Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Atf1-mediated active gene response to H2O2 challenge.

ABSTRACT: 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. . Expression level of genes in triplicates at 0min (without stress) is compared with that at 10, 30, 60, and 120min after stress treatment. ChIP-chip analyses is done for Atf1-HA, pcr1-HA, sty1-HA, Sty1-HA allele in the atf1D or pcr1D background without and with H2O2 (0.5mM for 30min).

ORGANISM(S): Schizosaccharomyces pombe

SUBMITTER: Majid Eshaghi

PROVIDER: E-GEOD-13053 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Genomic binding profiling of the fission yeast stress-activated MAPK Sty1 and the bZIP transcriptional activator Atf1 in response to H2O2.

Eshaghi Majid M Lee Jong Hoon JH Zhu Lei L Poon Suk Yean SY Li Juntao J Cho Kwang-Hyun KH Chu Zhaoqing Z Karuturi R Krishna M RK Liu Jianhua J

PloS one 20100716 7

<h4>Background</h4>The evolutionally conserved MAPK Sty1 and bZIP transcriptional activator Atf1 are known to play a pivotal role in response to the reactive oxygen species in S. pombe. However, it is unclear whether all of the H(2)O(2)-induced genes are directly regulated by the Sty1-Atf1 pathway and involved in growth fitness under H(2)O(2)-induced stress conditions.<h4>Methodology/principal findings</h4>Here we present the study on ChIP-chip mapping of the genomic binding sites for Sty1, Atf1 ...[more]

PMID: 20661279

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Project description:Oxidative stress plays a crucial role in preeclampsia (PE) pathogenesis. Evidence indicates altered microRNAs (miRNAs) expression in PE, however, the relationship between oxidative stress and miRNA changes in placenta as a potential mechanism involved in PE is not fully elucidated. In the present study, we investigate the impact of increased oxidative stress on miRNA and mRNA expression profiles of genes known to be associated with PE in villous 3A first trimester trophoblast cells. Cells were exposed to H2O2 at 10 different concentrations (0-1 mM) for 0.5, 4, 24, and 48 h. Cytotoxicity was determined using the SRB assay and data was used to calculate the IC50 of H2O2. Total RNA was extracted after short-term exposure (4 h) to H2O2 for miRNA expression profiling. H2O2 exerted a concentration and time-dependent cytotoxicity on 3A trophoblast cells. Short-term exposure of 3A cells to low concentration of H2O2 (5% of IC50) significantly altered miRNA profile as evidenced by significant changes in 195 out of 595 evaluatable miRNAs. Short-term exposure of villous first trimester trophoblasts to low concentrations of H2O2 significantly alters miRNA profile. Oxidative stress plays a crucial role in preeclampsia (PE) pathogenesis. Evidence indicates altered microRNAs (miRNAs) expression in PE, however, the relationship between oxidative stress and miRNA changes in placenta as a potential mechanism involved in PE is not fully elucidated. In the present study, we investigate the impact of increased oxidative stress on miRNA and mRNA expression profiles of genes known to be associated with PE in villous 3A first trimester trophoblast cells. Cells were exposed to H2O2 at 10 different concentrations (0-1 mM) for 0.5, 4, 24, and 48 h. Cytotoxicity was determined using the SRB assay and data was used to calculate the IC50 of H2O2. Total RNA was extracted after short-term exposure (4 h) to H2O2 for miRNA expression profiling. H2O2 exerted a concentration and time-dependent cytotoxicity on 3A trophoblast cells. Short-term exposure of 3A cells to low concentration of H2O2 (5% of IC50) significantly altered miRNA profile as evidenced by significant changes in 195 out of 595 evaluatable miRNAs. Short-term exposure of villous first trimester trophoblasts to low concentrations of H2O2 significantly alters miRNA profile. Cells were grown to 90% confluency in 75 cm2 flasks and exposed to 25 ÂµM H2O2 in complete medium for 4 h. Total RNA was isolated using the Qiagen miRNEasy Mini Kit and quality/quantity measured in the Molecular Genomics Core at UTMB. RNA was quantitated spectrophotometrically using a NanoDrop ND-1000 (NanoDrop Techniologies, DE). Quality of the purified RNA was assessed by visualization of 18S and 28S RNA bands using an Agilent BioAnalyzer 2100 (Agilent Technologies, CA). Resulting electroperograms were used in the calculation of the 28S/18S ratio and the RNA Integrity Number. Reverse transcription was carried out using either the miScript II RT kit or RT2 First Strand and subsequent SYBR green based real-time PCR on a BioRad Chromo4 Real-Time PCR Detector per manufacturerâs recommendation. The miRNA profile screening was performed using miScript Human miRNome PCR Array (MIHS-3216Z, Qiagen, Valencia, CA). Data was analyzed using the ÎÎCT method with the miScript miRNA PCR Array Data Analysis version 3.5 (SABiosciences, Valencia CA).

Dataset Information

Atf1-mediated active gene response to H2O2 challenge.

Publications

Genomic binding profiling of the fission yeast stress-activated MAPK Sty1 and the bZIP transcriptional activator Atf1 in response to H2O2.

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