| 1. |
|
|
| 2. |
- Kristell, Carolina, et al.
(författare)
-
Nitrogen depletion in the fission yeast Schizosaccharomyces pombe causes nucleosome loss in both promoters and coding regions of activated genes
- 2010
-
Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 20:3, s. 361-371
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 3. |
|
|
| 4. |
- Orzechowski Westholm, Jakub, 1977-, et al.
(författare)
-
Combinatorial control of gene expression by the three yeast repressors Mig1, Mig2 and Mig3
- 2008
-
Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 9, s. 601-
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Expression of a large number of yeast genes is repressed by glucose. The zinc finger protein Mig1 is the main effector in glucose repression, but yeast also has two related proteins: Mig2 and Mig3. We have used microarrays to study global gene expression in all possible combinations of mig1, mig2 and mig3 deletion mutants. Results: Mig1 and Mig2 repress a largely overlapping set of genes on 2% glucose. Genes that are upregulated in a mig1 mig2 double mutant were grouped according to the contribution of Mig2. Most of them show partially redundant repression, with Mig1 being the major repressor, but some genes show complete redundancy, and some are repressed only by Mig1. Several redundantly repressed genes are involved in phosphate metabolism. The promoters of these genes are enriched for Pho4 sites, a novel GGGAGG motif, and a variant Mig1 site which is absent from genes repressed only by Mig1. Genes repressed only by Mig1 on 2% glucose include the hexose transporter gene HXT4, but Mig2 contributes to HXT4 repression on 10% glucose. HXT6 is one of the few genes that are more strongly repressed by Mig2. Mig3 does not seem to overlap in function with Mig1 and Mig2. Instead, Mig3 downregulates the SIR2 gene encoding a histone deacetylase involved in gene silencing and the control of aging. Conclusions: Mig2 fine-tunes glucose repression by targeting a subset of the Mig1-repressed genes, and by responding to higher glucose concentrations. Mig3 does not target the same genes as Mig1 and Mig2, but instead downregulates the SIR2 gene.
|
|
| 5. |
- Orzechowski Westholm, Jakub
(författare)
-
Genome-wide Studies of Transcriptional Regulation in Yeast
- 2009
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this thesis, nutrient signalling in yeast is used as a model to study several features of gene regulation, such as combinatorial gene regulation, the role of motif context and chromatin modifications. The nutrient signalling system in yeast consists of several pathways that transmit signals about the availability of key nutrients, and regulate the transcription of a large part of the genome. Some of the signalling pathways are also conserved in other eukaryotic species where they are implicated in processes such as aging and in human disease. Combinatorial gene regulation is examined in papers I and II. In paper I, the role of Mig1, Mig2 and Mig3 is studied. To elucidate how the three proteins contribute to the control of gene expression, we used microarrays to study the expression of all yeast genes in the wild type and in all seven possible combinations of mig1, mig2 and mig3 deletions. In paper II, a similar strategy is used to investigate Gis1 and Rph1, two related transcription factors. Our results reveal that Rph1 is involved in nutrient signalling together with Gis1, and we find that both the activities and the target specificities of Gis1 and Rph1 depend on the growth phase. Paper III describes ContextFinder, a program for identifying constraints on sequence motif locations and orientations. ContextFinder was used to analyse over 300 cases of motifs that are enriched in experimentally selected groups of yeast promoters. Our results suggest that motif context frequently is important for stable DNA binding and/or regulatory activity of transcription factors. In paper IV, we investigated how gene expression changes resulting from nitrogen starvation are accompanied by chromatin modifications. Activation of gene expression is concentrated to specific genomic regions. It is associated with nucleosome depletion (in both promoters and coding regions) and increased levels of H3K9ac (but not H4K5ac).
|
|
| 6. |
- Orzechowski Westholm, Jakub, et al.
(författare)
-
Gis1 and Rph1 Regulate Glycerol and Acetate Metabolism in Glucose Depleted Yeast Cells
- 2012
-
Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 7:2, s. e31577-
-
Tidskriftsartikel (refereegranskat)abstract
- Aging in organisms as diverse as yeast, nematodes, and mammals is delayed by caloric restriction, an effect mediated by the nutrient sensing TOR, RAS/cAMP, and AKT/Sch9 pathways. The transcription factor Gis1 functions downstream of these pathways in extending the lifespan of nutrient restricted yeast cells, but the mechanisms involved are still poorly understood. We have used gene expression microarrays to study the targets of Gis1 and the related protein Rph1 in different growth phases. Our results show that Gis1 and Rph1 act both as repressors and activators, on overlapping sets of genes as well as on distinct targets. Interestingly, both the activities and the target specificities of Gis1 and Rph1 depend on the growth phase. Thus, both proteins are associated with repression during exponential growth, targeting genes with STRE or PDS motifs in their promoters. After the diauxic shift, both become involved in activation, with Gis1 acting primarily on genes with PDS motifs, and Rph1 on genes with STRE motifs. Significantly, Gis1 and Rph1 control a number of genes involved in acetate and glycerol formation, metabolites that have been implicated in aging. Furthermore, several genes involved in acetyl CoA metabolism are downregulated by Gis1.
|
|
| 7. |
|
|
| 8. |
- Rennel, Emma, et al.
(författare)
-
Endocan is a VEGF-A and PI3K regulated gene with increased expression in human renal cancer
- 2007
-
Ingår i: Experimental Cell Research. - : Elsevier BV. - 0014-4827 .- 1090-2422. ; 313:7, s. 1285-1294
-
Tidskriftsartikel (refereegranskat)abstract
- An in vitro model of VEGF-A-induced angiogenesis was used to generate transcription profiles of human microvascular endothelial cells. Microarray analysis showed increased transcription of genes known to regulate angiogenesis, but also genes that previously have not been firmly associated with angiogenesis such as endocan, pinin, plakophilin, phosphodiesterase 4B and gelsolin. Increased endocan mRNA levels in response to VEGF-A in endothelial cells and in human renal cancer have previously been reported. We now show increased endocan protein levels in VEGF-A treated endothelial cells and in human renal clear cell carcinoma. Increased protein expression was observed both in tumor cells and in a subset of tumor vessels, while expression in normal kidney tissue was low. VEGF-A seemed to be a specific inducer of endocan transcription since FGF-2, PDGF-BB, HGF/SF and EGF did not alter expression levels. Inhibition of PI3K with LY294002 caused a 12-fold increase in endocan transcription suggesting a repressive function of PI3K. In contrast inhibition of Src or MEK, which are signaling pathways activated by VEGF-A, did not influence basal or VEGF-A-induced endocan levels. In conclusion our study shows that, among angiogenic growth factors, VEGF-A is a specific inducer of endocan transcription which is translated into increased protein levels in VEGF-A treated endothelial cells. Increased endocan protein expression in human renal cancer suggests a role in tumor growth.
|
|
| 9. |
|
|
| 10. |
- Westholm, Jakub Orzechowski, et al.
(författare)
-
Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation.
- 2008
-
Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 9, s. 484-
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND The rate of mRNA transcription is controlled by transcription factors that bind to specific DNA motifs in promoter regions upstream of protein coding genes. Recent results indicate that not only the presence of a motif but also motif context (for example the orientation of a motif or its location relative to the coding sequence) is important for gene regulation. RESULTS In this study we present ContextFinder, a tool that is specifically aimed at identifying cases where motif context is likely to affect gene regulation. We used ContextFinder to examine the role of motif context in S. cerevisiae both for DNA binding by transcription factors and for effects on gene expression. For DNA binding we found significant patterns of motif location bias, whereas motif orientations did not seem to matter. Motif context appears to affect gene expression even more than it affects DNA binding, as biases in both motif location and orientation were more frequent in promoters of co-expressed genes. We validated our results against data on nucleosome positioning, and found a negative correlation between preferred motif locations and nucleosome occupancy. CONCLUSION We conclude that the requirement for stable binding of transcription factors to DNA and their subsequent function in gene regulation can impose constraints on motif context.
|
|
