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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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Scc2 is important for repression of DSB proximal genes. (A) Schematic illustration of the region immediately surrounding the DSB on Chr. VI (adapted from Sacchcaromyces Genome Database). Gray arrow points at the HO recognition site. (B) Relative gene expression of indicated genes was measured by qRT-PCR. Expression of respective gene for both WT and scc2–4 in the presence of break was related to its own absence of break sample that was set to 1. (C) Relative gene expression of indicated genes was measured by qRT-PCR. Expression of respective gene for scc2–4 cells in the absence of break was related to the WT absence of break sample that was set to 1. (B and C) Data are mean values from 3 independent experiments with the respective deviation (*, P ≤ 0.05, **, P ≤ 0.01, ***, P ≤ 0.005).
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f0005: Scc2 is important for repression of DSB proximal genes. (A) Schematic illustration of the region immediately surrounding the DSB on Chr. VI (adapted from Sacchcaromyces Genome Database). Gray arrow points at the HO recognition site. (B) Relative gene expression of indicated genes was measured by qRT-PCR. Expression of respective gene for both WT and scc2–4 in the presence of break was related to its own absence of break sample that was set to 1. (C) Relative gene expression of indicated genes was measured by qRT-PCR. Expression of respective gene for scc2–4 cells in the absence of break was related to the WT absence of break sample that was set to 1. (B and C) Data are mean values from 3 independent experiments with the respective deviation (*, P ≤ 0.05, **, P ≤ 0.01, ***, P ≤ 0.005).

Mentions: It has previously been reported that transcription of genes in close vicinity of the natural HO-cleavage site, localized at the MAT locus, are repressed in response to break induction. This was suggested to be due to resection of the DNA ends.29 In line with this, the microarray result for the genes surrounding the inserted HO recognition site on Chr. VI showed a similar pattern, where the majority of the genes in WT cells, LSB3, HIS2, CDC14, and PTR3 all showed reduced expression after break induction (data set S7;Fig. 5A). Somewhat surprisingly, we found that this was not true for the 2 genes located closest to the break on each side, where the expression of ULI1 was increased and no change in expression of ECO1 could be detected. Furthermore, when considering the microarray data for transcription over the same genes in Scc2 deficient cells, 3 out of the 6 closest genes (LSB3, HIS2, and PTR3) were not transcriptionally repressed after break induction (data set S8;Fig. 5A). In addition, ECO1 was shown to be upregulated after break induction in scc2–4 cells. However, CDC14 was repressed and ULI1 induced in response to the break in both WT and Scc2 deficient cells.Figure 5.


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)

Scc2 is important for repression of DSB proximal genes. (A) Schematic illustration of the region immediately surrounding the DSB on Chr. VI (adapted from Sacchcaromyces Genome Database). Gray arrow points at the HO recognition site. (B) Relative gene expression of indicated genes was measured by qRT-PCR. Expression of respective gene for both WT and scc2–4 in the presence of break was related to its own absence of break sample that was set to 1. (C) Relative gene expression of indicated genes was measured by qRT-PCR. Expression of respective gene for scc2–4 cells in the absence of break was related to the WT absence of break sample that was set to 1. (B and C) Data are mean values from 3 independent experiments with the respective deviation (*, P ≤ 0.05, **, P ≤ 0.01, ***, P ≤ 0.005).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f0005: Scc2 is important for repression of DSB proximal genes. (A) Schematic illustration of the region immediately surrounding the DSB on Chr. VI (adapted from Sacchcaromyces Genome Database). Gray arrow points at the HO recognition site. (B) Relative gene expression of indicated genes was measured by qRT-PCR. Expression of respective gene for both WT and scc2–4 in the presence of break was related to its own absence of break sample that was set to 1. (C) Relative gene expression of indicated genes was measured by qRT-PCR. Expression of respective gene for scc2–4 cells in the absence of break was related to the WT absence of break sample that was set to 1. (B and C) Data are mean values from 3 independent experiments with the respective deviation (*, P ≤ 0.05, **, P ≤ 0.01, ***, P ≤ 0.005).
Mentions: It has previously been reported that transcription of genes in close vicinity of the natural HO-cleavage site, localized at the MAT locus, are repressed in response to break induction. This was suggested to be due to resection of the DNA ends.29 In line with this, the microarray result for the genes surrounding the inserted HO recognition site on Chr. VI showed a similar pattern, where the majority of the genes in WT cells, LSB3, HIS2, CDC14, and PTR3 all showed reduced expression after break induction (data set S7;Fig. 5A). Somewhat surprisingly, we found that this was not true for the 2 genes located closest to the break on each side, where the expression of ULI1 was increased and no change in expression of ECO1 could be detected. Furthermore, when considering the microarray data for transcription over the same genes in Scc2 deficient cells, 3 out of the 6 closest genes (LSB3, HIS2, and PTR3) were not transcriptionally repressed after break induction (data set S8;Fig. 5A). In addition, ECO1 was shown to be upregulated after break induction in scc2–4 cells. However, CDC14 was repressed and ULI1 induced in response to the break in both WT and Scc2 deficient cells.Figure 5.

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