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Genome-wide characterisation of the Gcn5 histone acetyltransferase in budding yeast during stress adaptation reveals evolutionarily conserved and diverged roles
Södertörn University, School of Life Sciences, Molecular biology. Karolinska Institutet.
Södertörn University, School of Life Sciences, Molecular biology. Karolinska Intitutet.
Karolinska Institutet.
Södertörn University, School of Life Sciences, Molecular biology. Karolinska Institutet.
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2010 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 11, 200Article in journal (Refereed) Published
Abstract [en]

Background: Gcn5 is a transcriptional coactivator with histone cetyltransferase activity that is conserved with regard to structure as ell as its histone substrates throughout the eukaryotes. Gene egulatory networks within cells are thought to be evolutionarily iverged. The use of evolutionarily divergent yeast species, such as S. erevisiae and S. pombe, which can be studied under similar nvironmental conditions, provides an opportunity to examine the nterface between conserved regulatory components and their cellular pplications in different organisms. esults: We show that Gcn5 is important for a common set of stress esponses in evolutionarily diverged yeast species and that the activity f the conserved histone acetyltransferase domain is required. We define group of KCl stress response genes in S. cerevisiae that are pecifically dependent on Gcn5. Gcn5 is localised to many Gcn5-dependent enes including Gcn5 repressed targets such as FLO8. Gcn5 regulates ivergent sets of KCl responsive genes in S. cerevisiae and S. pombe. enome-wide localization studies showed a tendency for redistribution of cn5 during KCl stress adaptation in S. cerevisiae from short genes to he transcribed regions of long genes. An analogous redistribution was ot observed in S. pombe. onclusions: Gcn5 is required for the regulation of divergent sets of Cl stress-response genes in S. cerevisiae and S. pombe even though it s required a common group of stress responses, including the response o KCl. Genes that are physically associated with Gcn5 require its ctivity for their repression or activation during stress adaptation, roviding support for a role of Gcn5 as a corepressor as well as a oactivator. The tendency of Gcn5 to re-localise to the transcribed egions of long genes during KCl stress adaptation suggests that Gcn5 lays a specific role in the expression of long genes under adaptive onditions, perhaps by regulating transcriptional elongation as has been een for Gcn5 in S. pombe. Interestingly an analogous redistribution of cn5 is not seen in S. pombe. The study thus provides important new nsights in relation to why coregulators like Gcn5 are required for the orrect expression of some genes but not others.

Place, publisher, year, edition, pages
2010. Vol. 11, 200
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
URN: urn:nbn:se:sh:diva-13712DOI: 10.1186/1471-2164-11-200ISI: 000277270600002PubMedID: 2861062ScopusID: 2-s2.0-77952260641OAI: oai:DiVA.org:sh-13712DiVA: diva2:462187
Note

Som manuskript i avhandling. As manuscript in dissertation.

Functional aspects of the Gcn5 histone acetyltransferase in stress responses of evolutionarily diverged yest species

Available from: 2011-12-06 Created: 2011-12-06 Last updated: 2016-09-15Bibliographically approved
In thesis
1. Characterization of Gcn5 histone acetyltransferase in Schizosaccharomyces pombe
Open this publication in new window or tab >>Characterization of Gcn5 histone acetyltransferase in Schizosaccharomyces pombe
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The organisation of eukaryotic DNA into chromatin provides a natural barrier that prevents full access to the DNA thereby inhibiting events such as transcription, replication and repair. In order for these DNA-related events to occur, the chromatin needs to be modified by chromatin remodelling or, by reversible post-translational modifications. Histone acetylation is such a modification and is essential of numerous DNA related events. The enzymes involved in this event are conserved throughout evolution, underscoring their importance. This thesis describes the role of the conserved histone acetyltransferase (HAT) Gcn5 in transcriptional regulation in Schizosaccharomyces pombe. Here we show that Gcn5 plays an important role in stress response. We map genome-wide Gcn5 occupancy and show that Gcn5 is predominantly localized to coding regions of highly transcribed genes. We also map H3K14 acetylation during salt stress and show that Gcn5 collaborates antagonistically with the class-II histone deacetylase, Clr3, to modulate H3K14ac levels and transcriptional elongation. The interplay between Gcn5 and Clr3 is crucial for the regulation of many stress-response genes. Our findings suggest a new role for Gcn5 during transcriptional elongation, in addition to its known role in transcriptional initiation. We also investigate the interactions between Gcn5 and other histone deacetylases and acetyltransferases and show overlapping functionality between Gcn5 and another histone acetyltransferase, Mst2, in stress response, regulation of subtelomeric genes and DNA damage repair. Finally, we show that the role of Gcn5 in stress response is mediated by its catalytic activity and that its function in stress response is conserved among yeast species.

Place, publisher, year, edition, pages
Stockholm: Karolinska instiutet, 2009. 31 p.
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:sh:diva-30871 (URN)9789174095494 (ISBN)
Public defence
2009-08-28, 10:00
Opponent
Supervisors
Available from: 2016-09-15 Created: 2016-09-15 Last updated: 2016-09-15Bibliographically approved
2. DNA microarray approaches to understanding the regulation and evolution of gene expression networks
Open this publication in new window or tab >>DNA microarray approaches to understanding the regulation and evolution of gene expression networks
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

DNA microarray technology allows biological and medical research to shift from investigation of individual functions of a few related genes to the whole genome level. This creates opportunities for discovery of complex and coordinated transcriptional networks in biological systems. The aim of this thesis has been to study gene regulation and evolution using yeast responses to environmental cues as a model system. We first developed and validated a fission yeast cDNA microarray for genome-wide expression analysis (Paper I). It is the first commercially available fission yeast microarray, which presents a useful resouce for yeast researchers and provides information required to contruct the array from scratch. Next, we characterised the gene regulatory networks involved in the pheromone response (Paper II) and investigate the role of Gcn5 transcription co-regulator, a histone acetyltransferase (HAT), in re-programming gene expression during the salt stress response in fission yeast (Paper III). We further investigated evolutionary conservation and divergence of Gcn5 in gene regulation by comparing its role in the evolutionarily distantly related yeast species. The parallel study of the fission yeast and budding yeast showed that Gcn5 has a conserved physiological role in salt stress responses, but it regulates diverged sets of stress response genes potentially via distinct mechanisms (paper IV). Finally, we investigated interactions between different HATs and between HATs and HDACs (histone deacetylases). Phenotypic studies and gene expression profiling revealed that Gcn5 has overlapping functions with another HAT, Mst2, in the stress response and DNA damage repair (Paper V). We found that the HDAC Clr3 acts antagonistically to Gcn5 in transcriptional elongation and stress responses (Paper VI).

Place, publisher, year, edition, pages
Stockholm: Karolinska Institutet, 2009. 46 p.
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:sh:diva-30873 (URN)978-91-7409-554-8 (ISBN)
Public defence
2009-09-29, 10:00
Available from: 2016-09-15 Created: 2016-09-15 Last updated: 2016-09-15Bibliographically approved

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