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Histone deacetylases and their co-regulators in schizosaccharomyces pombe
Södertörn University, School of Life Sciences.
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The DNA in every eukaryotic cell is wrapped around eight core histones to form the nucleosome. Therefore all events that involve DNA must also involve chromatin and nucleosomes. By regulating chromatin structure the cell can regulate the reactivity of the DNA. One of the most common ways of altering nucleosomes is the acetylation of lysine residues. Two enzymes are required to maintain the correct equilibrium for optimal cell growth: histone acetyltransferases (HATs) and histone deacetyltransferases (HDACs). In general, histone hypoacetylation is correlated with transcriptional inactivation, while hyperacetylation is correlated with active gene transcription. In Schizosaccharomyces pombe, mating type loci are silenced. Deletion of HDAC Hos2 had previously been shown to slightly increase silencing at the mating type locus. To assess whether any other HDAC was necessary for mating type silencing, cells were treated with HDAC poison Trichostatin A (TSA). TSA was found to cause a mild derepression of the mating type locus, indicating that another HDAC was responsible for silencing in this region. The RNA interference nuclease Dcr1 was later identified, and showed to degrade double stranded RNA into small nucleotide fragments. Deletion of dcr1 caused chromosome segregation defects and derepression of centromeric silencing. Rpd3 in S. cerevisiae is recruited to genomic targets by interacting with co-regulator Sin3. S. pombe has three Sin3 homologs. Pst1 interacts with the HDAC Clr6, and like Clr6 is an essential gene, mutants of which display chromosome mis-segregation and derepression of centromeric silencing. Pst1 was required for centromeric cohesion, and localized to centromeres in late S phase. Thus a co-repressor paradigm could be applied to centromere silencing as well. A comparative characterization of HDACs in S. pombe showed that the HDACs had different localizations and histone specificities. The comparison of HDACs was taken further with a genome wide expression analysis and histone density study of mutants. Results indicated that Clr6 was most often involved in promoter initiated gene repression, whereas Hos2 promoted the high expression of growth related genes by deacetylating H4K16ac in their coding regions. A class II HDAC, Clr3, was found to act cooperatively with Sir2 throughout the genome. Using a genomic approach to analyze Pst3, it was established that Clr6 and Pst3 could cooperate to negatively regulate genes by binding to their promoter regions. On the other hand, Pst3 was also involved in the up-regulation of ribosome biosynthesis genes, and could bind to the rDNA.

Place, publisher, year, edition, pages
Stockholm: Karolinska Institutet , 2007. , 37 p.
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:sh:diva-31262ISBN: 978-91-7357-140-1 (print)OAI: oai:DiVA.org:sh-31262DiVA: diva2:1051217
Public defence
2007-03-23, MA636, Alfred Nobels allé 7, Huddinge, 13:00 (English)
Opponent
Supervisors
Available from: 2016-12-01 Created: 2016-12-01 Last updated: 2016-12-01Bibliographically approved
List of papers
1. Transient inhibition of histone deacetylase activity overcomes silencing in the mating-type region in fission yeast
Open this publication in new window or tab >>Transient inhibition of histone deacetylase activity overcomes silencing in the mating-type region in fission yeast
1999 (English)In: Current Genetics, ISSN 0172-8083, E-ISSN 1432-0983, Vol. 35, no 2, 82-87 p.Article in journal (Refereed) Published
Abstract [en]

We have investigated the effects of inhibition of histone de-acetylase activity on silencing at the silent mating-type loci in fission yeast. Treatment of exponentially growing cells with the histone deacetylase inhibitor, trichostatin A (TSA), resulted in derepression of a marker gene inserted 150 bp distal from the silent mat3-M locus. The natural targets for the silencing mechanism in this region were only partially derepressed and the activation appeared to be asymmetric. i.e. the mat2-P cassette remained silent at concentrations that clearly partially derepressed the mat3-M cassette. We further noted that treatment of wild-type h(90) cells resulted in the generation of altered sporulation phenotypes, indicating that the treatment affected the expression of mating-type genes and/or mating-type switching. The results are discussed in the light of recent accumulated data regarding the role of deacetylation for silencing in other species.

Keyword
trichostatin A, repression, Schizosaccharomyces pombe, heterochromatin
National Category
Biological Sciences
Identifiers
urn:nbn:se:sh:diva-31263 (URN)10.1007/s002940050436 (DOI)000079273500004 ()10079326 (PubMedID)2-s2.0-0033061968 (ScopusID)
Available from: 2016-12-01 Created: 2016-12-01 Last updated: 2016-12-01Bibliographically approved
2. Dicer is required for chromosome segregation and gene silencing in fission yeast cells
Open this publication in new window or tab >>Dicer is required for chromosome segregation and gene silencing in fission yeast cells
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2002 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 99, no 26, 16648-16653 p.Article in journal (Refereed) Published
Abstract [en]

RNA interference is a form of gene silencing in which the nuclease Dicer cleaves double-stranded RNA into small interfering RNAs. Here we report a role for Dicer in chromosome segregation of fission yeast. Deletion of the Dicer (dcr1(+)) gene caused slow growth, sensitivity to thiabendazole, lagging chromosomes during anaphase, and abrogated silencing of centromeric repeats. As Dicer in other species, Dcr1p degraded double-stranded RNA into approximate to23 nucleotide fragments in vitro, and dcr1Delta cells were partially rescued by expression of human Dicer, indicating evolutionarily conserved functions. Expression profiling demonstrated that dcr1(+) was required for silencing of two genes containing a conserved motif.

National Category
Natural Sciences
Identifiers
urn:nbn:se:sh:diva-15719 (URN)10.1073/pnas.212633199 (DOI)000180101600028 ()12482946 (PubMedID)2-s2.0-0037168521 (ScopusID)
Available from: 2012-03-08 Created: 2012-03-06 Last updated: 2016-12-29Bibliographically approved
3. A new role for the transcriptional corepressor SIN3; Regulation of centromeres
Open this publication in new window or tab >>A new role for the transcriptional corepressor SIN3; Regulation of centromeres
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2003 (English)In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 13, no 1, 68-72 p.Article in journal (Refereed) Published
Abstract [en]

Centromeres play a vital role in maintaining the genomic stability of eukaryotes by coordinating the equal distribution of chromosomes to daughter cells during mitosis and meiosis. Fission yeast (S. pombe) centromeres consist of a 4-9 kb central core region and 30-100 kb of flanking inner (imr/B) and outer (otr/K) repeats [1-3]. These sequences direct a laminar kinetochore structure similar to that of human centromeres [4, 5]. Centromeric heterochromatin is generally underacetylated [6, 7]. We have previously shown that inhibition of histone deacetylases (HDACs) caused hyperacetylation of centromeres and defective chromosome segregation [8]. SIN3 is a HDAC corepressor that has the ability to mediate HDAC targeting in the repression of promoters. In this study, we have characterized S. pombe sin three corepressors (Pst1p and Pst2p) to investigate whether SIN3-HDAC is required in the regulation of centromeres. We show that only pst1-1 and not pst2Delta cells displayed anaphase defects and thiabendazole sensitivity. pst1-1 cells showed reduced centromeric silencing, increased histone acetylation in centromeric chromatin, and defective centromeric sister chromatid cohesion. The HDAC Clr6p and Pst1p coimmunoprecipitated, and Pst1p colocalized with centromeres, particularly in binucleate cells. These data are consistent with a model in which Pst1 pClr6p temporally associate with centromeres to carry out the initial deacetylation necessary for subsequent steps in heterochromatin formation.

National Category
Biochemistry and Molecular Biology Cell Biology
Identifiers
urn:nbn:se:sh:diva-17667 (URN)10.1016/S0960-9822(02)01401-X (DOI)000180915600025 ()12526748 (PubMedID)2-s2.0-0346034996 (ScopusID)
Available from: 2012-12-14 Created: 2012-12-14 Last updated: 2016-12-01Bibliographically approved
4. Functional divergence between histone deacetylases in fission yeast by distinct cellular localization and in vivo specificity
Open this publication in new window or tab >>Functional divergence between histone deacetylases in fission yeast by distinct cellular localization and in vivo specificity
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2002 (English)In: Molecular and Cellular Biology, ISSN 0270-7306, E-ISSN 1098-5549, Vol. 22, no 7, 2170-2181 p.Article in journal (Refereed) Published
Abstract [en]

Histone deacetylases (HDACs) are important for gene regulation and the maintenance of heterochromatin in eukaryotes. Schizosaccharomyces pombe was used as a model system to investigate the functional divergence within this conserved enzyme family. S. pombe has three HDACs encoded by the hda1(+), clr(3+), and clr6(+) genes. Strains mutated in these genes have previously been shown to display strikingly different phenotypes when assayed for viability, chromosome loss, and silencing. Here, conserved differences in the substrate binding pocket identify Clr6 and Hda1 as class I HDACs, while Clr3 belongs in the class II family. Furthermore, these HDACs were shown to have strikingly different subcellular localization patterns. Hda1 was localized to the cytoplasm, while most of Clr3 resided throughout the nucleus. Finally, Clr6 was localized exclusively on the chromosomes in a spotted pattern. Interestingly, Clr3, the only HDAC present in the nucleolus, was required for ribosomal DNA (rDNA) silencing. Clr3 presumably acts directly on heterochromatin, since it colocalized with the centromere, mating-type region, and rDNA as visualized by in situ hybridization. In addition, Clr3 could be cross-linked to mat3 in chromatin immunoprecipitation experiments. Western analysis of bulk histone preparations indicated that Hda1 (class I) had a generally low level of activity in vivo and Clr6 (class 1) had a high level of activity and broad in vivo substrate specificity, whereas Clr3 (class II) displayed its main activity on acetylated lysine 14 of histone H3. Thus, the distinct functions of the S. pombe HDACs are likely explained by their distinct cellular localization and their different in vivo specificities.

National Category
Biological Sciences
Identifiers
urn:nbn:se:sh:diva-15808 (URN)10.1128/MCB.22.7.2170-2181.2002 (DOI)000174407500020 ()11884604 (PubMedID)2-s2.0-0036122494 (ScopusID)
Available from: 2012-03-08 Created: 2012-03-07 Last updated: 2016-12-01Bibliographically approved
5. Genomewide analysis of nucleosome density histone acetylation and HDAC function in fission yeast
Open this publication in new window or tab >>Genomewide analysis of nucleosome density histone acetylation and HDAC function in fission yeast
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2005 (English)In: EMBO Journal, ISSN 0261-4189, E-ISSN 1460-2075, Vol. 24, no 16, 2906-2918 p.Article in journal (Refereed) Published
Abstract [en]

We have conducted a genomewide investigation into the enzymatic specificity, expression profiles, and binding locations of four histone deacetylases (HDACs), representing the three different phylogenetic classes in fission yeast ( Schizosaccharomyces pombe). By directly comparing nucleosome density, histone acetylation patterns and HDAC binding in both intergenic and coding regions with gene expression profiles, we found that Sir2 ( class III) and Hos2 ( class I) have a role in preventing histone loss; Clr6 ( class I) is the principal enzyme in promoter-localized repression. Hos2 has an unexpected role in promoting high expression of growth-related genes by deacetylating H4K16Ac in their open reading frames. Clr3 ( class II) acts cooperatively with Sir2 throughout the genome, including the silent regions: rDNA, centromeres, mat2/3 and telomeres. The most significant acetylation sites are H3K14Ac for Clr3 and H3K9Ac for Sir2 at their genomic targets. Clr3 also affects subtelomeric regions which contain clustered stress- and meiosis-induced genes. Thus, this combined genomic approach has uncovered different roles for fission yeast HDACs at the silent regions in repression and activation of gene expression.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:sh:diva-14447 (URN)10.1038/sj.emboj.7600758 (DOI)000231789300007 ()16079916 (PubMedID)2-s2.0-72949109535 (ScopusID)
Available from: 2012-01-19 Created: 2011-12-23 Last updated: 2016-12-29Bibliographically approved
6. Sin3: a flexible regulator of global gene expression and genome stability
Open this publication in new window or tab >>Sin3: a flexible regulator of global gene expression and genome stability
2005 (English)In: Current Genetics, ISSN 0172-8083, E-ISSN 1432-0983, Vol. 47, no 1, 1-17 p.Article in journal (Refereed) Published
Abstract [en]

SIN3 was first identified genetically as a global regulator of transcription. Sin3 is a large protein composed mainly of protein-interaction domains, whose function is to provide structural support for a heterogeneous Sin3/histone deacetylase (HDAC) complex. The core Sin3/HDAC complex is conserved from yeast to man and consists of eight proteins. In addition to HDACs, Sin3 can sequester other enzymatic functions, including nucleosome remodeling, DNA methylation, N-acetylglucoseamine transferase activity, and histone methylation. Since the Sin3/HDAC complex lacks any DNA-binding activity, it must be targeted to gene promoters by interacting with DNA-binding proteins. Although most research on Sin3 has focused on its role as a corepressor, mounting evidence suggests that Sin3 can also positively regulate transcription. Furthermore, Sin3 is key to the propagation of epigenetically silenced domains and is required for centromere function. Thus, Sin3 provides a platform to deliver multiple combinations modifications to the chromatin, using both sequence-specific and sequence-independent mechanisms.

National Category
Genetics
Identifiers
urn:nbn:se:sh:diva-14396 (URN)10.1007/s00294-004-0541-5 (DOI)000225895200001 ()15565322 (PubMedID)2-s2.0-11244271837 (ScopusID)
Available from: 2011-12-22 Created: 2011-12-21 Last updated: 2016-12-01Bibliographically approved

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  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
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  • nn-NB
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  • Other locale
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