silence a second ura4+ allele in trans is strongly inhibited by the conserved siRNA nuclease, Eri1. Surprisingly, silencing of tethered ura4+, or ura4+ inserted within centromeric heterochromatin, or some of the endogenous centromeric repeat promoters, is not associated with changes in RNA polymerase II occupancy. These findings support a model in which targeting of nascent transcripts by RITS mediates chromatin modifications and suggest that cotranscriptional processing events play a primary role in the silencing mechanism.
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Affiliation(s)
- Marc Bühler
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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22
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Klenov MS, Gvozdev VA. Heterochromatin formation: role of short RNAs and DNA methylation. BIOCHEMISTRY (MOSCOW) 2006; 70:1187-98. [PMID: 16336177 DOI: 10.1007/s10541-005-0247-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The role of small double-stranded RNAs is considered in formation of silent chromatin structure. Small RNAs are implicated in the regulation of individual gene transcription, suppression of transposon expression, and in maintaining functional structure of extended heterochromatic regions. Interrelations between short RNA-dependent gene silencing, histone modifications, and DNA methylation are discussed. Specific features of RNA-induced chromatin repression in various eucaryotes are also described.
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Affiliation(s)
- M S Klenov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
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23
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Gómez EB, Espinosa JM, Forsburg SL. Schizosaccharomyces pombe mst2+ encodes a MYST family histone acetyltransferase that negatively regulates telomere silencing. Mol Cell Biol 2005; 25:8887-903. [PMID: 16199868 PMCID: PMC1265769 DOI: 10.1128/mcb.25.20.8887-8903.2005] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Histone acetylation and deacetylation are associated with transcriptional activity and the formation of constitutively silent heterochromatin. Increasingly, histone acetylation is also implicated in other chromosome transactions, including replication and segregation. We have cloned the only Schizosaccharomyces pombe MYST family histone acetyltransferase genes, mst1(+) and mst2(+). Mst1p, but not Mst2p, is essential for viability. Both proteins are localized to the nucleus and bound to chromatin throughout the cell cycle. Deltamst2 genetically interacts with mutants that affect heterochromatin, cohesion, and telomere structure. Mst2p is a negative regulator of silencing at the telomere but does not affect silencing in the centromere or mating type region. We generated a census of proteins and histone modifications at wild-type telomeres. A histone acetylation gradient at the telomeres is lost in Deltamst2 cells without affecting the distribution of Taz1p, Swi6p, Rad21p, or Sir2p. We propose that the increased telomeric silencing is caused by histone hypoacetylation and/or an increase in the ratio of methylated to acetylated histones. Although telomere length is normal, meiosis is aberrant in Deltamst2 diploid homozygote mutants, suggesting that telomeric histone acetylation contributes to normal meiotic progression.
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Affiliation(s)
- Eliana B Gómez
- Molecular & Computational Biology Section, University of Southern California, Los Angeles, 90089-2910, USA
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24
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Shin JA, Choi ES, Kim HS, Ho JCY, Watts FZ, Park SD, Jang YK. SUMO Modification Is Involved in the Maintenance of Heterochromatin Stability in Fission Yeast. Mol Cell 2005; 19:817-28. [PMID: 16168376 DOI: 10.1016/j.molcel.2005.08.021] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2005] [Revised: 08/09/2005] [Accepted: 08/17/2005] [Indexed: 10/25/2022]
Abstract
Several studies have suggested that SUMO may participate in the regulation of heterochromatin, but direct evidence is lacking. Here, we present a direct link between sumoylation and heterochromatin stability. SUMO deletion impaired silencing at heterochromatic regions and induced histone H3 Lys4 methylation, a hallmark of active chromatin in fission yeast. Our findings showed that the SUMO-conjugating enzyme Hus5/Ubc9 interacted with the conserved heterochromatin proteins Swi6, Chp2 (a paralog of Swi6), and Clr4 (H3 Lys9 methyltransferase). Moreover, chromatin immunoprecipitation (ChIP) revealed that Hus5 was highly enriched in heterochromatic regions in a heterochromatin-dependent manner, suggesting a direct role of Hus5 in heterochromatin formation. We also found that Swi6, Chp2, and Clr4 themselves can be sumoylated in vivo and defective sumoylation of Swi6 or Chp2 compromised silencing. These results indicate that Hus5 associates with heterochromatin through interactions with heterochromatin proteins and modifies substrates whose sumoylations are required for heterochromatin stability, including heterochromatin proteins themselves.
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Affiliation(s)
- Jin A Shin
- Research Institute, National Cancer Center, Goyang, Gyeonggi 411-764, Republic of Korea
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25
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Abstract
Epigenetic events that contribute to the assembly and maintenance of silent chromatin structures have been defined through genetic, molecular, and cytological studies in a variety of eukaryotic model organisms. However, the precise cascade of events responsible for converting a developmentally regulated gene from an active euchromatic state to a heritably silent heterochromatic state remains to be elucidated. To establish a molecular framework for studying this cascade, we examined the temporal order of events associated with silencing of the murine terminal transferase (Dntt) gene during thymocyte maturation. This article describes our findings in the context of current knowledge of gene silencing mechanisms.
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Affiliation(s)
- Ruey-Chyi Su
- Howard Hughes Medical Institute, Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, USA
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26
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Schweinsberg S, Hagstrom K, Gohl D, Schedl P, Kumar RP, Mishra R, Karch F. The enhancer-blocking activity of the Fab-7 boundary from the Drosophila bithorax complex requires GAGA-factor-binding sites. Genetics 2005; 168:1371-84. [PMID: 15579691 PMCID: PMC1448804 DOI: 10.1534/genetics.104.029561] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the work reported here we have analyzed the role of the GAGA factor [encoded by the Trithorax-like (Trl) gene] in the enhancer-blocking activity of Frontabdominal-7 (Fab-7), a domain boundary element from the Drosophila melanogaster bithorax complex (BX-C). One of the three nuclease hypersensitive sites in the Fab-7 boundary, HS1, contains multiple consensus-binding sequences for the GAGA factor, a protein known to be involved in the formation and/or maintenance of nucleosome-free regions of chromatin. GAGA protein has been shown to localize to the Fab-7 boundary in vivo, and we show that it recognizes sequences from HS1 in vitro. Using two different transgene assays we demonstrate that GAGA-factor-binding sites are necessary but not sufficient for full Fab-7 enhancer-blocking activity. We show that distinct GAGA sites are required for different enhancer-blocking activities at different stages of development. We also show that the enhancer-blocking activity of the endogenous Fab-7 boundary is sensitive to mutations in the gene encoding the GAGA factor Trithorax-like.
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Affiliation(s)
- Susan Schweinsberg
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08540, USA
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27
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Duraisingh MT, Voss TS, Marty AJ, Duffy MF, Good RT, Thompson JK, Freitas-Junior LH, Scherf A, Crabb BS, Cowman AF. Heterochromatin Silencing and Locus Repositioning Linked to Regulation of Virulence Genes in Plasmodium falciparum. Cell 2005; 121:13-24. [PMID: 15820675 DOI: 10.1016/j.cell.2005.01.036] [Citation(s) in RCA: 363] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2004] [Revised: 10/06/2004] [Accepted: 01/14/2005] [Indexed: 11/26/2022]
Abstract
The malaria parasite Plasmodium falciparum undergoes antigenic variation to evade host immune responses through switching expression of variant surface proteins encoded by the var gene family. We demonstrate that both a subtelomeric transgene and var genes are subject to reversible gene silencing. Var gene silencing involves the SIR complex as gene disruption of PfSIR2 results in activation of this gene family. We also demonstrate that perinuclear gene activation involves chromatin alterations and repositioning into a location that may be permissive for transcription. Together, this implies that locus repositioning and heterochromatic silencing play important roles in the epigenetic regulation of virulence genes in P. falciparum.
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Affiliation(s)
- Manoj T Duraisingh
- The Walter and Eliza Hall Institute of Medical Research, Melbourne 3050, Australia
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28
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Freeman-Cook LL, Gómez EB, Spedale EJ, Marlett J, Forsburg SL, Pillus L, Laurenson P. Conserved locus-specific silencing functions of Schizosaccharomyces pombe sir2+. Genetics 2005; 169:1243-60. [PMID: 15545655 PMCID: PMC1449530 DOI: 10.1534/genetics.104.032714] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2004] [Accepted: 11/22/2004] [Indexed: 01/09/2023] Open
Abstract
In Schizosaccharomyces pombe, three genes, sir2(+), hst2(+), and hst4(+), encode members of the Sir2 family of conserved NAD(+)-dependent protein deacetylases. The S. pombe sir2(+) gene encodes a nuclear protein that is not essential for viability or for resistance to treatment with UV or a microtubule-destabilizing agent. However, sir2(+) is essential for full transcriptional silencing of centromeres, telomeres, and the cryptic mating-type loci. Chromatin immunoprecipitation results suggest that the Sir2 protein acts directly at these chromosomal regions. Enrichment of Sir2p at silenced regions does not require the HP1 homolog Swi6p; instead, Swi6-GFP localization to telomeres depends in part on Sir2p. The phenotype of sir2 swi6 double mutants supports a model whereby Sir2p functions prior to Swi6p at telomeres and the silent mating-type loci. However, Sir2p does not appear to be essential for the localization of Swi6p to centromeric foci. Cross-complementation experiments showed that the Saccharomyces cerevisiae SIR2 gene can function in place of S. pombe sir2(+), suggesting overlapping deacetylation substrates in both species. These results also suggest that, despite differences in most of the other molecules required, the two distantly related yeast species share a mechanism for targeting Sir2p homologs to silent chromatin.
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Affiliation(s)
- Lisa L Freeman-Cook
- Division of Biological Sciences, Section of Molecular Biology and UCSD Center for Cancer Research, University of California, San Diego, 92093-0347, USA.
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29
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Martin AM, Pouchnik DJ, Walker JL, Wyrick JJ. Redundant roles for histone H3 N-terminal lysine residues in subtelomeric gene repression in Saccharomyces cerevisiae. Genetics 2005; 167:1123-32. [PMID: 15280228 PMCID: PMC1470950 DOI: 10.1534/genetics.104.026674] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The transcription of genes located in subtelomeric regions of yeast chromosomes is repressed relative to the rest of the genome. This repression requires wild-type nucleosome levels but not the telomere silencing factors Sir2, Sir3, Sir4, and Rap1. Subtelomeric heterochromatin is characterized by the absence of acetylation or methylation of histone H3 lysine residues, but it is not known whether histone H3 hypoacetylation or hypomethylation is a prerequisite for the establishment of subtelomeric heterochromatin. We have systematically mutated the N-terminal tails of histone H3 and H4 in Saccharomyces cerevisiae and characterized the effects each mutant has on genome-wide expression. Our results show that subtelomeric transcriptional repression is dependent on the histone H3 N-terminal domain, but not the histone H4 N-terminal domain. Mutating lysine-4, lysine-9, lysine-14, lysine-18, lysine-23, and lysine-27 to glycine in histone H3 is also sufficient to significantly reduce subtelomeric gene repression. Individual histone H3 lysine mutations, however, have little effect on subtelomeric gene repression or genome-wide expression, indicating that these six lysine residues have redundant functions. We propose that acetylation and methylation of histone H3 N-terminal lysine residues act as redundant mechanisms to demarcate regions of euchromatin from heterochromatin.
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Affiliation(s)
- Amy M Martin
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, USA
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30
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Jia S, Yamada T, Grewal SIS. Heterochromatin regulates cell type-specific long-range chromatin interactions essential for directed recombination. Cell 2004; 119:469-80. [PMID: 15537537 DOI: 10.1016/j.cell.2004.10.020] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Revised: 09/24/2004] [Accepted: 10/07/2004] [Indexed: 11/22/2022]
Abstract
Mating-type switching in Schizosaccharomyces pombe involves replacing genetic information at the expressed mat1 locus with sequences copied from one of two silent donor loci, mat2-P or mat3-M, located within a 20-kb heterochromatic domain. Donor selection is dictated by cell type: mat2 is the preferred donor in M cells, and mat3 is the preferred donor in P cells. Here we show that a recombination-promoting complex (RPC) containing Swi2 and Swi5 proteins exhibits cell type-specific localization pattern at the silent mating-type region and this differential localization modulates donor preference during mating-type switching. In P cells, RPC localization is restricted to a recombination enhancer located adjacent to mat3, but in M cells, RPC spreads in cis across the entire silent mating-type interval in a heterochromatin-dependent manner. Our analyses implicate heterochromatin in long-range regulatory interactions and suggest that heterochromatin imposes at the mating-type region structural organization that is important for the donor-choice mechanism.
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Affiliation(s)
- Songtao Jia
- Laboratory of Molecular Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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31
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Abstract
Exclusive gene expression, where only one member of a gene or gene cassette family is selected for expression, plays an important role in the establishment of cell identity in several biological systems. Here, we compare four such systems: mating-type switching in fission and budding yeast, where cells choose between expressing one of the two different mating-type cassettes, and immunoglobulin and odorant receptor gene expression in mammals, where the number of gene choices is substantially higher. The underlying mechanisms that establish this selective expression pattern in each system differ in almost every detail. In all four systems, once a successful gene activation event has taken place, a feedback mechanism affects the fate of the cell. In the mammalian systems, feedback is mediated by the expressed cell surface receptor to ensure monoallelic gene expression, whereas in the yeasts, the expressed gene cassette at the mating-type locus affects donor choice during the subsequent switching event.
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32
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Abstract
Soon after its discovery 75 years ago, heterochromatin, a dense chromosomal material, was found to silence genes. But its importance in regulating gene expression was controversial. Long thought to be inert, heterochromatin is now known to give rise to small RNAs, which, by means of RNA interference, direct the modification of proteins and DNA in heterochromatic repeats and transposable elements. Heterochromatin has thus emerged as a key factor in epigenetic regulation of gene expression, chromosome behaviour and evolution.
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Affiliation(s)
- Zachary Lippman
- Watson School of Biological Sciences and Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724 USA
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33
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Sadaie M, Iida T, Urano T, Nakayama JI. A chromodomain protein, Chp1, is required for the establishment of heterochromatin in fission yeast. EMBO J 2004; 23:3825-35. [PMID: 15372076 PMCID: PMC522800 DOI: 10.1038/sj.emboj.7600401] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2004] [Accepted: 08/17/2004] [Indexed: 11/09/2022] Open
Abstract
The chromodomain is a conserved motif that functions in the epigenetic control of gene expression. Here, we report the functional characterization of a chromodomain protein, Chp1, in the heterochromatin assembly in fission yeast. We show that Chp1 is a structural component of three heterochromatic regions-centromeres, the mating-type region, and telomeres-and that its localization in these regions is dependent on the histone methyltransferase Clr4. Although deletion of the chp1(+) gene causes centromere-specific decreases in Swi6 localization and histone H3-K9 methylation, we show that the role of Chp1 is not exclusive to the centromeres. We found that some methylation persists in native centromeric regions in the absence of Chp1, which is also true for the mating-type region and telomeres, and determined that Swi6 and Chp2 are critical to maintaining this residual methylation. We also show that Chp1 participates in the establishment of repressive chromatin in all three chromosomal regions. These results suggest that different heterochromatic regions share common structural properties, and that centromeric heterochromatin requires Chp1-mediated establishment steps differently than do other heterochromatic regions.
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Affiliation(s)
- Mahito Sadaie
- PRESTO, Japan Science and Technology Corporation, Japan
| | - Tetsushi Iida
- Laboratory for Chromatin Dynamics, Center for Developmental Biology, RIKEN, Kobe, Japan
| | - Takeshi Urano
- Department of Biochemistry II, Nagoya University School of Medicine, Nagoya, Japan
| | - Jun-ichi Nakayama
- PRESTO, Japan Science and Technology Corporation, Japan
- Laboratory for Chromatin Dynamics, Center for Developmental Biology, RIKEN, Kobe, Japan
- Laboratory for Chromatin Dynamics, Center for Developmental Biology, RIKEN, 2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan. Tel.: +81 78 306 3205; Fax: +81 78 306 3208; E-mail:
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34
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Jia S, Noma KI, Grewal SIS. RNAi-Independent Heterochromatin Nucleation by the Stress-Activated ATF/CREB Family Proteins. Science 2004; 304:1971-6. [PMID: 15218150 DOI: 10.1126/science.1099035] [Citation(s) in RCA: 243] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
At the silent mating-type interval of fission yeast, the RNA interference (RNAi) machinery cooperates with cenH, a DNA element homologous to centromeric repeats, to initiate heterochromatin formation. However, in RNAi mutants, heterochromatin assembly can still occur at low efficiency. Here, we report that Atf1 and Pcr1, two ATF/CREB family proteins, act in a parallel mechanism to the RNAi pathway for heterochromatin nucleation. Deletion of atf1 or pcr1 alone has little effect on silencing at the mating-type region, but when combined with RNAi mutants, double mutants fail to nucleate heterochromatin assembly. Moreover, deletion of atf1 or pcr1 in combination with cenH deletion causes loss of silencing and heterochromatin formation. Furthermore, Atf1 and Pcr1 bind to the mating-type region and target histone H3 lysine-9 methylation and the Swi6 protein essential for heterochromatin assembly. These analyses link ATF/CREB family proteins, involved in cellular response to environmental stresses, to nucleation of constitutive heterochromatin.
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Affiliation(s)
- Songtao Jia
- Laboratory of Molecular Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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35
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Cheutin T, Gorski SA, May KM, Singh PB, Misteli T. In vivo dynamics of Swi6 in yeast: evidence for a stochastic model of heterochromatin. Mol Cell Biol 2004; 24:3157-67. [PMID: 15060140 PMCID: PMC381678 DOI: 10.1128/mcb.24.8.3157-3167.2004] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The mechanism for transcriptional silencing of pericentric heterochromatin is conserved from fission yeast to mammals. Silenced genome regions are marked by epigenetic methylation of histone H3, which serves as a binding site for structural heterochromatin proteins. In the fission yeast Schizosaccharomyces pombe, the major structural heterochromatin protein is Swi6. To gain insight into Swi6 function in vivo, we have studied its dynamics in the nucleus of living yeast. We demonstrate that, in contrast to mammalian cells, yeast heterochromatin domains undergo rapid, large-scale motions within the nucleus. Similar to the situation in mammalian cells, Swi6 does not permanently associate with these chromatin domains but binds only transiently to euchromatin and heterochromatin. Swi6 binding dynamics are dependent on growth status and on the silencing factors Clr4 and Rik1, but not Clr1, Clr2, or Clr3. By comparing the kinetics of mutant Swi6 proteins in swi6(-) and swi6(+) strains, we demonstrate that homotypic protein-protein interactions via the chromoshadow domain stabilize Swi6 binding to chromatin in vivo. Kinetic modeling allowed quantitative estimation of residence times and indicated the existence of at least two kinetically distinct populations of Swi6 in heterochromatin. The observed dynamics of Swi6 binding are consistent with a stochastic model of heterochromatin and indicate evolutionary conservation of heterochromatin protein binding properties from mammals to yeast.
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Affiliation(s)
- Thierry Cheutin
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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Bose ME, McConnell KH, Gardner-Aukema KA, Müller U, Weinreich M, Keck JL, Fox CA. The origin recognition complex and Sir4 protein recruit Sir1p to yeast silent chromatin through independent interactions requiring a common Sir1p domain. Mol Cell Biol 2004; 24:774-86. [PMID: 14701749 PMCID: PMC343803 DOI: 10.1128/mcb.24.2.774-786.2004] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Sir1p is one of four SIR (silent information regulator) proteins required for silencing the cryptic mating-type locus HMRa in the budding yeast Saccharomyces cerevisiae. A Sir1p interaction with Orc1p, the largest subunit of the origin recognition complex (ORC), is critical for Sir1p's ability to bind HMRa and function in the formation of silent chromatin. Here we show that a discrete domain within Sir1p, the ORC interaction region (OIR), was necessary and sufficient for a Sir1p-ORC interaction. The OIR contains the originally defined silencer recognition-defective region as well as additional amino acids. In addition, a Sir1p-Sir4p interaction required a larger region of Sir1p that included the OIR. Amino acid substitutions causing defects in either a Sir1p-Orc1p or a Sir1p-Sir4p interaction reduced HMRa silencing and Sir1p binding to HMRa in chromatin. These data support a model in which Sir1p's association with HMRa is mediated by separable Sir1p-ORC and Sir1p-Sir4p interactions requiring a common Sir1p domain, and they indicate that a Sir1p-ORC interaction is restricted to silencers, at least in part, through interactions with Sir4p.
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Affiliation(s)
- Melissa E Bose
- Department of Biomolecular Chemistry, 587 MSC, University of Wisconsin Medical School, 1300 University Avenue, Madison, WI 43706-1532, USA
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37
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Ueno M, Murase T, Kibe T, Ohashi N, Tomita K, Murakami Y, Uritani M, Ushimaru T, Harata M. Fission yeast Arp6 is required for telomere silencing, but functions independently of Swi6. Nucleic Acids Res 2004; 32:736-41. [PMID: 14757838 PMCID: PMC373355 DOI: 10.1093/nar/gkh234] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The actin-related proteins (Arps), which are subdivided into at least eight subfamilies, are conserved from yeast to humans. A member of the Arp6 subfamily in Drosophila, Arp4/Arp6, co-localizes with heterochromatin protein 1 (HP1) in pericentric heterochromatin. Fission yeast Schizosaccharomyces pombe possesses both an HP1 homolog and an Arp6 homolog. However, the function of S.pombe Arp6 has not been characterized yet. We found that deletion of arp6(+) impaired telomere silencing, but did not affect centromere silencing. Chromatin immunoprecipitation assays revealed that Arp6 bound to the telomere region. However, unlike Drosophila Arp4/Arp6, S.pombe Arp6 was distributed throughout nuclei. The binding of Arp6 to telomere DNA was not affected by deletion of swi6(+). Moreover, the binding of Swi6 to telomere ends was not affected by deletion of arp6(+). These results suggest that Arp6 and Swi6 function independently at telomere ends. We propose that the Arp6-mediated repression mechanism works side by side with Swi6-based telomere silencing in S.pombe.
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Affiliation(s)
- Masaru Ueno
- Department of Chemistry, Shizuoka University, 836 Oya, Shizuoka 422-8529, Japan.
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38
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Cam H, Grewal SIS. RNA interference and epigenetic control of heterochromatin assembly in fission yeast. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2004; 69:419-27. [PMID: 16117676 DOI: 10.1101/sqb.2004.69.419] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Affiliation(s)
- H Cam
- Laboratory of Molecular Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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39
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Shankaranarayana GD, Motamedi MR, Moazed D, Grewal SIS. Sir2 regulates histone H3 lysine 9 methylation and heterochromatin assembly in fission yeast. Curr Biol 2003; 13:1240-6. [PMID: 12867036 DOI: 10.1016/s0960-9822(03)00489-5] [Citation(s) in RCA: 153] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Hypoacetylated histones are a hallmark of heterochromatin in organisms ranging from yeast to humans. Histone deacetylation is carried out by both NAD(+)-dependent and NAD(+)-independent enzymes. In the budding yeast Saccharomyces cerevisiae, deacetylation of histones in heterochromatic chromosomal domains requires Sir2, a phylogenetically conserved NAD(+)-dependent deacetylase. In the fission yeast Schizosaccharomyces pombe, NAD(+)-independent histone deacetylases are required for the formation of heterochromatin, but the role of Sir2-like deacetylases in this process has not been evaluated. Here, we show that spSir2, the S. pombe Sir2-like protein that is the most closely related to the S. cerevisiae Sir2, is an NAD(+)-dependent deacetylase that efficiently deacetylates histone H3 lysine 9 (K9) and histone H4 lysine 16 (K16) in vitro. In sir2 Delta cells, silencing at the donor mating-type loci, telomeres, and the inner centromeric repeats (imr) is abolished, while silencing at the outer centromeric repeats (otr) and rDNA is weakly reduced. Furthermore, Sir2 is required for hypoacetylation and methylation of H3-K9 and for the association of Swi6 with the above loci in vivo. Our findings suggest that the NAD(+)-dependent deacetylase Sir2 plays an important and conserved role in heterochromatin assembly in eukaryotes.
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Nakayama JI, Xiao G, Noma KI, Malikzay A, Bjerling P, Ekwall K, Kobayashi R, Grewal SIS. Alp13, an MRG family protein, is a component of fission yeast Clr6 histone deacetylase required for genomic integrity. EMBO J 2003; 22:2776-87. [PMID: 12773392 PMCID: PMC156745 DOI: 10.1093/emboj/cdg248] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The post-translational modifications of histones are key to the modulation of chromatin structure. Distinct patterns of modifications established by histone-modifying enzymes control diverse chromosomal processes. Here, we report the purification and molecular characterization of the fission yeast Clr6 histone deacetyl ase involved in higher order chromatin assembly. We show that a chromodomain protein Alp13, which belongs to the conserved MRG protein family linked to cellular senescence in humans, is associated with Clr6. In addition, Clr6 interacts with homologs of the mammalian transcriptional co-repressors Sin3, Pst1 and Pst2, and a WD40 repeat-containing protein, Prw1. Alp13, Pst2 and Prw1 form a stable complex with Clr6 in the nucleus. Deletion of any of these factors causes progressive loss of viability and sensitivity to DNA-damaging agents, and impairs condensation/resolution of chromosomes during mitosis. This is accompanied by hyperacetylation of histones and a reduction in histone H3 Ser10 phosphorylation, which correlates with chromosome condensation during mitosis. These results link the MRG family protein Alp13 to histone deacetylation, and suggest that Clr6 and its associated factors are essential for fundamental chromosomal events.
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Affiliation(s)
- Jun-Ichi Nakayama
- Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, NY 11724, USA
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41
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Ayoub N, Noma KI, Isaac S, Kahan T, Grewal SIS, Cohen A. A novel jmjC domain protein modulates heterochromatization in fission yeast. Mol Cell Biol 2003; 23:4356-70. [PMID: 12773576 PMCID: PMC156127 DOI: 10.1128/mcb.23.12.4356-4370.2003] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The heterochromatin domain at the mat locus of Schizosaccharomyces pombe is bounded by the IR-L and IR-R barriers. A genetic screen for mutations that promote silencing beyond IR-L revealed a novel gene named epe1, encoding a conserved nuclear protein with a jmjC domain. Disruption of epe1 promotes continuous spreading of heterochromatin-associated histone modifications and Swi6 binding to chromatin across heterochromatic barriers. It also enhances position effect variegation at heterochromatic domains, suppresses mutations in silencing genes, and stabilizes the repressed epigenetic state at the mat locus. However, it does not enhance silencing establishment. Our analysis suggests that the jmjC domain is essential for Epe1 activity and that Epe1 counteracts transcriptional silencing by negatively affecting heterochromatin stability. Consistent with this proposition, the meiotic stability of established heterochromatin beyond IR-L is diminished by Epe1 activity, and overexpression of Epe1 disrupts heterochromatin through acetylation of H3-K9 and H3-K14 and methylation of H3-K4. Furthermore, overexpression of Epe1 elevates the rate of chromosome loss. We propose that Epe1 helps control chromatin organization by down-regulating the stability of epigenetic marks that govern heterochromatization.
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Affiliation(s)
- Nabieh Ayoub
- Department of Molecular Biology, The Hebrew University-Hadassah Medical School, Jerusalem, Israel 91010
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42
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Nicolas E, Roumillac C, Trouche D. Balance between acetylation and methylation of histone H3 lysine 9 on the E2F-responsive dihydrofolate reductase promoter. Mol Cell Biol 2003; 23:1614-22. [PMID: 12588981 PMCID: PMC151719 DOI: 10.1128/mcb.23.5.1614-1622.2003] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Epigenetic marks that specify silent heterochromatic domains in eucaryotic genomes include methylation of histone H3 lysine 9. Strikingly, active loci in the vicinity of silent domains are sometimes characterized by acetylation of histone H3 lysine 9, suggesting that the balance between these two competitive modifications is important for the establishment of specific chromatin structures. Some euchromatic genes, targeted by the retinoblastoma protein Rb, are also believed to be regulated by histone H3 lysine 9 methylation. Here, we study the dihydrofolate reductase promoter, which is repressed in G0 and at the beginning of G1 by p107 or p130, two Rb-related proteins. We found that these two pocket proteins share with Rb the ability to associate with the histone methyl transferase SUV39H1. SUV39H1 can be recruited to the E2F transcription factor and functions as a transcriptional corepressor. With ChIP assays followed by real-time PCR, we showed that K9 of histone H3 evolves from a hypermethylated state in G0 to a hyperacetylated state at the G1/S transition. Taken together, these results indicate that the temporal regulation of euchromatic promoters may involve controlling the balance between methylation and acetylation of histone H3 lysine 9, a feature previously described for the spatial regulation of chromatin function.
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Affiliation(s)
- Estelle Nicolas
- Laboratoire de Biologie Moléculaire Eucaryote, UMR 5099 CNRS, IFR 109, Toulouse, France
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43
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Blanton J, Gaszner M, Schedl P. Protein:protein interactions and the pairing of boundary elements in vivo. Genes Dev 2003; 17:664-75. [PMID: 12629048 PMCID: PMC196003 DOI: 10.1101/gad.1052003] [Citation(s) in RCA: 159] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Although it is now well-established that boundary elements/insulators function to subdivide eukaryotic chromosomes into autonomous regulatory domains, the underlying mechanisms remain elusive. One idea is that boundaries act as barriers, preventing the processive spreading of "active" or "silenced" chromatin between domains. Another is that the partitioning into autonomous functional units is a consequence of an underlying structural subdivision of the chromosome into higher order "looped" domains. In this view, boundaries are thought to delimit structural domains by interacting with each other or with some other nuclear structure. The studies reported here provide support for the looped domain model. We show that the Drosophila scs and scs' boundary proteins, Zw5 and BEAF, respectively, interact with each other in vitro and in vivo. Moreover, consistent with idea that this protein:protein interaction might facilitate pairing of boundary elements, we find that that scs and scs' are in close proximity to each other in Drosophila nuclei.
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Affiliation(s)
- Jason Blanton
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08540, USA
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44
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Noma KI, Grewal SIS. Histone H3 lysine 4 methylation is mediated by Set1 and promotes maintenance of active chromatin states in fission yeast. Proc Natl Acad Sci U S A 2002; 99 Suppl 4:16438-45. [PMID: 12193658 PMCID: PMC139906 DOI: 10.1073/pnas.182436399] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Methylation of histone H3 at lysine 4 (H3 Lys-4) or lysine 9 (H3 Lys-9) is known to define active and silent chromosomal domains respectively from fission yeast to humans. However, in budding yeast, H3 Lys-4 methylation is also necessary for silent chromatin assembly at telomeres and ribosomal DNA. Here we demonstrate that deletion of set1, which encodes a protein containing an RNA recognition motif at its amino terminus and a SET domain at the carboxy terminus, abolishes H3 Lys-4 methylation in fission yeast. Unlike in budding yeast, Set1-mediated H3 Lys-4 methylation is not required for heterochromatin assembly at the silent mating-type region and centromeres in fission yeast. Our analysis suggests that H3 Lys-4 methylation is a stable histone modification present throughout the cell cycle, including mitosis. The loss of H3 Lys-4 methylation in set1Delta cells is correlated with a decrease in histone H3 acetylation levels, suggesting a mechanistic link between H3 Lys-4 methylation and acetylation of the H3 tail. We suggest that methylation of H3 Lys-4 primarily acts in the maintenance of transcriptionally poised euchromatic domains, and that this modification is dispensable for heterochromatin formation in fission yeast, which instead utilizes H3 Lys-9 methylation.
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Affiliation(s)
- Ken-ichi Noma
- Cold Spring Harbor Laboratory, P.O. Box 100, NY 11724, USA
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45
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Singh G, Klar AJS. The 2.1-kb inverted repeat DNA sequences flank the mat2,3 silent region in two species of Schizosaccharomyces and are involved in epigenetic silencing in Schizosaccharomyces pombe. Genetics 2002; 162:591-602. [PMID: 12399374 PMCID: PMC1462298 DOI: 10.1093/genetics/162.2.591] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The mat2,3 region of the fission yeast Schizosaccharomyces pombe exhibits a phenomenon of transcriptional silencing. This region is flanked by two identical DNA sequence elements, 2.1 kb in length, present in inverted orientation: IRL on the left and IRR on the right of the silent region. The repeats do not encode any ORF. The inverted repeat DNA region is also present in a newly identified related species, which we named S. kambucha. Interestingly, the left and right repeats share perfect identity within a species, but show approximately 2% bases interspecies variation. Deletion of IRL results in variegated expression of markers inserted in the silent region, while deletion of the IRR causes their derepression. When deletions of these repeats were genetically combined with mutations in different trans-acting genes previously shown to cause a partial defect in silencing, only mutations in clr1 and clr3 showed additive defects in silencing with the deletion of IRL. The rate of mat1 switching is also affected by deletion of repeats. The IRL or IRR deletion did not cause significant derepression of the mat2 or mat3 loci. These results implicate repeats for maintaining full repression of the mat2,3 region, for efficient mat1 switching, and further support the notion that multiple pathways cooperate to silence the mat2,3 domain.
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Affiliation(s)
- Gurjeet Singh
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702-1201, USA
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46
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Abstract
DNA repetitions may provoke heterochromatinization. We explore here a model in which multiple cis-acting sequences that display no silencing activity on their own (protosilencers) may cooperate to establish and maintain a heterochromatin domain efficiently. Protosilencers, first defined in budding yeast, have now been found in a wide range of genomes where they appear to stabilize and to extend the propagation of heterochromatin domains. Strikingly, isolated or moderately repeated protosilencers can also be found in promoters where they participate in transcriptional activation and have insulation functions. This suggests that the proper juxtaposition of a threshold number of protosilencers converts them from neutral or transactivating elements into ones that nucleate heterochromatin. Interactions might be transient or permanent, and are likely to occur over distances by looping. This model provides a conceptual framework for as varied phenomena as telomere-driven silencing in Drosophila, X inactivation in mammals, and rDNA silencing in S. cerevisiae. It may also account for the silencing that occurs when multiple copies of a transgene are inserted in tandem.
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47
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Nielsen IS, Nielsen O, Murray JM, Thon G. The fission yeast ubiquitin-conjugating enzymes UbcP3, Ubc15, and Rhp6 affect transcriptional silencing of the mating-type region. EUKARYOTIC CELL 2002; 1:613-25. [PMID: 12456009 PMCID: PMC118003 DOI: 10.1128/ec.1.4.613-625.2002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2001] [Accepted: 06/04/2002] [Indexed: 11/20/2022]
Abstract
Genes transcribed by RNA polymerase II are silenced when introduced near the mat2 or mat3 mating-type loci of the fission yeast Schizosaccharomyces pombe. Silencing is mediated by a number of gene products and cis-acting elements. We report here the finding of novel trans-acting factors identified in a screen for high-copy-number disruptors of silencing. Expression of cDNAs encoding the putative E2 ubiquitin-conjugating enzymes UbcP3, Ubc15 (ubiquitin-conjugating enzyme), or Rhp6 (Rad homolog pombe) from the strong nmt1 promoter derepressed the silent mating-type loci mat2 and mat3 and reporter genes inserted nearby. Deletion of rhp6 slightly derepressed an ade6 reporter gene placed in the mating-type region, whereas disruption of ubcP3 or ubc15 had no obvious effect on silencing. Rhp18 is the S. pombe homolog of Saccharomyces cerevisiae Rad18p, a DNA-binding protein that physically interacts with Rad6p. Rhp18 was not required for the derepression observed when UbcP3, Ubc15, or Rhp6 was overproduced. Overexpressing Rhp6 active-site mutants showed that the ubiquitin-conjugating activity of Rhp6 is essential for disruption of silencing. However, high dosage of UbcP3, Ubc15, or Rhp6 was not suppressed by a mutation in the 26S proteasome, suggesting that loss of silencing is not due to an increased degradation of silencing factors but rather to the posttranslational modification of proteins by ubiquitination. We discuss the implications of these results for the possible modes of action of UbcP3, Ubc15, and Rhp6.
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Affiliation(s)
- Inga Sig Nielsen
- Department of Genetics, Institute of Molecular Biology, University of Copenhagen, DK-1353 Copenhagen K, Denmark
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48
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Nakagawa H, Lee JK, Hurwitz J, Allshire RC, Nakayama JI, Grewal SIS, Tanaka K, Murakami Y. Fission yeast CENP-B homologs nucleate centromeric heterochromatin by promoting heterochromatin-specific histone tail modifications. Genes Dev 2002; 16:1766-78. [PMID: 12130537 PMCID: PMC186399 DOI: 10.1101/gad.997702] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Heterochromatin is a functionally important chromosomal component, especially at centromeres. In fission yeast, conserved heterochromatin-specific modifications of the histone H3 tail, involving deacetylation of Lys 9 and Lys 14 and subsequent methylation of Lys 9, promote the recruitment of a heterochromatin protein, Swi6, a homolog of the Drosophila heterochromatin protein 1. However, the primary determinants of the positioning of heterochromatin are still unclear. The fission yeast proteins Abp1, Cbh1, and Cbh2 are homologs of the human protein CENP-B that bind to centromeric alpha-satellite DNA and associate with centromeric heterochromatin. We show that the CENP-B homologs are functionally redundant at centromeres, and that Abp1 binds specifically to centromeric heterochromatin. In the absence of Abp1 or Cbh1, the centromeric association of Swi6 is diminished, resulting in a decrease in silencing of the region. CENP-B-homolog double disruptants show a synergistic reduction of Swi6 at centromeric heterochromatin, indicating that the three proteins are functionally redundant in the recruitment of Swi6. Furthermore, using chromatin immunoprecipitation assays, we show that disruption of CENP-B homologs causes a decrease in heterochromatin-specific modifications of histone H3. These results indicate that the CENP-B homologs act as site-specific nucleation factors for the formation of centromeric heterochromatin by heterochromatin-specific modifications of histone tails.
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Affiliation(s)
- Hiromi Nakagawa
- Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
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49
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Abstract
In eukaryotes, chromatin is essential for heredity. Chromatin architecture is sometimes "epistatic" over the DNA and imparts a different heritable state to the same DNA sequence or the same functional state to unrelated DNA sequences. This has been documented recently in a wide variety of studies focused on regulation of the yeast mating type, the function of Polycomb and trithorax group proteins, the specification of eukaryotic centromeres and neocentromeres, and genomic imprinting.
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Affiliation(s)
- Giacomo Cavalli
- Institut de Génétique Humaine-CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France.
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50
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Huang Y. Transcriptional silencing in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Nucleic Acids Res 2002; 30:1465-82. [PMID: 11917007 PMCID: PMC101825 DOI: 10.1093/nar/30.7.1465] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Transcriptional silencing is a heritable form of gene inactivation that involves the assembly of large regions of DNA into a specialized chromatin structure that inhibits transcription. This phenomenon is responsible for inhibiting transcription at silent mating-type loci, telomeres and rDNA repeats in both budding yeast Saccharomyces cerevisiae and fission yeast Schizosaccharomyces pombe, as well as at centromeres in fission yeast. Although transcriptional silencing in both S.cerevisiae and S.pombe involves modification of chromatin, no apparent amino acid sequence similarities have been reported between the proteins involved in establishment and maintenance of silent chromatin in these two distantly related yeasts. Silencing in S.cerevisiae is mediated by Sir2p-containing complexes, whereas silencing in S.pombe is mediated primarily by Swi6-containing complexes. The Swi6 complexes of S.pombe contain proteins closely related to their counterparts in higher eukaryotes, but have no apparent orthologs in S.cerevisiae. Silencing proteins from both yeasts are also actively involved in other chromosome-related nuclear functions, including DNA repair and the regulation of chromatin structure.
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