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High-throughput genetic interaction mapping in the fission yeast Schizosaccharomyces pombe
University of California, San Francisco, USA.
Södertörn University, School of Life Sciences. Karolinska Institute / University of California, San Francisco, United States .
University of California, San Francisco, USA.
University of California, San Francisco, USA.
2007 (English)In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 4, no 10, 861-866 p.Article in journal (Refereed) Published
Abstract [en]

Epistasis analysis, which reports on the extent to which the function of one gene depends on the presence of a second, is a powerful tool for studying the functional organization of the cell. Systematic genome-wide studies of epistasis, however, have been limited, with the majority of data being collected in the budding yeast, Saccharomyces cerevisiae. Here we present two 'pombe epistasis mapper' strategies, PEM-1 and PEM-2, which allow for high-throughput double mutant generation in the fission yeast, S. pombe. These approaches take advantage of a previously undescribed, recessive, cycloheximide-resistance mutation. Both systems can be used for genome-wide screens or for the generation of high-density, quantitative epistatic miniarray profiles (E-MAPs). Since S. cerevisiae and S. pombe are evolutionary distant, this methodology will provide insight into conserved biological pathways that are present in S. pombe, but not S. cerevisiae, and will enable a comprehensive analysis of the conservation of genetic interaction networks.

Place, publisher, year, edition, pages
2007. Vol. 4, no 10, 861-866 p.
Keyword [en]
cycloheximide, article, controlled study, fungal genetics, fungus mutant, gene interaction, gene mutation, genetic conservation, genetic epistasis, nonhuman, priority journal, quantitative analysis, recessive inheritance, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Epistasis, Genetic, Genes, Lethal, Genome, Fungal, Genomics, Mutation, Schizosaccharomyces, Transformation, Genetic, Saccharomycetales, Schizosaccharomycetaceae
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:sh:diva-22585DOI: 10.1038/nmeth1098ISI: 000249778200023PubMedID: 17893680ScopusID: 2-s2.0-35848940244OAI: oai:DiVA.org:sh-22585DiVA: diva2:704565
Available from: 2014-03-12 Created: 2014-03-03 Last updated: 2016-08-04Bibliographically 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

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