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Hog1 bypasses stress-mediated down-regulation of transcription by PolII redistribution and chromatin remodeling

ABSTRACT: Cells are subjected to dramatic changes on gene expression upon environmental changes. Stress causes a general down-regulation of gene expression together with the induction of a set of stress-responsive genes. Genome wide localisation studies showed major changes on Pol II localisation towards stress-responsive genes in contrast to housekeeping genes. Pol II relocalisation requires of the Hog1 SAPK, which also associates at stress-responsive loci. Chromatin structure was not significantly altered upon stress except for those genes that displayed Hog1 association. Together, Hog1 serves to bypass the general down-regulation of gene expression by targeting RNA Pol II machinery and inducing chromatin remodeling at stress-responsive loci.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE41494 | GEO | 2012/10/30

SECONDARY ACCESSION(S): PRJNA177335

REPOSITORIES: GEO

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Hog1 bypasses stress-mediated down-regulation of transcription by PolII redistribution and chromatin remodeling

Project description:Cells are subjected to dramatic changes on gene expression upon environmental changes. Stress causes a general down-regulation of gene expression together with the induction of a set of stress-responsive genes. Genome wide localisation studies showed major changes on Pol II localisation towards stress-responsive genes in contrast to housekeeping genes. Pol II relocalisation requires of the Hog1 SAPK, which also associates at stress-responsive loci. Chromatin structure was not significantly altered upon stress except for those genes that displayed Hog1 association. Together, Hog1 serves to bypass the general down-regulation of gene expression by targeting RNA Pol II machinery and inducing chromatin remodeling at stress-responsive loci. Hog1 and Pol II ChIP-Seq and Mnase-Seq experiments in both strains WT and Hog1 mutant, for 2 conditions: Exposed and not exposed to osmostress

2012-10-30 | E-GEOD-41494 | biostudies-arrayexpress

Hog1 controls global reallocation of RNA Pol II upon osmotic shock

2012-07-15 | GSE38208 | GEO

Hog1 controls global reallocation of RNA Pol II upon osmotic shock

Project description:When challenged with osmotic shock, S. cerevisiae induces hundreds of genes, despite a global reduction in transcriptional capacity. The mechanisms that regulate this rapid reallocation of transcriptional resources are not known. Here we show that redistribution of RNA Pol II upon stress requires the stress-responsive MAP kinase Hog1. We find that Hog1 and RNA Pol II co-localize to open reading frames that bypass global transcriptional repression, and that these targets are specified by two osmotic stress-responsive transcription factors. The combination of reduced global transcription with a gene-specific override mechanism allows cells to rapidly switch their transcriptional program in response to stress. ChIP-sequencing of S. cervisiae RNA Pol II, Hog1, Sko1 and Hot1 Processed data file descriptions: ORFcounts.txt: table of summed ChIP-seq reads that align to each ORF (normalized by reads per kilobase per million) promoter_counts.txt: table of summed ChIP-seq reads that align to each promoter (1kb upstream, normalized by reads per kilobase per million) downstream_counts.txt: table of summed ChIP-seq reads that align 3' regions (50-500 bp downstream, normalized by reads per kilobase per million) Sko1_peak_list.txt: table of peaks found by PeakSeq Hot1_peak_list.txt: table of peaks found by PeakSeq

2012-07-15 | E-GEOD-38208 | biostudies-arrayexpress

Hog1 bypasses stress-mediated downregulation of transcription by PolII redistribution and chromatin remodeling

Project description:Hog1 bypasses stress-mediated downregulation of transcription by PolII redistribution and chromatin remodeling Keyword: genetic modification

2012-10-30 | GSE41451 | GEO

Hog1 bypasses stress-mediated downregulation of transcription by PolII redistribution and chromatin remodeling

Project description:Hog1 bypasses stress-mediated downregulation of transcription by PolII redistribution and chromatin remodeling Keyword: genetic modification Three independent 200 ml cultures of wild-type strain were grown to mid-log phase in YPD rich medium at 30ºC

2012-10-30 | E-GEOD-41451 | biostudies-arrayexpress

Structure and Function of a Transcriptional Network Activated by Hog1

2008-07-29 | GSE12270 | GEO

Structure and Function of a Transcriptional Network Activated by Hog1

Project description:Cells regulate gene expression using a complex network of signaling pathways, transcription factors and promoters. To gain insight into the structure and function of these networks we analyzed gene expression in single and multiple mutant strains to build a quantitative model of the Hog1 MAPK-dependent osmotic stress response in budding yeast. Our model reveals that the Hog1 and general stress (Msn2/4) pathways interact, at both the signaling and promoter level, to integrate information and create a context-dependent response. Keywords: Stress response network analysis using genetically modified cells 85 samples were used to dissect the structure and function of the Hog1 network (Critical Samples measured in triplicate). The overall strategy was to double mutant or epistasis analysis to break down the influence that genes in the Hog1 network have on each other and the genome-wide stress response. This was done by comparing the expression in strains with different combinations of genes deleted and fitting the data to quantitative models. See Capaldi et. al. Nature Genetics 2008 for details.

2008-07-29 | E-GEOD-12270 | biostudies-arrayexpress

hog1 mutant 3 hour exposure to zymolyase

Project description:We did transcription profiling on the effect of hog1 deletion, gene involved in cell osmotic stress and cell wall stress response Keywords: cell wall stress response

2008-09-06 | GSE9931 | GEO

Transcription profiling of wild type and hog1 Candida albicans subjected to environmental stresses that are known to activate the Hog1 Stress-activated Protein Kinase

Project description:Based on studies in S. pombe (Chen et al., 2003), we predicted that conditions which activate C. albicans Hog1 would result in the induction of a common set of genes that are regulated by this SAPK (Smith et al., 2004). Hence in this study we compared the global transcriptional responses of wild-type and hog1 C. albicans cells to environmental stresses that are known to activate the Hog1 SAPK. We compared the homozygous hog1/hog1 null mutant (JC50) with the isogenic HOG1 reintegrant (hog1/hog1/HOG1: JC52) because this controlled for any secondary mutations that might have been introduced during the construction of the null mutant. We have shown that this reintegrant is indistinguishable from its parental wild-type strain RM1000 (HOG1/HOG1) with respect to their stress phenotypes (Smith et al., 2004) and their expression of stress genes (Supplementary Data). Three conditions were chosen for transcript profiling: osmotic stress imposed by 0.3 M NaCl, oxidative stress imposed by 5 mM H2O2, and heavy metal stress imposed by 0.5 mM CdSO4. Each of these treatments stimulates the phosphorylation and nuclear accumulation of this Hog1 SAPK within a 10-min time frame (Smith et al., 2004). Furthermore, significant differences in stress regulated gene expression are observed within this time scale (Enjalbert et al., 2003; Smith et al., 2004). Hence, we analyzed the C. albicans transcriptome after a 10-min exposure to each stress condition. Although some stress genes might be missed by analyzing a single time point, most C. albicans stress genes are induced within 10 min (Enjalbert et al., 2003). At least four independent biological replicates were analyzed for each condition

2007-07-05 | E-MEXP-1134 | biostudies-arrayexpress

Nuclear Localization of Hog1 MAPK is Not Necessary for Resistance to Hyperosmotic Stress

Project description:In budding yeast, this signaling pathway— the high-osmolarity glycerol (HOG) response —culminates in dual phosphorylation and nuclear translocation of the MAPK, Hog1 (ortholog of mammalian p38/SAPK). Induction of at least 50 genes requires nuclear Hog1, implying that transcriptional up-regulation is necessary to cope with hyperosmotic stress. Contrary to this expectation, we found that cells lacking the karyopherin (Nmd5) required for Hog1 nuclear import or in which Hog1 was permanently anchored at the plasma membrane(HOG1-CCAAX) (or both) withstood hyperosmotic challenge by three different solutes (1 M sorbitol, KCl or NaCl). In cells where activated Hog1 is excluded from the nucleus, there was little change in transcriptional program after exposure to hyperosmotic shock (comparable to hog1∆ cells), as judged by examining several diagnostic mRNAs and by global transcript measurements using microarrays. Systematic genetic analysis ruled out the need for any transcription factor known to be influenced by Hog1 (Hot1, Msn2, Msn4, Sko1 and Smp1). Keywords: Time course of stress response gene expression array

2008-06-01 | GSE8703 | GEO

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