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The yeast Snt2 protein helps coordinate the transcriptional response to hydrogen-peroxide mediated oxidative stress (H2O2)

ABSTRACT: Snt2 is a yeast chromatin-interacting protein whose function has not been well characterized, that was recently shown to associate with Ecm5 and the Rpd3 deacetylase. Using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq), we show that in response to H2O2, Snt2 and Ecm5 colocalize to promoters of genes involved in various aspects of the environmental stress response. By integrating these ChIP-seq results with expression analysis, we identify a key set of target genes that require Snt2 for proper expression after H2O2 stress. Finally, by mapping Snt2 and Ecm5 localization before and after rapamycin treatment, we identify a subset of H2O2-specific Snt2 and Ecm5 target promoters that are also targeted in response to rapamycin. Our results establish a function for Snt2 in regulating transcriptional changes in response to oxidative stress, and suggest Snt2 may have a role in additional stress pathways.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE42971 | GEO | 2013/07/24

SECONDARY ACCESSION(S): PRJNA184039

REPOSITORIES: GEO

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The yeast Snt2 protein helps coordinate the transcriptional response to hydrogen-peroxide mediated oxidative stress (H2O2)

Project description:Snt2 is a yeast chromatin-interacting protein whose function has not been well characterized, that was recently shown to associate with Ecm5 and the Rpd3 deacetylase. Using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq), we show that in response to H2O2, Snt2 and Ecm5 colocalize to promoters of genes involved in various aspects of the environmental stress response. By integrating these ChIP-seq results with expression analysis, we identify a key set of target genes that require Snt2 for proper expression after H2O2 stress. Finally, by mapping Snt2 and Ecm5 localization before and after rapamycin treatment, we identify a subset of H2O2-specific Snt2 and Ecm5 target promoters that are also targeted in response to rapamycin. Our results establish a function for Snt2 in regulating transcriptional changes in response to oxidative stress, and suggest Snt2 may have a role in additional stress pathways. Crosslinking ChIP analysis to identify sites of Snt2 or Ecm5 genomic localization before, 0.5 hours after, or 4 hours after treatment with H2O2 (final concentration 0.4 mM). Snt2 and Ecm5 were genomically tagged with a 13Myc tag at their C termini. ChIPs were performed using a Myc antibody on either Snt2-Myc or Ecm5-Myc strains, or on an untagged wildtype strain (BY4741) as a control. Inputs and ChIPs from untagged strain were sequenced as controls.

2013-07-24 | E-GEOD-42971 | biostudies-arrayexpress

The yeast Snt2 protein helps coordinate the transcriptional response to hydrogen-peroxide mediated oxidative stress (RNA-seq)

Project description:Snt2 is a yeast chromatin-interacting protein whose function has not been well characterized, that was recently shown to associate with Ecm5 and the Rpd3 deacetylase. Using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq), we show that in response to H2O2, Snt2 and Ecm5 colocalize to promoters of genes involved in various aspects of the environmental stress response. By integrating these ChIP-seq results with expression analysis, we identify a key set of target genes that require Snt2 for proper expression after H2O2 stress. Finally, by mapping Snt2 and Ecm5 localization before and after rapamycin treatment, we identify a subset of H2O2-specific Snt2 and Ecm5 target promoters that are also targeted in response to rapamycin. Our results establish a function for Snt2 in regulating transcriptional changes in response to oxidative stress, and suggest Snt2 may have a role in additional stress pathways. RNA-seq analysis to look at gene expression levels in wild-type, snt2 deletion, or ecm5 deletion strains before or 0.5 hours after treatment with H2O2 (final concentration 0.4 mM). This sequencing was done on biological triplicate samples.

2013-07-24 | E-GEOD-42983 | biostudies-arrayexpress

The yeast Snt2 protein helps coordinate the transcriptional response to hydrogen-peroxide mediated oxidative stress (RNA-seq)

2013-07-24 | GSE42983 | GEO

The yeast Snt2 protein helps coordinate the transcriptional response to hydrogen-peroxide mediated oxidative stress (rapamycin or DMSO)

2013-07-24 | GSE43001 | GEO

The yeast Snt2 protein helps coordinate the transcriptional response to hydrogen-peroxide mediated oxidative stress (rapamycin or DMSO)

Project description:Snt2 is a yeast chromatin-interacting protein whose function has not been well characterized, that was recently shown to associate with Ecm5 and the Rpd3 deacetylase. Using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq), we show that in response to H2O2, Snt2 and Ecm5 colocalize to promoters of genes involved in various aspects of the environmental stress response. By integrating these ChIP-seq results with expression analysis, we identify a key set of target genes that require Snt2 for proper expression after H2O2 stress. Finally, by mapping Snt2 and Ecm5 localization before and after rapamycin treatment, we identify a subset of H2O2-specific Snt2 and Ecm5 target promoters that are also targeted in response to rapamycin. Our results establish a function for Snt2 in regulating transcriptional changes in response to oxidative stress, and suggest Snt2 may have a role in additional stress pathways. Crosslinking ChIP analysis to identify sites of Snt2 or Ecm5 genomic localization before, 0.5 hours after, or 4 hours after treatment with rapamycin (final concentration 5 nM) or with DMSO as a control. Snt2 and Ecm5 were genomically tagged with a 13Myc tag at their C termini. ChIPs were performed using a Myc antibody on either Snt2-Myc or Ecm5-Myc strains, or on untagged wildtype strain (BY4741) as a control. Inputs and ChIPs from untagged strain were sequenced as controls.

2013-07-24 | E-GEOD-43001 | biostudies-arrayexpress

RNA sequencing of hydrogen peroxide (H2O2)-treated melanocytes

Project description:Purpose: Determine the mechanism of H2O2-induced signaling in melanocytes. Method: Primary human epidermal melanocytes were treated with H2O2 (200 μM) and incubated for 24 h. Total RNA (500 ng) from melanocytes were extracted and subjected to library synthesis. Results: H2O2-treated melanocytes exhibited upregulation of cell death and type 1 interferon-related genes. Conclusion: H2O2-induced melanocyte signaling was well evaluated using RNA sequencing.

2023-07-28 | GSE216447 | GEO

Halobacterium NRC-1, H2O2 Stress Response

Project description:50mM H2O2 was added to mid-log phase Halobacterium NRC-1 cultures. After constant stress of H2O2 for 30 minutes, cultures were spun down and pellets were resuspended in same volume of GN101 media. Samples for RNA preparation were collected during recovery time points at 0, 10, 20, 30, 40, 60 and 120 minutes. Keywords: stress response

2008-01-03 | GSE7610 | GEO

Expression data from yeast wild type (WT) and sod1M-NM-^T strains after treatment with hydrogen peroxide (H2O2)

Project description:An important cellular defense mechanism against oxidative stress is the induction of genes involved in ROS resistance and DNA damage repair. Under normal conditions, Sod1 is localized mainly in the cytosol. However, we found that Sod1 translocates into the nucleus after oxidative stress. To address the physiological role of Sod1, we performed DNA microarray analysis of global gene expression in wild type (WT) and sod1M-NM-^T cells before and after treatment with H2O2. Early log phase WT and sod1M-NM-^T cells were treated with or without H2O2 for 20 min and RNA samples were extracted and subjected to hybridization on Affymetrix microarrays. We then compared the dataset of WT +/- H2O2 with SOD1 deleted cells +/- H2O2 to identify the H2O2-responsive genes whose induction was attenuated in sod1M-NM-^T cells by more than 50%.

2014-03-18 | E-GEOD-55081 | biostudies-arrayexpress

Atf1-mediated active gene response to H2O2 challenge.

Project description:Here we present the study on ChIP-chip mapping of the genomic binding sites for Sty1, Atf1, and the Atf1's binding partner Pcr1; the genome-wide transcriptional profiling of the atf1 and pcr1 strains in response to H2O2; and the phenotypic assessment of ~90 Atf1/Pcr1-bound or unbound genes for growth fitness under H2O2 conditions. ChIP-chip analysis shows that Atf1 and Pcr1 binding sites are overlapped in the genome and constitutively present before H2O2 stress. On the other hand, Sty1 recruitment primarily occurs at the Atf1/Pcr1 binding sites and is induced by H2O2. We found that Atf1/Pcr1 is clearly responsible for the high-level transcriptional response to H2O2. Furthermore, phenotypic assessment indicates that among the H2O2-induced genes, Atf1/Pcr1-bound genes exhibit a higher likelihood of functional requirement for growth fitness under the stress condition than the Atf1/Pcr1-unbound genes do. Notably, we found that the Atf1/Pcr1-bound genes regardless of their responsiveness to H2O2 show a high probability of requirement for growth fitness. .

2010-07-19 | GSE13053 | GEO

Atf1-mediated active gene response to H2O2 challenge.

2010-07-19 | E-GEOD-13053 | biostudies-arrayexpress

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