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Chromatin Dynamics in the Fission Yeast, Schizosaccharomyces pombe
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In the eukaryotic cell nucleus, spatial organization and dynamics of the genome is important in the regulation of gene expression. This thesis describes the use of the fission yeast, Schizosaccharomyces pombe, to study chromatin regulation and dynamics.

We used nitrogen starvation to induce transcription of genes in fission yeast cells. In induced genes, nucleosomes get evicted in both the promoter and in the open reading frame (ORF). In the genes with the highest expression more nucleosomes get evicted from the ORF than from the promoter. This indicates that large rearrangements of the chromatin are occurring during a drastic gene induction.

Many of the genes that become expressed early after nitrogen starvation are located together in clusters. In a cell where nitrogen is present in the surrounding media the gene clusters locate close to the nuclear periphery. When the nitrogen source is removed from the media, the clusters move to a more internal position. Thus rearrangement of chromatin due to gene induction, described in the first study, is accompanied by subnuclear changes of localization.

Another type of regulation is the silencing of genes. We have studied a factor necessary for correct repression of genes located in silent chromatin, in S. pombe. The protein, Clr2, is part of the SHREC complex containing a remodeler (Mit1) and a histone deacetylase (Clr3). By bioinformatic analysis of Clr2 and newly sequenced fungi genomes, three motifs were identified. To gather more information about important parts of the Clr2 protein, deletions were made. When removing from about 20 to 100 amino acids in the middle of the protein, silencing of a reporter gene inserted at the mating-type region, inner repeats of centromere 1 and at the central core of centromere 2, failed. This indicates that Clr2 has an important role in establishing silent chromatin.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis , 2011. , 58 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 698
Keyword [en]
Chromatin, Gene induction, Silencing, Subnuclear localization, Stress
National Category
Biochemistry and Molecular Biology
Research subject
Molecular Genetics
URN: urn:nbn:se:uu:diva-158084ISBN: 978-91-554-8143-8OAI: diva2:438055
Public defence
2011-10-14, B21, BMC, Husargatan 3, Uppsala, 09:15 (English)
Available from: 2011-09-22 Created: 2011-08-30 Last updated: 2011-11-03Bibliographically approved
List of papers
1. Nitrogen depletion in the fission yeast Schizosaccharomyces pombe causes nucleosome loss in both promoters and coding regions of activated genes
Open this publication in new window or tab >>Nitrogen depletion in the fission yeast Schizosaccharomyces pombe causes nucleosome loss in both promoters and coding regions of activated genes
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2010 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 20, no 3, 361-371 p.Article in journal (Refereed) Published
Abstract [en]

Gene transcription is associated with local changes in chromatin, both in nucleosome positions and in chemical modifications of the histones. Chromatin dynamics has mostly been studied on a single-gene basis. Those genome-wide studies that have been made primarily investigated steady-state transcription. However, three studies of genome-wide changes in chromatin during the transcriptional response to heat shock in the budding yeast Saccharomyces cerevisiae revealed nucleosome eviction in promoter regions but only minor effects in coding regions. Here, we describe the short-term response to nitrogen starvation in the fission yeast Schizosaccharomyces pombe. Nitrogen depletion leads to a fast induction of a large number of genes in S. pombe and is thus suitable for genome-wide studies of chromatin dynamics during gene regulation. After 20 min of nitrogen removal, 118 transcripts were up-regulated. The distribution of regulated genes throughout the genome was not random; many up-regulated genes were found in clusters, while large parts of the genome were devoid of up-regulated genes. Surprisingly, this up-regulation was associated with nucleosome eviction of equal magnitudes in the promoters and in the coding regions. The nucleosome loss was not limited to induction by nitrogen depletion but also occurred during cadmium treatment. Furthermore, the lower nucleosome density persisted for at least 60 min after induction. Two highly induced genes, urg1(+) and urg2(+), displayed a substantial nucleosome loss, with only 20% of the nucleosomes being left in the coding region. We conclude that nucleosome loss during transcriptional activation is not necessarily limited to promoter regions.

National Category
Medical and Health Sciences
urn:nbn:se:uu:diva-137146 (URN)10.1101/gr.098558.109 (DOI)000275124600008 ()20086243 (PubMedID)
Available from: 2010-12-15 Created: 2010-12-15 Last updated: 2011-11-03Bibliographically approved
2. Reorganization of chromatin is an early response to nitrogen starvation in Schizosaccharomyces pombe
Open this publication in new window or tab >>Reorganization of chromatin is an early response to nitrogen starvation in Schizosaccharomyces pombe
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2009 (English)In: Chromosoma, ISSN 0009-5915, E-ISSN 1432-0886, Vol. 118, no 1, 99-112 p.Article in journal (Refereed) Published
Abstract [en]

There are several documented events of changes in subnuclear localization during gene activation. However, there are conflicting data on whether the nuclear periphery is a compartment for gene repression or activation, and whether genes are moved to the pores at the nuclear membrane (NM) or not during gene activation. Nitrogen starvation of fission yeast serves as a good model system for studying gene induction since it causes fast regulation of hundreds of genes. In this study the subnuclear localization of two gene clusters repressed by nitrogen was investigated. During normal growth conditions the gene clusters localized to the nuclear periphery at the opposite side of the nucleus as compared to the spindle pole body (SPB). This constrained localization was dependent on the histone deacetylase Clr3, known to transcriptionally repress genes in these clusters. Already 20 minutes after nitrogen depletion drastic changes in subnuclear localization of the two loci were observed, away from the NM towards the nuclear interior. At least for one of the clusters the movement was clearly transcription dependent. Data presented here illustrates how interconnected events of gene activation and nuclear reorganization are, as well as provides a suggestion of how nuclear organization might be maintained.

National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
urn:nbn:se:uu:diva-107289 (URN)10.1007/s00412-008-0180-6 (DOI)000262504300009 ()
Available from: 2009-08-05 Created: 2009-08-05 Last updated: 2011-11-03Bibliographically approved
3. Functional study of the Clr2 silencing protein
Open this publication in new window or tab >>Functional study of the Clr2 silencing protein
(English)Manuscript (preprint) (Other academic)
Fission yeast, Schizosaccharomyces pombe, Silencing, Chromatin
Research subject
Molecular Genetics
urn:nbn:se:uu:diva-157970 (URN)
Available from: 2011-08-30 Created: 2011-08-29 Last updated: 2011-11-03

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