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- Alfredsson-Timmins, Jenny, 1976-, et al.
(author)
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Reorganization of chromatin is an early response to nitrogen starvation in Schizosaccharomyces pombe
- 2009
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In: Chromosoma. - : Springer Science and Business Media LLC. - 0009-5915 .- 1432-0886. ; 118:1, s. 99-112
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Journal article (peer-reviewed)abstract
- 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.
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| 2. |
- Kristell, Carolina, 1979-
(author)
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Chromatin Dynamics in the Fission Yeast, Schizosaccharomyces pombe
- 2011
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Doctoral thesis (other academic/artistic)abstract
- 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.
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| 5. |
- Kristell, Carolina, et al.
(author)
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Nitrogen depletion in the fission yeast Schizosaccharomyces pombe causes nucleosome loss in both promoters and coding regions of activated genes
- 2010
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In: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 20:3, s. 361-371
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Journal article (peer-reviewed)abstract
- 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.
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| 7. |
- Steinhauf, Daniel, et al.
(author)
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Silencing Motifs in the Clr2 Protein from Fission Yeast, Schizosaccharomyces pombe
- 2014
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In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:1, s. e86948-
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Journal article (peer-reviewed)abstract
- The fission yeast, Schizosaccharomyces pombe, is a well-established model for heterochromatin formation, but the exact sequence of events for initiation remains to be elucidated. The essential factors involved include RNA transcribed from repeated sequences together with the methyltransferase Clr4. In addition, histone deacetylases, like Clr3, found in the SHREC complex are also necessary for transcriptional silencing. Clr2 is another crucial factor required for heterochromatin formation found in the SHREC complex. The function of Clr2 has been difficult to establish due to the lack of conserved domains or homology to proteins of known molecular function. Using a bioinformatics approach, three conserved motifs in Clr2 were identified, which contained amino acids important for transcriptional repression. Analysis of clr2 mutant strains revealed a major role for Clr2 in mating-type and rDNA silencing, and weaker effects on centromeric silencing. The effect on mating-type silencing showed variegation in several of the strains with mutated versions of Clr2 indicating an establishment or maintenance defect. Moreover, the critical amino acids in Clr2 were also necessary for transcriptional repression in a minimal system, by the tethering of Clr4 upstream of a reporter gene, inserted into the euchromatic part of the genome. Finally, in silico modeling suggested that the mutations in Clr2 cause disruption of secondary structures in the Clr2 protein. Identification of these critical amino acids in the protein provides a useful tool to explore the molecular mechanism behind the role of Clr2 in heterochromatin formation.
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