Dataset Information

Expression data from wild-type and rph1-deleted yeasts

ABSTRACT: Cells respond to environmental signals by alteration of gene expression through action of transcription factors. A JmjC-domain-containing protein Rph1 belongs to the C2H2 zinc finger protein family and functions to repress transcription of PHR1 via histone demethylation. However, additional targets of Rph1 remain largely unknown. Here, we investigate the regulatory network of Rph1 by microarray analyses. More than 75% of Rph1-regulated genes showed increased expression in rph1Δ, suggesting Rph1 serves as a transcriptional repressor under physiological conditions. The binding motif of Rph1 resembling the STress Response Element (STRE) was over-represented in the promoters of Rph1-repressed genes. In addition, significant proportions of Rph1-regulated genes responded to DNA damage and environmental stress, implying a repressive role of Rph1 in the cross-protection of stress responses.

ORGANISM(S): Saccharomyces cerevisiae Schizosaccharomyces pombe

PROVIDER: GSE39950 | GEO | 2013/11/06

SECONDARY ACCESSION(S): PRJNA172145

REPOSITORIES: GEO

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Project description:The diverse mixture of contaminants frequently present in estuarine wetlands complicates their assessment by routine chemical or biological analyses. We investigated the use of gene expression to assess contaminant exposure and the condition of southern California (USA) estuarine fish. Liver gene expression, plasma estradiol concentrations and gonad histopathology were used to investigate the biological condition of longjaw mudsuckers (Gillichthys mirabilis). A wide array of metals, legacy organochlorine pesticides, PCBs and contaminants of emerging concern were detected in sediments and whole fish. Overall gene expression patterns were characteristic to each of four sites investigated in this study. Differentially expressed genes belonged to several functional categories including xenobiotic metabolism, detoxification, disease and stress responses. In general, plasma estradiol concentrations were similar among fish from all areas. Some fish gonads had pathologic changes (e.g. infection, inflammation) that could indicate weakened immune systems and chronic stress. The differential expression of some genes involved in stress responses correlated with the prevalence of histologic gonad lesions. This study indicates that sentinel fish gene expression data is a promising tool for assessing the biological condition of fish exposed to environmental contaminants. Key Words: Gene expression, fish, contaminants, estuaries. This abstract belongs to a manuscript that has been submitted to Environmental Science and Technology. The manuscript has been invited as part of an especial Omics Issue which is expected to be published in 2012. In this study, we used hepatic gene expression in wild longjaw mudsuckers (Gillichthys mirabilis) to assess biological responses from anthropogenically influenced wetlands. We investigated the relationships among gene expression responses, chemical exposure and additional biological responses in this species. We studied estuarine wetlands that had diverse contaminant characteristics and received three main types of contaminant inputs in different proportions: agricultural runoff, urban runoff and municipal wastewater.

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Expression data from wild-type and rph1-deleted yeasts

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