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Genomewide analysis of nucleosome density histone acetylation and HDAC function in fission yeast
Södertörn University, School of Life Sciences. Karolinska Institutet.
Södertörn University, School of Life Sciences. Karolinska Institutet.
Södertörn University, School of Life Sciences. Karolinska Institutet.
Södertörn University, School of Life Sciences. Karolinska Institutet.
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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.

Place, publisher, year, edition, pages
2005. Vol. 24, no 16, 2906-2918 p.
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:sh:diva-14447DOI: 10.1038/sj.emboj.7600758ISI: 000231789300007PubMedID: 16079916ScopusID: 2-s2.0-72949109535OAI: oai:DiVA.org:sh-14447DiVA: diva2:480532
Available from: 2012-01-19 Created: 2011-12-23 Last updated: 2016-12-01Bibliographically approved
In thesis
1. Genome-wide study of HDACs and transcription in Schizosaccharomyces pombe
Open this publication in new window or tab >>Genome-wide study of HDACs and transcription in Schizosaccharomyces pombe
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The eukaryotic genome has to be organized to fit into the cell and this is achieved by packing of DNA into chromatin. The basic repeating structural unit of chromatin is the nucleosome, which consists of DNA wrapped around histone proteins. Histones are subjected to multiple covalent posttranslational modifications including, acetylation, methylation, phosphorylation, and ubiquitination. These modifications take part in gene regulation by changing the structure of chromatin and by recruiting gene regulatory proteins. Histone acetylation can be removed by histone deacetylases (HDACs), which are highly conserved enzymes that regulate a diverse number of biological processes including gene expression and chromosome segregation, and have shown to be closely linked to major diseases like cancer. This thesis described the genome-wide role of HDACs and transcription in S. pombe. We studied the genome wide binding targets and enzymatic specificity of different S. pombe HDACs and uncovered different roles for the enzymes at silent regions and in repression and activation of gene expression. We proposed that independent of gene length, a typical fission yeast gene shows a 5 to 3 polarity, i.e., the histone acetylation levels peak near the ATG and gradually decrease in the coding regions. We also observed that different HDACs are responsible for different position within the ORF regions. Our genome-wide study of two different Mediator complexes reviled that they displayed similar binding patterns, and interactions with promoters and upstream activating sequences correlated with increased transcription activity. We also found that Mediator associates with the downstream coding region of many genes. We finally developed a method, E-map, which made it possible to systematically construct haploid double mutants. This method was used for constructing genome-wide genetic interaction maps of HDACs in S. pombe. From our preliminary results we discovered a new link between the Class III HDACs and a biosynthesis protein. Our data also suggest that different HDACs are involved in distinct biological processes.

Place, publisher, year, edition, pages
Stockholm: Karolinska Institutet, 2010. 51 p.
National Category
Biological Sciences
Identifiers
urn:nbn:se:sh:diva-30694 (URN)978-91-7409-970-6 (ISBN)
Supervisors
Available from: 2016-08-04 Created: 2016-08-04 Last updated: 2016-08-04Bibliographically approved
2. Genome-wide patterns of histone modifications in fission yeast
Open this publication in new window or tab >>Genome-wide patterns of histone modifications in fission yeast
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

DNA is wrapped almost two times around a group of proteins called histones to form a chromosomal structure known as the nucleosome. Both DNA and histones can be modified with different chemical tags by several enzymes to activate or suppress a particular gene or group of genes. Histones can be covalently modified at several places. Among many different types of post-translational histone modifications, histone acetylation and methylation are two important modification types that are associated with transcriptional activation and repression. Histone acetylation and methylation can be added by histone acetyltransferases (HATs) and histone methyletransferases (HMTs), whereas these modifications can be removed by histone deacetylases (HDACs) and histone demethylases (HDMs). Histone modifications are not only involved in the regulation of gene expression, but also in DNA-based processes, such as replication, repair, and the formation and maintenance of heterochromatin. Combinations of modified and unmodified states of histones can form distinct histone modification patterns. In many different genome-wide studies, it was observed that a distinctive pattern of histone modification in various organisms is important for gene regulation, DNA replication, chromosome segregation and heterochromatin-mediated silencing. In this thesis, we have conducted several genome-wide investigations to uncover different histone modification patterns and their roles in transcriptional control in fission yeast. Our analysis of six different HDACs in fission yeast showed that Clr6 and Clr3 are mainly involved in keeping repressed genes silent; Sir2 and Hst2 repress non-expressed genes, and Hst4 acts globally to reduce gene expression, whereas Hos2 is required for the activation of gene expression. By investigating the influence of each HDAC on nucleosome density, we found that all sirtuins and Hos2 enzymes are required to maintain normal nucleosome density and distribution in the S. pombe genome. We have reported that histone acetylation patterns show a 5` to 3` polarity, i.e., the modification levels peak near the ATG and gradually decrease in the coding regions. We also found that histone acetylation patterns depend on gene expression but are independent of gene length. Comparing our data with other published datasets, we observed that different HDAC mutants affect acetylation in different parts of open reading frames (ORFs). We have demonstrated that histone H4 acetylation proceeds in the direction from K16 to K5, consistent with a `zip` model that may be involved in transcriptional control. Our analysis revealed antagonistic crosstalk between H3K36me2/me3 and H3K27ac at promoter regions. We observed that histone H3 K18, K27 and K9 acetylation positively correlate with gene expression, and a conserved pattern was also reported in other organisms. Finally, we report that histone H4K20me1 is strongly linked to active genes, whereas H4K20me3 is associated with weakly expressed genes. Our analysis further shows that H4K20me1 modification levels peak at 3‟UTR regions in active genes. Thus, our analysis revealed many different aspects of histone modification patterns and their roles in transcriptional control in fission yeast.

Place, publisher, year, edition, pages
Stockholm: Karolinska Institutet, 2010. 59 p.
National Category
Biological Sciences
Identifiers
urn:nbn:se:sh:diva-30695 (URN)
Supervisors
Available from: 2016-08-05 Created: 2016-08-04 Last updated: 2016-08-05Bibliographically approved
3. Histone deacetylases and their co-regulators in schizosaccharomyces pombe
Open this publication in new window or tab >>Histone deacetylases and their co-regulators in schizosaccharomyces pombe
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:nbn:se:sh:diva-31262 (URN)978-91-7357-140-1 (ISBN)
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

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