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Inactivation of the budding yeast cohesin loader Scc2 alters gene expression both globally and in response to a single DNA double strand break.

Lindgren E, Hägg S, Giordano F, Björkegren J, Ström L - Cell Cycle (2014)

Bottom Line: In yeast it has been suggested that the proteins in the cohesin network would effect transcription based on its role as insulator.We found that not only the DNA damage specific transcriptional response is distorted after inactivation of Scc2 but also the overall transcription profile.Interestingly, these alterations did not correlate with changes in cohesin binding.

View Article: PubMed Central - PubMed

Affiliation: a Department of Cell and Molecular Biology; Karolinska Institutet ; Stockholm , Sweden.

ABSTRACT
Genome integrity is fundamental for cell survival and cell cycle progression. Important mechanisms for keeping the genome intact are proper sister chromatid segregation, correct gene regulation and efficient repair of damaged DNA. Cohesin and its DNA loader, the Scc2/4 complex have been implicated in all these cellular actions. The gene regulation role has been described in several organisms. In yeast it has been suggested that the proteins in the cohesin network would effect transcription based on its role as insulator. More recently, data are emerging indicating direct roles for gene regulation also in yeast. Here we extend these studies by investigating whether the cohesin loader Scc2 is involved in regulation of gene expression. We performed global gene expression profiling in the absence and presence of DNA damage, in wild type and Scc2 deficient G2/M arrested cells, when it is known that Scc2 is important for DNA double strand break repair and formation of damage induced cohesion. We found that not only the DNA damage specific transcriptional response is distorted after inactivation of Scc2 but also the overall transcription profile. Interestingly, these alterations did not correlate with changes in cohesin binding.

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Related in: MedlinePlus

Inactivation of Scc2 causes global changes in gene expression. (A) Correlation plot illustrating correlations between WT and Scc2 deficient cells and induction of DSB. White color represents perfect correlation (ρ = 1) and black represents no correlation (ρ=0). Higher correlation is seen within each cell type, independent of DSB induction. (B) Summary of the number of probes/genes significantly affected when comparing WT and scc2–4 cells in the absence and presence of DSB. (C and D) Bioinformatic analysis using SGD GO slim mapping. Up- and downregulated genes were sorted according to biological process. Processes were regarded as significantly enhanced if FDR ≤ 0.05 (*, P ≤ 0.05, **, P ≤ 0.01, ***, P ≤ 0.005). (C) Biological processes of upregulated genes in Scc2 deficient cells compared to WT. (D) Biological processes of downregulated genes in Scc2 deficient cells compared to WT.
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f0002: Inactivation of Scc2 causes global changes in gene expression. (A) Correlation plot illustrating correlations between WT and Scc2 deficient cells and induction of DSB. White color represents perfect correlation (ρ = 1) and black represents no correlation (ρ=0). Higher correlation is seen within each cell type, independent of DSB induction. (B) Summary of the number of probes/genes significantly affected when comparing WT and scc2–4 cells in the absence and presence of DSB. (C and D) Bioinformatic analysis using SGD GO slim mapping. Up- and downregulated genes were sorted according to biological process. Processes were regarded as significantly enhanced if FDR ≤ 0.05 (*, P ≤ 0.05, **, P ≤ 0.01, ***, P ≤ 0.005). (C) Biological processes of upregulated genes in Scc2 deficient cells compared to WT. (D) Biological processes of downregulated genes in Scc2 deficient cells compared to WT.

Mentions: Samples were collected and prepared as described (Fig. 1). For comparisons between the different conditions gene expression data were pre-processed using limma and the rma (Robust Multichip Average) procedure.30-32 Samples were tested for differential expression (FDR ≤ 0.05) between different strains, and within strains but between absence and presence of DSB. A correlation graph is presented in Figure 2A where the strongest correlation is depicted white and the weakest black. The best correlations were found within the groups of either WT or scc2–4 cell, indicating that the effect of the induced DSB within the same cell type was diluted in the much larger lack of correlation between WT and scc2–4 cells (Fig. 2A).Figure 2.


Inactivation of the budding yeast cohesin loader Scc2 alters gene expression both globally and in response to a single DNA double strand break.

Lindgren E, Hägg S, Giordano F, Björkegren J, Ström L - Cell Cycle (2014)

Inactivation of Scc2 causes global changes in gene expression. (A) Correlation plot illustrating correlations between WT and Scc2 deficient cells and induction of DSB. White color represents perfect correlation (ρ = 1) and black represents no correlation (ρ=0). Higher correlation is seen within each cell type, independent of DSB induction. (B) Summary of the number of probes/genes significantly affected when comparing WT and scc2–4 cells in the absence and presence of DSB. (C and D) Bioinformatic analysis using SGD GO slim mapping. Up- and downregulated genes were sorted according to biological process. Processes were regarded as significantly enhanced if FDR ≤ 0.05 (*, P ≤ 0.05, **, P ≤ 0.01, ***, P ≤ 0.005). (C) Biological processes of upregulated genes in Scc2 deficient cells compared to WT. (D) Biological processes of downregulated genes in Scc2 deficient cells compared to WT.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4612677&req=5

f0002: Inactivation of Scc2 causes global changes in gene expression. (A) Correlation plot illustrating correlations between WT and Scc2 deficient cells and induction of DSB. White color represents perfect correlation (ρ = 1) and black represents no correlation (ρ=0). Higher correlation is seen within each cell type, independent of DSB induction. (B) Summary of the number of probes/genes significantly affected when comparing WT and scc2–4 cells in the absence and presence of DSB. (C and D) Bioinformatic analysis using SGD GO slim mapping. Up- and downregulated genes were sorted according to biological process. Processes were regarded as significantly enhanced if FDR ≤ 0.05 (*, P ≤ 0.05, **, P ≤ 0.01, ***, P ≤ 0.005). (C) Biological processes of upregulated genes in Scc2 deficient cells compared to WT. (D) Biological processes of downregulated genes in Scc2 deficient cells compared to WT.
Mentions: Samples were collected and prepared as described (Fig. 1). For comparisons between the different conditions gene expression data were pre-processed using limma and the rma (Robust Multichip Average) procedure.30-32 Samples were tested for differential expression (FDR ≤ 0.05) between different strains, and within strains but between absence and presence of DSB. A correlation graph is presented in Figure 2A where the strongest correlation is depicted white and the weakest black. The best correlations were found within the groups of either WT or scc2–4 cell, indicating that the effect of the induced DSB within the same cell type was diluted in the much larger lack of correlation between WT and scc2–4 cells (Fig. 2A).Figure 2.

Bottom Line: In yeast it has been suggested that the proteins in the cohesin network would effect transcription based on its role as insulator.We found that not only the DNA damage specific transcriptional response is distorted after inactivation of Scc2 but also the overall transcription profile.Interestingly, these alterations did not correlate with changes in cohesin binding.

View Article: PubMed Central - PubMed

Affiliation: a Department of Cell and Molecular Biology; Karolinska Institutet ; Stockholm , Sweden.

ABSTRACT
Genome integrity is fundamental for cell survival and cell cycle progression. Important mechanisms for keeping the genome intact are proper sister chromatid segregation, correct gene regulation and efficient repair of damaged DNA. Cohesin and its DNA loader, the Scc2/4 complex have been implicated in all these cellular actions. The gene regulation role has been described in several organisms. In yeast it has been suggested that the proteins in the cohesin network would effect transcription based on its role as insulator. More recently, data are emerging indicating direct roles for gene regulation also in yeast. Here we extend these studies by investigating whether the cohesin loader Scc2 is involved in regulation of gene expression. We performed global gene expression profiling in the absence and presence of DNA damage, in wild type and Scc2 deficient G2/M arrested cells, when it is known that Scc2 is important for DNA double strand break repair and formation of damage induced cohesion. We found that not only the DNA damage specific transcriptional response is distorted after inactivation of Scc2 but also the overall transcription profile. Interestingly, these alterations did not correlate with changes in cohesin binding.

Show MeSH
Related in: MedlinePlus