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A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift
Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
Max-Plank Institute for Molecular Genetics, Berlin, Germany.
Eurogentec SA, Seraing, Belgium.
Karolinska Institute.
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2004 (English)In: Yeast, ISSN 0749-503X, E-ISSN 1097-0061, Vol. 21, no 1, 25-39 p.Article in journal (Refereed) Published
Abstract [en]

Completion of the fission yeast genome sequence has opened up possibilities for post-genomic approaches. We have constructed a DNA microarray for genome-wide gene expression analysis in fission yeast. The microarray contains DNA fragments, PCR-amplified from a genomic DNA template, that represent >99% of the 5000 or so annotated fission yeast genes, as well as a number of control sequences. The GenomePRIDE software used attempts to design similarly sized DNA fragments corresponding to gene regions within single exons, near the 3'-end of genes that lack homology to other fission yeast genes. To validate the design and utility of the array, we studied expression changes after a 2 h temperature shift from 25degreesC to 36degreesC, conditions widely used when studying temperature-sensitive mutants. Obligingly, the vast majority of genes do not change more than two-fold, supporting the widely held view that temperature-shift experiments specifically reveal phenotypes associated with temperature-sensitive mutants. However, we did identify a small group of genes that showed a reproducible change in expression. Importantly, most of these corresponded to previously characterized heat-shock genes, whose expression has been reported to change after more extreme temperature shifts than those used here.. We conclude that the DNA microarray represents a useful resource for fission yeast researchers as well as the broader yeast community, since it will facilitate comparison with the distantly related budding yeast, Saccharomyces cerevisiae. To maximize the utility of this resource, the array and its component parts are fully described in On-line Supplementary Information and are also available commercially.

Place, publisher, year, edition, pages
2004. Vol. 21, no 1, 25-39 p.
National Category
Biochemistry and Molecular Biology Microbiology
Identifiers
URN: urn:nbn:se:sh:diva-15500DOI: 10.1002/yea.1053ISI: 000188635600003PubMedID: 14745780ScopusID: 2-s2.0-0742289927OAI: oai:DiVA.org:sh-15500DiVA: diva2:504346
Available from: 2012-02-20 Created: 2012-02-20 Last updated: 2016-09-15Bibliographically approved
In thesis
1. 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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