ChIP-chip and gene expression model of the MoCRZ1 mediated circuit for Ca2+/calcineurin signaling in rice blast fungus
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ABSTRACT:
PROVIDER: PRJNA119505 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE18080: ChIP-chip of MoCRZ1 GSE18185: Ca2+/calcineurin/CRZ1 dependent gene expression in Magnaporthe oryzae Refer to individual Series
2010-09-17 | E-GEOD-18193 | biostudies-arrayexpress
Project description:The Ca2+/calcineurin signaling pathway is a central conduit regulating growth, development, and virulence of fungal pathogens infecting plants and human. We have analyzed global gene expression profiles during Ca2+ treatment in the rice blast fungus, Magnaporthe oryzae. An immunosuppressive drug, FK506, and the knock-out mutant of a transcription factor, MoCRZ1, were included to analyze calcineurin- and/or CRZ1-dependent gene expression, respectively. About 1,400 genes were up or down regulated by Ca2+ treatment, while about 200 genes seemed to be up-regulated in a calcineurin/CRZ1-dependent manner.
2010-09-17 | GSE18185 | GEO
Project description:The Ca2+/calcineurin signaling pathway is a central conduit regulating growth, development, and virulence of fungal pathogens infecting plants and human. We have analyzed global gene expression profiles during Ca2+ treatment in the rice blast fungus, Magnaporthe oryzae. An immunosuppressive drug, FK506, and the knock-out mutant of a transcription factor, MoCRZ1, were included to analyze calcineurin- and/or CRZ1-dependent gene expression, respectively. About 1,400 genes were up or down regulated by Ca2+ treatment, while about 200 genes seemed to be up-regulated in a calcineurin/CRZ1-dependent manner. This study analyzes global gene expression dynamics during Ca2+ treatment in the rice blast fungus. We have used Agilent M. grisea 2.0 4×44K Microarrays using a single channel hybridization design. An immunosuppressive drug, FK506, and the knock out mutant of a transcription factor, MoCRZ1, were included to analyze calcineurin- and/or CRZ1-dependent gene expression, respectively. To know the time point at which the gene expression fluctuates most significantly, we treated mycelia with CaCl2 for 0, 15, 30, and 60 min. PMC1 expression level was checked by RT-PCR with the highest expression at 30 min time point. Four biological replicates of wild type and mutant mycelia were harvested after 30 min treatment with chemicals. Pairwise comparisons between Ca2+ treated vs. control and Ca2+ vs. Ca2+/FK506 in wild type (WT), and Ca2+ treated in WT vs. in mutant were conducted.
2010-09-17 | E-GEOD-18185 | biostudies-arrayexpress
Project description:CRZ1 (Calcineurin Responsive Zinc finger 1) is a conserved transcription factor that relays Ca2+/calcineurin signals within the cell. To catalog genome wide locations that MoCRZ1 binds to, we have conducted chromatin immunoprecipitation coupled with microarray (ChIP-chip) in the rice blast fungus, Magnaporthe oryzae. Fungal mycelia were treated with 200mM CaCl2 to activate translocation of MoCRZ1 to the nucleus, thereby binding to the promoter regions of downstream genes, and CaCl2 together with 10ug/ml FK506 to block these phenomena. Using ChIP-chip, we were able to identify over 100 direct targets of MoCRZ1 which include well known downstream genes as well as previously unknown genes.
2010-09-17 | GSE18080 | GEO
Project description:CRZ1 (Calcineurin Responsive Zinc finger 1) is a conserved transcription factor that relays Ca2+/calcineurin signals within the cell. To catalog genome wide locations that MoCRZ1 binds to, we have conducted chromatin immunoprecipitation coupled with microarray (ChIP-chip) in the rice blast fungus, Magnaporthe oryzae. Fungal mycelia were treated with 200mM CaCl2 to activate translocation of MoCRZ1 to the nucleus, thereby binding to the promoter regions of downstream genes, and CaCl2 together with 10ug/ml FK506 to block these phenomena. Using ChIP-chip, we were able to identify over 100 direct targets of MoCRZ1 which include well known downstream genes as well as previously unknown genes. Fungal mycelia expressing MoCRZ1::GFP under its native promoter were treated with 200mM CaCl2. MoCRZ1 bound DNA fragments which were immunoprecipitated with antiGFP-antibody were compared with 30% input DNA. Mycelia treated with 200mM CaCl2 and 10ug/ml FK506 were processed as the same way and used as negative control treatment.
2010-09-17 | E-GEOD-18080 | biostudies-arrayexpress
Project description:In Saccharomyces cerevisiae, the Ca2+/calmodulin-dependent protein phosphatase, calcineurin, is activated by specific environmental conditions, including exposure to Ca2+ and Na+, and induces gene expression by regulating the Crz1p/Tcn1p transcription factor. We used DNA microarrays to perform a comprehensive analysis of calcineurin/Crz1p-dependent gene expression following addition of Ca2+ (200 mM) or Na+ (0.8 M) to yeast. 163 genes exhibited increased expression that was reduced 50% or more by calcineurin inhibition. These calcineurin dependent genes function in signaling pathways, ion/small molecule transport, cell wall maintenance, vesicular transport, and include many open reading frames of heretofore-unknown function. Three distinct gene classes were defined: 28 genes displayed calcineurin-dependent induction in response to Ca2+ and Na+, 125 showed calcineurin-dependent expression following Ca2+ but not Na+ addition, and 10 were regulated by calcineurin in response to Na+ but not Ca2+. Analysis of crz1D cells established Crz1p as the major effecter of calcineurin-regulated gene expression in yeast. We identified the Crz1p binding site as 5-GNGGC(G/T)CA-3 by in vitro site selection. A similar sequence, 5-GAGGCTG-3, was identified as a common sequence motif in the upstream regions of calcineurin/Crz1p-dependent genes. This finding is consistent with direct regulation of these genes by Crz1p. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Computed
2005-10-15 | E-GEOD-3456 | biostudies-arrayexpress
Project description:Calcineurin is a highly conserved Ca2+/calmodulin-dependent serine/threonine-specific protein phosphatase that orchestrates cellular Ca2+ signaling responses. In Cryptococcus neoformans, calcineurin is activated by multiple stresses including high temperature, and is essential for stress adaptation and virulence. The transcription factor Crz1 is a major calcineurin effector in Saccharomyces cerevisiae and other fungi. Calcineurin dephosphorylates Crz1, thereby enabling Crz1 nuclear translocation and transcription of target genes. Here we show that Crz1 is dephosphorylated by calcineurin, and crz1Δ mutants display phenotypes intermediate between wild-type and calcineurin mutants. RNA-sequencing revealed 102 genes that are regulated in a calcineurin/Crz1-dependent manner at 37°C. 99 genes were down-regulated in cna1Δ and crz1Δ mutants, indicating these genes are normally activated by the calcineurin/Crz1 pathway at high temperature. About 58% of calcineurin-Crz1 target genes have unknown functions, while genes with known or predicted functions are involved in cell wall remodeling, calcium transport, and pheromone production. Surprisingly, only five genes have orthologs known to be calcineurin/Crz1-dependent in S. cerevisiae. 393 genes are independently regulated by calcineurin, and Crz1 regulates 59 genes independently of calcineurin. Taken together, these results indicate that the calcineurin/Crz1-dependent pathway controls a transcriptional circuit that has been extensively rewired in C. neoformans compared to S. cerevisiae. Given the intermediate crz1Δ mutant phenotype, and our recent evidence for a calcineurin regulatory network impacting mRNA in P-bodies and stress granules independently of Crz1, calcineurin likely acts on factors beyond Crz1 that govern mRNA expression/stability to operate a branched transcriptional/post-transcriptional stress response network necessary for fungal virulence. Taken together, our findings reveal the core calcineurin-Crz1 stress response cascade is maintained from ascomycetes to a pathogenic basidiomycete fungus, but its output has been extensively rewired to promote fungal virulence.
2017-04-07 | GSE93005 | GEO
Project description:In Saccharomyces cerevisiae, the Ca2+/calmodulin-dependent protein phosphatase, calcineurin, is activated by specific environmental conditions, including exposure to Ca2+ and Na+, and induces gene expression by regulating the Crz1p/Tcn1p transcription factor. We used DNA microarrays to perform a comprehensive analysis of calcineurin/Crz1p-dependent gene expression following addition of Ca2+ (200 mM) or Na+ (0.8 M) to yeast. 163 genes exhibited increased expression that was reduced 50% or more by calcineurin inhibition. These calcineurin dependent genes function in signaling pathways, ion/small molecule transport, cell wall maintenance, vesicular transport, and include many open reading frames of heretofore-unknown function. Three distinct gene classes were defined: 28 genes displayed calcineurin-dependent induction in response to Ca2+ and Na+, 125 showed calcineurin-dependent expression following Ca2+ but not Na+ addition, and 10 were regulated by calcineurin in response to Na+ but not Ca2+. Analysis of crz1D cells established Crz1p as the major effecter of calcineurin-regulated gene expression in yeast. We identified the Crz1p binding site as 5-GNGGC(G/T)CA-3 by in vitro site selection. A similar sequence, 5-GAGGCTG-3, was identified as a common sequence motif in the upstream regions of calcineurin/Crz1p-dependent genes. This finding is consistent with direct regulation of these genes by Crz1p. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
2005-10-15 | GSE3456 | GEO
Project description: Not available
| S-EPMC2873923 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2010-09-17 | GSE18193 | GEO