Data-driven identification of inherent features of eukaryotic stress-responsive genes
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PROVIDER: PRJNA719547 | ENA |
REPOSITORIES: ENA
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Project description:Virtually all living organisms are challenged by changes in their environment, such as sudden increases in osmolarity. To survive, cells have developed stress-responsive mechanisms that tune functions such as metabolism and gene expression. The response of Saccharomyces cerevisiae to osmostress includes a massive reprogramming of gene expression. Identifying the inherent features of stress-responsive genes is of significant interest for understanding the basic principles underlying the rewiring of gene expression upon stress. Here we generated a comprehensive catalog of osmotress-responsive genes from 5 independent RNA-seq experiments. We explored 30 features of yeast genes and found that 25 (83.34%) were distinct in osmostress-responsive genes. We then identified a subset of 13 non-redundant minimal osmostress gene traits and used statistical modeling to generate a ranking of the most stress-predictive features. Our findings reveal that the most relevant features of osmostress-responsive genes are the number of transcription factors targeting a gene and gene conservation. The same features that define yeast osmostress-responsive genes can also be used to predict osmostress-responsive genes in humans, although the most predictive features in humans are GC content and mRNA half-life. Our study provides a holistic understanding of the basic principles of the regulation of stress-responsive gene expression across eukaryotes.
2022-02-14 | GSE171427 | GEO
Project description:Eukaryotic cytosine methylation represses transposable elements, but also occurs in bodies of active genes. The extent to which these processes are conserved is unclear, and little is known about methylation outside of mammals, Arabidopsis thaliana, and Neurospora crassa. Utilizing deep bisulfite sequencing, we have quantified DNA methylation in five plant, seven animal, and five fungal genomes. We find that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons has evolved independently in the vertebrate lineage. We show that methylation of plant transposons in the CHG context extends to green algae, and present evidence for RNA-directed DNA methylation of fungal genes. We also show that antagonism between DNA methylation and histone H2A.Z is conserved between plants and animals. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes. Keywords: Epigenetics Examination of DNA methylation and transcription in plant, animal, and fungal genomes, and examination of how H2A.Z deposition relates to both methylation and transcription in puffer fish. Descriptions of the Samples' raw and processed data (provided as supplementary files) can be found in GSE19824_README.txt at the foot of this record.
2010-04-15 | E-GEOD-19824 | biostudies-arrayexpress
Project description:Observations of scarce surface ocean concentrations of dissolved zinc (Zn) have raised the possibility that Zn may co-limit the growth of oceanic phytoplankton, yet testing this hypothesis has been difficult because Zn is highly prone to contamination. Biomarkers of micro-nutrient stress can serve as an alternate means to assay, though biomarker proteins for Zn stress in marine algae are currently uncharacterized. In this study we identified two Zn-responsive proteins in four marine diatom species that became abundant under Zn and Co limitation, but were scarce or undetectable in replete conditions. We refer to these proteins as ZCRP-A and ZCRP-B (Zn/Co Responsive Protein A and B). Sequence similarity of ZCRP-A to the Escherichia coli model COG0523 protein YjiA suggests a Zn2+ binding capability using conserved metal binding sites. Cellular localization by fluorescent tagging and overexpression of these proteins showed that ZCRP-B is part of a membrane-bound transport complex and that ZCRP-A serves as a Zn/Co chaperone with a chloroplastic target. These results imply that ZCRP-A and ZCRP-B are important in intracellular Zn trafficking and high-affinity transport, respectively. Metaproteomic detection of ZCRP-A and ZCRP-B homologs in a variety of eukaryotic protists along a South Pacific Ocean transect demonstrated that both proteins were more abundant in the euphotic zone (0-200m) where dZn and dCo were scarce. These findings describe widely distributed marine algal proteins linked to Zn and Co metabolism that together contribute to our understanding of Zn homeostasis in important marine phytoplankton.
2022-03-02 | PXD026953 | Pride
Project description:Eukaryotic cytosine methylation represses transposable elements, but also occurs in bodies of active genes. The extent to which these processes are conserved is unclear, and little is known about methylation outside of mammals, Arabidopsis thaliana, and Neurospora crassa. Utilizing deep bisulfite sequencing, we have quantified DNA methylation in five plant, seven animal, and five fungal genomes. We find that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons has evolved independently in the vertebrate lineage. We show that methylation of plant transposons in the CHG context extends to green algae, and present evidence for RNA-directed DNA methylation of fungal genes. We also show that antagonism between DNA methylation and histone H2A.Z is conserved between plants and animals. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes. Keywords: Epigenetics
2010-04-15 | GSE19824 | GEO
Project description:BACKGROUND: Lithospermum erythrorhizon, popularly known as Gromwell, is a perennial herb belonging to the family of Boraginaceae and its extract is known to have diverse pharmacological, cosmetic, and nutritional values for human. Nevertheless the biological influence of Gromwell extract on general physiology of eukaryotic cells remains unknown. In this study, we for the first time performed a global transcriptome analysis by using DNA microarray analysis to identify genes affected by the addition of Gromwell extract (GE) by using a eukaryotic microorganism, basidiomycete fungus Cryptococcus neoformans, as a model system. RESULTS: The transcriptome analysis revealed that a total of 1932 genes are differentially regulated in a statistically significant manner and expressions of 715 genes are up- (315 genes) or down-regulated (457 genes) more than twofold upon GE treatment. In response to GE treatment, genes involved in signal transduction genes are immediately regulated and the evolutionarily conserved set of genes involved in the core cellular functions, including DNA replication, RNA transcription/processing, and protein translation/processing, are generally upregulated. In contrast, a number of genes involved in carbohydrate metabolism and transport, inorganic ion transport and metabolism, post-translational modification/protein turnover/chaperone functions, and signal transduction are downregulated by the GE treatment. Among the GE-responsive genes that are also evolutionarily conserved in the human genome, we confirmed expression patterns of YSA1, TPO2, FET5 (CFO1), and PZF1 by Northern blot analysis. Based on the functional characterization of some GE-responsive genes through phenotypic analysis of gene knockout mutants, we found that GE treatment may promote cellular tolerance against a variety of environmental stresses in eukaryotes. CONCLUSIONS: A significant portion of the Cryptococcus genome is affected in expression levels by treatment of GE, implying that the general physiology of eukaryotic cells is significantly affected by the GE treatment.
2013-01-10 | GSE43370 | GEO
Project description:BACKGROUND: Lithospermum erythrorhizon, popularly known as Gromwell, is a perennial herb belonging to the family of Boraginaceae and its extract is known to have diverse pharmacological, cosmetic, and nutritional values for human. Nevertheless the biological influence of Gromwell extract on general physiology of eukaryotic cells remains unknown. In this study, we for the first time performed a global transcriptome analysis by using DNA microarray analysis to identify genes affected by the addition of Gromwell extract (GE) by using a eukaryotic microorganism, basidiomycete fungus Cryptococcus neoformans, as a model system. RESULTS: The transcriptome analysis revealed that a total of 1932 genes are differentially regulated in a statistically significant manner and expressions of 715 genes are up- (315 genes) or down-regulated (457 genes) more than twofold upon GE treatment. In response to GE treatment, genes involved in signal transduction genes are immediately regulated and the evolutionarily conserved set of genes involved in the core cellular functions, including DNA replication, RNA transcription/processing, and protein translation/processing, are generally upregulated. In contrast, a number of genes involved in carbohydrate metabolism and transport, inorganic ion transport and metabolism, post-translational modification/protein turnover/chaperone functions, and signal transduction are downregulated by the GE treatment. Among the GE-responsive genes that are also evolutionarily conserved in the human genome, we confirmed expression patterns of YSA1, TPO2, FET5 (CFO1), and PZF1 by Northern blot analysis. Based on the functional characterization of some GE-responsive genes through phenotypic analysis of gene knockout mutants, we found that GE treatment may promote cellular tolerance against a variety of environmental stresses in eukaryotes. CONCLUSIONS: A significant portion of the Cryptococcus genome is affected in expression levels by treatment of GE, implying that the general physiology of eukaryotic cells is significantly affected by the GE treatment. There are more than 95% of genome homology between JEC21 and H99. Therefore 6 slides of JEC21 (Cryptococcus neoformans var. neoformans serotype D) 70-mer oligo are used in this analysis, 3 biological replicate experiments are performed, total RNAs are extracted from H99 (H99 Wild type strain (Cryptococcus neoformans var. grubii serotype A)) with 6.4 mg/ml Gromwell extract in 0, 10, 30, 60 min. We use the mixed all of total RNAs from this experiment as a control RNA. We use Cy3 as Sample dye and Cy5 as a control dye.
2013-01-10 | E-GEOD-43370 | biostudies-arrayexpress
Project description:eukaryotic metagenome Raw sequence reads
| PRJNA602127 | ENA
Project description:Human Oral Eukaryotic Metagenome sequences
| PRJNA609043 | ENA