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  • 1
    Language: English
    In: Nature communications, 2014-06-09, Vol.5 (1), p.4091-4091
    Description: DNA double-strand break (DSB) repair is a highly regulated process performed predominantly by non-homologous end joining (NHEJ) or homologous recombination (HR) pathways. How these pathways are coordinated in the context of chromatin is unclear. Here we uncover a role for histone H3K36 modification in regulating DSB repair pathway choice in fission yeast. We find Set2-dependent H3K36 methylation reduces chromatin accessibility, reduces resection and promotes NHEJ, while antagonistic Gcn5-dependent H3K36 acetylation increases chromatin accessibility, increases resection and promotes HR. Accordingly, loss of Set2 increases H3K36Ac, chromatin accessibility and resection, while Gcn5 loss results in the opposite phenotypes following DSB induction. Further, H3K36 modification is cell cycle regulated with Set2-dependent H3K36 methylation peaking in G1 when NHEJ occurs, while Gcn5-dependent H3K36 acetylation peaks in S/G2 when HR prevails. These findings support an H3K36 chromatin switch in regulating DSB repair pathway choice.
    Subject(s): Acetylation ; Acetyltransferases - metabolism ; Chromatin - metabolism ; DNA End-Joining Repair ; DNA Repair ; DNA, Fungal - metabolism ; Histone-Lysine N-Methyltransferase - metabolism ; Histones - metabolism ; Methylation ; Recombinational DNA Repair ; Schizosaccharomyces - genetics ; Schizosaccharomyces - metabolism ; Schizosaccharomyces pombe Proteins - metabolism
    ISSN: 2041-1723
    E-ISSN: 2041-1723
    Source: Nature Open Access
    Source: PubMed Central
    Source: DOAJ Directory of Open Access Journals - Not for CDI Discovery
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  • 2
    Language: English
    In: Genetics (Austin), 2016-08, Vol.203 (4), p.1669-1678
    Description: Uncontrolled propagation of retrotransposons is potentially detrimental to host genome integrity. Therefore, cells have evolved surveillance mechanisms to restrict the mobility of these elements. In Schizosaccharomyces pombe the Tf2 LTR retrotransposons are transcriptionally silenced and are also clustered in the nucleus into structures termed Tf bodies. Here we describe the impact of silencing and clustering on the mobility of an endogenous Tf2 element. Deletion of genes such as set1(+) (histone H3 lysine 4 methyltransferase) or abp1(+) (CENP-B homolog) that both alleviate silencing and clustering, result in a corresponding increase in mobilization. Furthermore, expression of constitutively active Sre1, a transcriptional activator of Tf2 elements, also alleviates clustering and induces mobilization. In contrast, clustering is not disrupted by loss of the HIRA histone chaperone, despite high levels of expression, and in this background, mobilization frequency is only marginally increased. Thus, mutations that compromise transcriptional silencing but not Tf bodies are insufficient to drive mobilization. Furthermore, analyses of mutant alleles that separate the transcriptional repression and clustering functions of Set1 are consistent with control of Tf2 propagation via a combination of silencing and spatial organization. Our results indicate that host surveillance mechanisms operate at multiple levels to restrict Tf2 retrotransposon mobilization.
    Subject(s): Chromatin ; Chromatin - genetics ; Deoxyribonucleic acid ; DNA ; DNA methylation ; DNA-Binding Proteins - genetics ; Epigenetics ; Gene Expression Regulation, Fungal ; Genetic aspects ; Genome, Fungal ; Genomes ; Genomic Instability ; higher-order chromatin organization ; Histone-Lysine N-Methyltransferase - biosynthesis ; Histone-Lysine N-Methyltransferase - genetics ; Investigations ; Laboratories ; Mutation ; Proteins ; Research ; Retroelements - genetics ; retrotransposition ; Retrotransposons ; RNA polymerase ; Schizosaccharomyces - genetics ; Schizosaccharomyces pombe ; Schizosaccharomyces pombe Proteins - biosynthesis ; Schizosaccharomyces pombe Proteins - genetics ; Tf2 LTR retrotransposons ; Transcription Factors - biosynthesis ; Transcription Factors - genetics ; transcriptional silencing ; Yeast ; Yeast fungi
    ISSN: 1943-2631
    ISSN: 0016-6731
    E-ISSN: 1943-2631
    Source: Alma/SFX Local Collection
    Source: Genetics Society of America
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  • 3
    Language: English
    In: PloS one, 2015-07-13, Vol.10 (7), p.e0132240
    Description: Synthetic genetic array (SGA) has been successfully used to identify genetic interactions in S . cerevisiae and S . pombe . In S . pombe , SGA methods use either cycloheximide ( C ) or heat shock ( HS ) to select double mutants before measuring colony size as a surrogate for fitness. Quantitative Fitness Analysis (QFA) is a different method for determining fitness of microbial strains. In QFA, liquid cultures are spotted onto solid agar and growth curves determined for each spot by photography and model fitting. Here, we compared the two S . pombe SGA methods and found that the HS method was more reproducible for us. We also developed a QFA procedure for S . pombe . We used QFA to identify genetic interactions affecting two temperature sensitive, telomere associated query mutations ( taz1Δ and pot1-1 ). We identify exo1∆ and other gene deletions as suppressors or enhancers of S . pombe telomere defects. Our study identifies known and novel gene deletions affecting the fitness of strains with telomere defects. The interactions we identify may be relevant in human cells.
    Subject(s): Agar ; Cycloheximide ; Defects ; Deoxyribonucleic acid ; DNA ; Enhancers ; Fitness ; Genes ; Genetic engineering ; Genomes ; Growth curves ; Heat shock ; Medical research ; Medical schools ; Melanoma ; Methods ; Microorganisms ; Mutants ; Mutation ; Photography ; Quantitative genetics ; Skin cancer ; Suppressors ; Yeast
    ISSN: 1932-6203
    E-ISSN: 1932-6203
    Source: Academic Search Ultimate
    Source: PubMed Central
    Source: DOAJ Directory of Open Access Journals - Not for CDI Discovery
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  • 4
    Language: English
    In: PloS one, 2010-10-18, Vol.5 (10), p.e13488
    Description: HIRA (or Hir) proteins are conserved histone chaperones that function in multi-subunit complexes to mediate replication-independent nucleosome assembly. We have previously demonstrated that the Schizosaccharomyces pombe HIRA proteins, Hip1 and Slm9, form a complex with a TPR repeat protein called Hip3. Here we have identified a new subunit of this complex. To identify proteins that interact with the HIRA complex, rapid affinity purifications of Slm9 were performed. Multiple components of the chaperonin containing TCP-1 complex (CCT) and the 19S subunit of the proteasome reproducibly co-purified with Slm9, suggesting that HIRA interacts with these complexes. Slm9 was also found to interact with a previously uncharacterised protein (SPBC947.08c), that we called Hip4. Hip4 contains a HRD domain which is a characteristic of the budding yeast and human HIRA/Hir-binding proteins, Hpc2 and UBN1. Co-precipitation experiments revealed that Hip4 is stably associated with all of the other components of the HIRA complex and deletion of hip4(+) resulted in the characteristic phenotypes of cells lacking HIRA function, such as temperature sensitivity, an elongated cell morphology and hypersensitivity to the spindle poison, thiabendazole. Moreover, loss of Hip4 function alleviated the heterochromatic silencing of reporter genes located in the mating type locus and centromeres and was associated with increased levels of non-coding transcripts derived from centromeric repeat sequences. Hip4 was also found to be required for the distinct form of silencing that controls the expression of Tf2 LTR retrotransposons. Overall, these results indicate that Hip4 is an integral component of the HIRA complex that is required for transcriptional silencing at multiple loci.
    Subject(s): Amino Acid Sequence ; Baking yeast ; Base Sequence ; Binding proteins ; Biology ; Cell Biology ; Cell morphology ; Centromeres ; Chaperones ; Chromatin Structure ; Chromatography, Liquid ; Chromosome Biology ; Chromosome Structure ; Chromosomes ; Clonal deletion ; Cytology ; Defects ; DNA Primers ; Elongation ; Epigenetics ; Gene Expression ; Gene Silencing ; Genetics and Genomics ; Histone Modification ; Hypersensitivity ; Loci ; Mating ; Molecular Biology ; Molecular Sequence Data ; Mutation ; Open Reading Frames ; Precipitation (Meteorology) ; Protein binding ; Proteins ; Proteomics ; Reverse Transcriptase Polymerase Chain Reaction ; Saccharomyces cerevisiae ; Schizosaccharomyces - physiology ; Schizosaccharomyces pombe ; Schizosaccharomyces pombe Proteins - physiology ; Sequence Homology, Amino Acid ; Tandem Mass Spectrometry ; Thiabendazole ; Transcription Factors - physiology ; Yeast
    ISSN: 1932-6203
    E-ISSN: 1932-6203
    Source: Academic Search Ultimate
    Source: PubMed Central
    Source: DOAJ Directory of Open Access Journals - Not for CDI Discovery
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  • 5
    Language: English
    In: EMBO reports, 2016-01, Vol.17 (1), p.79-93
    Description: Maintenance of the correct level and organisation of nucleosomes is crucial for genome function. Here, we uncover a role for a conserved bromodomain AAA‐ATPase, Abo1, in the maintenance of nucleosome architecture in fission yeast. Cells lacking abo1+ experience both a reduction and mis‐positioning of nucleosomes at transcribed sequences in addition to increased intragenic transcription, phenotypes that are hallmarks of defective chromatin re‐establishment behind RNA polymerase II. Abo1 is recruited to gene sequences and associates with histone H3 and the histone chaperone FACT. Furthermore, the distribution of Abo1 on chromatin is disturbed by impaired FACT function. The role of Abo1 extends to some promoters and also to silent heterochromatin. Abo1 is recruited to pericentromeric heterochromatin independently of the HP1 ortholog, Swi6, where it enforces proper nucleosome occupancy. Consequently, loss of Abo1 alleviates silencing and causes elevated chromosome mis‐segregation. We suggest that Abo1 provides a histone chaperone function that maintains nucleosome architecture genome‐wide. Synopsis Loss of Abo1 function—a bromodomain AAA‐ATPase—results in global perturbations to nucleosome occupancy and organisation with effects on transcription and heterochromatin function. Loss of Abo1 results in a global reduction of histone levels. Nucleosome organisation at gene sequences is perturbed in the absence of Abo1. Abo1 co‐purifies with FACT and suppresses cryptic intragenic transcription. Abo1 function is required for silent centromeric heterochromatin and accurate chromosome segregation. Loss of Abo1 function—a bromodomain AAA‐ATPase—results in global perturbations to nucleosome occupancy and organisation with effects on transcription and heterochromatin function.
    Subject(s): Abo1 ; Adenosine Triphosphatases - chemistry ; Adenosine Triphosphatases - genetics ; Adenosine Triphosphatases - metabolism ; bromodomain AAA-ATPases ; Chromatin ; Chromatin - genetics ; Chromatin - metabolism ; Chromatin Assembly and Disassembly ; Chromatin, Epigenetics, Genomics & Functional Genomics ; Chromosomal Proteins, Non-Histone - metabolism ; Chromosome Segregation ; DNA, Intergenic ; Gene Silencing ; Genes ; Genomes ; Histone Chaperones - genetics ; Histone Chaperones - metabolism ; Histones - genetics ; Histones - metabolism ; nucleosome mapping ; Nucleosomes - genetics ; Nucleosomes - metabolism ; Promoter Regions, Genetic ; RNA Polymerase II - genetics ; Schizosaccharomyces - genetics ; Schizosaccharomyces - metabolism ; Schizosaccharomyces pombe ; Schizosaccharomyces pombe Proteins - chemistry ; Schizosaccharomyces pombe Proteins - genetics ; Schizosaccharomyces pombe Proteins - metabolism ; Transcription Factors - metabolism ; Transcription, Genetic
    ISSN: 1469-221X
    E-ISSN: 1469-3178
    Source: HighWire Press (Free Journals)
    Source: Wiley Online Library All Journals
    Source: PubMed Central
    Source: Get It Now
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  • 6
    Language: English
    In: Molecular and Cellular Biology, 2009-09-15, Vol.29 (18), p.5158-5167
    Description: Article Usage Stats Services MCB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley Reddit StumbleUpon Twitter current issue Spotlights in the Current Issue MCB About MCB Subscribers Authors Reviewers Advertisers Inquiries from the Press Permissions & Commercial Reprints ASM Journals Public Access Policy MCB RSS Feeds 1752 N Street N.W. • Washington DC 20036 202.737.3600 • 202.942.9355 fax • journals@asmusa.org Print ISSN: 0270-7306 Online ISSN: 1098-5549 Copyright © 2014 by the American Society for Microbiology.   For an alternate route to MCB .asm.org, visit: MCB       
    Subject(s): Cell Cycle Proteins - genetics ; Cell Cycle Proteins - metabolism ; DNA Damage ; DNA Transposable Elements - genetics ; Down-Regulation ; Gene Expression Profiling ; Gene Expression Regulation, Fungal ; Gene Silencing - drug effects ; Histones - metabolism ; Molecular Chaperones - metabolism ; Mutagens - pharmacology ; Mutation - genetics ; Nuclear Proteins - genetics ; Nuclear Proteins - metabolism ; Promoter Regions, Genetic ; RNA, Antisense - genetics ; RNA, Messenger - genetics ; RNA, Messenger - metabolism ; Schizosaccharomyces - drug effects ; Schizosaccharomyces - genetics ; Schizosaccharomyces - metabolism ; Schizosaccharomyces pombe ; Schizosaccharomyces pombe Proteins - genetics ; Schizosaccharomyces pombe Proteins - metabolism ; Telomere - metabolism ; Terminal Repeat Sequences - genetics ; Transcription Factors - genetics ; Transcription Factors - metabolism ; Transcription, Genetic - drug effects
    ISSN: 0270-7306
    E-ISSN: 1098-5549
    Source: HighWire Press (Free Journals)
    Source: Hellenic Academic Libraries Link
    Source: PubMed Central
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  • 7
    Language: English
    In: Cell cycle (Georgetown, Tex.), 2015-01-02, Vol.14 (1), p.123-134
    Description: HIRA is an evolutionarily conserved histone chaperone that mediates replication-independent nucleosome assembly and is important for a variety of processes such as cell cycle progression, development, and senescence. Here we have used a chromatin sequencing approach to determine the genome-wide contribution of HIRA to nucleosome organization in Schizosaccharomyces pombe. Cells lacking HIRA experience a global reduction in nucleosome occupancy at gene sequences, consistent with the proposed role for HIRA in chromatin reassembly behind elongating RNA polymerase II. In addition, we find that at its target promoters, HIRA commonly maintains the full occupancy of the −1 nucleosome. HIRA does not affect global chromatin structure at replication origins or in rDNA repeats but is required for nucleosome occupancy in silent regions of the genome. Nucleosome organization associated with the heterochromatic (dg-dh) repeats located at the centromere is perturbed by loss of HIRA function and furthermore HIRA is required for normal nucleosome occupancy at Tf2 LTR retrotransposons. Overall, our data indicate that HIRA plays an important role in maintaining nucleosome architecture at both euchromatic and heterochromatic loci.
    Subject(s): Chromatin ; Chromatin - metabolism ; Chromatin Assembly and Disassembly ; heterochromatin ; HIRA ; histone chaperone ; Histones - metabolism ; nucleosome assembly ; Nucleosomes - metabolism ; Promoter Regions, Genetic ; Reports ; RNA Polymerase II - genetics ; RNA Polymerase II - metabolism ; S. pombe ; Schizosaccharomyces - metabolism ; Schizosaccharomyces pombe Proteins - genetics ; Schizosaccharomyces pombe Proteins - metabolism ; Transcription Factors - genetics ; Transcription Factors - metabolism
    ISSN: 1538-4101
    E-ISSN: 1551-4005
    Source: Taylor & Francis Open Access
    Source: PubMed Central
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  • 8
    Language: English
    In: PloS one, 2015, Vol.10 (9), p.e0137820-e0137820
    Description: Cbf11 and Cbf12, the fission yeast CSL transcription factors, have been implicated in the regulation of cell-cycle progression, but no specific roles have been described and their target genes have been only partially mapped. Using a combination of transcriptome profiling under various conditions and genome-wide analysis of CSL-DNA interactions, we identify genes regulated directly and indirectly by CSL proteins in fission yeast. We show that the expression of stress-response genes and genes that are expressed periodically during the cell cycle is deregulated upon genetic manipulation of cbf11 and/or cbf12. Accordingly, the coordination of mitosis and cytokinesis is perturbed in cells with genetically manipulated CSL protein levels, together with other specific defects in cell-cycle progression. Cbf11 activity is nutrient-dependent and Δcbf11-associated defects are mitigated by inactivation of the protein kinase A (Pka1) and stress-activated MAP kinase (Sty1p38) pathways. Furthermore, Cbf11 directly regulates a set of lipid metabolism genes and Δcbf11 cells feature a stark decrease in the number of storage lipid droplets. Our results provide a framework for a more detailed understanding of the role of CSL proteins in the regulation of cell-cycle progression in fission yeast.
    Subject(s): Analysis ; Biology ; Cell cycle ; Cellular stress response ; CSL protein ; Cyclic AMP-Dependent Protein Kinases - genetics ; Cytokinesis ; Deactivation ; Defects ; Deoxyribonucleic acid ; Deregulation ; DNA ; DNA binding proteins ; Fission ; Gene expression ; Gene Expression Profiling - methods ; Gene Expression Regulation, Fungal ; Gene mapping ; Genes ; Genetic engineering ; Genomes ; Genomics ; Inactivation ; Kinases ; Lipid metabolism ; Lipids ; Localization ; MAP kinase ; Metabolism ; Microscopy ; Mitogen-Activated Protein Kinases - genetics ; Mitosis ; Nutrient cycles ; Physiological aspects ; Protein kinase A ; Proteins ; Schizosaccharomyces - genetics ; Schizosaccharomyces - metabolism ; Schizosaccharomyces pombe Proteins - genetics ; Schizosaccharomyces pombe Proteins - metabolism ; Science ; Stress, Physiological ; Transcription factors ; Transcription Factors - genetics ; Transcription Factors - metabolism ; Yeast
    ISSN: 1932-6203
    E-ISSN: 1932-6203
    Source: Academic Search Ultimate
    Source: PubMed Central
    Source: DOAJ Directory of Open Access Journals - Not for CDI Discovery
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  • 9
    Language: English
    In: Cell cycle (Georgetown, Tex.), 2009-10-01, Vol.8 (19), p.3102-3106
    Description: The primary function of tRNA genes is to provide the templates for the transcription of essential tRNA molecules. However, there is now evidence that these dispersed repetitive elements have the potential to mediate the spatial and functional organization of the genome and to drive genome change and evolution. Indeed, tRNA genes and related Pol III promoter elements can occupy distinct subnuclear positions and also provide barriers which functionally separate domains of chromatin. Furthermore, tRNA genes can also represent barriers to DNA replication fork progression and accordingly, tRNA genes can contribute to the formation of genomic fragile sites and have been implicated in genome evolution. Here we give insight into our current understanding of these "extra transcriptional" functions of tRNA genes and discuss how these functions may impact upon genome regulation and evolution.
    Subject(s): Binding ; Biology ; Bioscience ; Calcium ; Cancer ; Cell ; Chromosome Fragile Sites ; Cycle ; DNA Polymerase III - genetics ; DNA Polymerase III - metabolism ; DNA Replication ; Genome ; Landes ; Organogenesis ; Promoter Regions, Genetic ; Proteins ; RNA, Transfer - genetics ; RNA, Transfer - metabolism ; Transcription Factors, TFIII - metabolism
    ISSN: 1538-4101
    E-ISSN: 1551-4005
    Source: PubMed Central
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  • 10
    Language: English
    In: PloS one, 2015, Vol.10 (12), p.e0144677-e0144677
    Description: In the fission yeast, two Tor isoforms, Tor1 and Tor2, oppositely regulate gene expression of amino acid permeases. To elucidate the transcriptional machinery for these regulations, here we have employed the cap analysis of gene expression (CAGE), a method of analyzing expression profiles and identifying transcriptional start sites (TSSs). The loss of Tor1 decreased, and Tor2 inhibition by its temperature sensitive mutation increased, mRNA expression of isp5+, per1+, put4+ and SPBPB2B2.01. In contrast, the loss of Tor1 increased, and Tor2 inhibition decreased, the expression of cat1+. These changes were confirmed by semi-quantitative RT-PCR. These opposite effects by the loss of Tor1 and Tor2 inhibition appeared to occur evenly across multiple TSSs for the respective genes. The motif discovery analysis based on the CAGE results identified the GATA motifs as a potential cis-regulatory element for Tor-mediated regulation. In the luciferase reporter assay, the loss of Tor1 reduced, and Tor2 inhibition and nitrogen depletion increased, the activity of isp5+ promoter as well as that of a GATAAG reporter. One of the GATAAG motifs in isp5+ promoter was critical for its transcriptional activity, and a GATA transcription factor Gaf1 was critical for the activities of isp5+ promoter and the GATAAG reporter. Furthermore, Tor2 inhibition and nitrogen depletion induced nuclear localization of Gaf1 from the cytosol and its dephosphorylation. These results suggest that Tor2 inhibition, which is known to be induced by nitrogen depletion, promotes nuclear localization of Gaf1, thereby inducing isp5+ transcription through Gaf1 binding to the GATAAG motif in its promoter. Since Gaf1 was also critical for transcription of per1+ and put4+, Tor-Gaf1 signaling may coordinate transcription of multiple amino acid permeases according to nutrient availability.
    Subject(s): Acids ; Amino Acid Transport Systems - biosynthesis ; Amino Acid Transport Systems - genetics ; Amino acids ; Baking yeast ; Cages ; Cell growth ; Cell Nucleus - genetics ; Cell Nucleus - metabolism ; Cellular signal transduction ; Cytosol ; Dephosphorylation ; Depletion ; Gene expression ; Genetic aspects ; Genetic regulation ; Genomics ; Inhibition ; Isoforms ; Kinases ; Localization ; Machinery ; Machinery and equipment ; Mutation ; Nitrogen ; Nutrient availability ; Period 1 protein ; Phosphatidylinositol 3-Kinases - genetics ; Phosphatidylinositol 3-Kinases - metabolism ; Physiological aspects ; Polymerase chain reaction ; Protein Kinases - genetics ; Protein Kinases - metabolism ; Research ; Response Elements - physiology ; Schizosaccharomyces - genetics ; Schizosaccharomyces - metabolism ; Schizosaccharomyces pombe Proteins - genetics ; Schizosaccharomyces pombe Proteins - metabolism ; Signal Transduction - physiology ; Signaling ; Trans-Activators - genetics ; Trans-Activators - metabolism ; Transcription factors ; Transcription, Genetic - physiology ; Yeast
    ISSN: 1932-6203
    E-ISSN: 1932-6203
    Source: Academic Search Ultimate
    Source: PubMed Central
    Source: DOAJ Directory of Open Access Journals - Not for CDI Discovery
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