Saccharomyces cerevisiae
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PROVIDER: PRJNA109829 | ENA |
REPOSITORIES: ENA
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Project description:The budding yeast Saccharomyces cerevisiae alters its gene expression profile in response to a change in nutrient availability. The PHO-system is a well-studied case in the transcriptional regulation responding to nutritional changes in which a set of genes (PHO genes) is expressed to activate phosphate (Pi) metabolism for adaptation to Pi-starvation. Pi-starvation triggers an inhibition of Pho85 kinase, leading to migration of unphosphorylated Pho4 transcriptional activator into the nucleus enabling expression of PHO genes. When Pi is sufficient, the Pho85 kinase phosphorylates Pho4 thereby excluding it from the nucleus and resulting in repression (i.e., lack of transcription) of PHO genes. The Pho85 kinase has a role in various cellular functions other than regulation of the PHO system, in that Pho85 monitors whether environmental conditions are adequate for cell growth, and represses inadequate (untimely) responses in these cellular processes. In contrast, Pho4 appears to activate some genes involved in stress-response and is required for G1 arrest caused by DNA damage. These facts suggest the antagonistic function of these two players on a more general scale when yeast cells must cope with stress conditions. To explore general involvement of Pho4 in stress-response, we tried to identify Pho4-dependent genes by a genome-wide mapping of Pho4- and Rpo21-binding (Rpo21 being the largest subunit of RNA polymerase II) using a yeast tiling array. In the course of this study, we found Pi- and Pho4-regulated intragenic and antisense RNAs that could modulate the Pi-signal transduction pathway. Low-Pi signal is transmitted via certain inositol polyphosphate (IP) species (IP7) that are synthesized by Vip1 IP6 kinase. We have shown that Pho4 activates transcription of antisense and intragenic RNAs in the KCS1 locus to downregulate the Kcs1 activity, another IP6 kinase, by producing truncated Kcs1 protein via hybrid formation with the KCS1 mRNA and translation of the intragenic RNA, thereby enabling Vip1 to utilize more IP6 to synthesize IP7 functioning in low-Pi signaling. Since Kcs1 also can phosphorylate these IP7 species to synthesize IP8, reduction in the Kcs1 activity can ensure accumulation of the IP7 species, leading to further stimulation of low Pi-signaling, i.e., forming a positive feedback loop. We also report that genes apparently not involved in the PHO system are regulated by Pho4 either dependent upon or independently of the Pi conditions, and many of the latter genes are involved in stress-response. In S. cerevisiae, a large-scale cDNA analysis and mapping of RNA polymerase II binding using a high-resolution tiling array have identified a large number of antisense RNA species whose functions are yet to be clarified. Here we have shown that nutrient-regulated antisense and intragenic RNAs, as well as direct regulation of structural gene transcription, function in the response to nutrient availability. Our findings also imply that Pho4 is present in the nucleus even under high-Pi condition to activate or repress transcription, which challenges our current understanding of Pho4 regulation. Wild type and pho4 deletion mutant were grown in low or high phosphate medium and distribution of Rpo21 was analyzed.
2008-12-23 | E-GEOD-13350 | biostudies-arrayexpress
Project description:The budding yeast Saccharomyces cerevisiae alters its gene expression profile in response to a change in nutrient availability. The PHO-system is a well-studied case in the transcriptional regulation responding to nutritional changes in which a set of genes (PHO genes) is expressed to activate phosphate (Pi) metabolism for adaptation to Pi-starvation. Pi-starvation triggers an inhibition of Pho85 kinase, leading to migration of unphosphorylated Pho4 transcriptional activator into the nucleus enabling expression of PHO genes. When Pi is sufficient, the Pho85 kinase phosphorylates Pho4 thereby excluding it from the nucleus and resulting in repression (i.e., lack of transcription) of PHO genes. The Pho85 kinase has a role in various cellular functions other than regulation of the PHO system, in that Pho85 monitors whether environmental conditions are adequate for cell growth, and represses inadequate (untimely) responses in these cellular processes. In contrast, Pho4 appears to activate some genes involved in stress-response and is required for G1 arrest caused by DNA damage. These facts suggest the antagonistic function of these two players on a more general scale when yeast cells must cope with stress conditions. To explore general involvement of Pho4 in stress-response, we tried to identify Pho4-dependent genes by a genome-wide mapping of Pho4- and Rpo21-binding (Rpo21 being the largest subunit of RNA polymerase II) using a yeast tiling array. In the course of this study, we found Pi- and Pho4-regulated intragenic and antisense RNAs that could modulate the Pi-signal transduction pathway. Low-Pi signal is transmitted via certain inositol polyphosphate (IP) species (IP7) that are synthesized by Vip1 IP6 kinase. We have shown that Pho4 activates transcription of antisense and intragenic RNAs in the KCS1 locus to downregulate the Kcs1 activity, another IP6 kinase, by producing truncated Kcs1 protein via hybrid formation with the KCS1 mRNA and translation of the intragenic RNA, thereby enabling Vip1 to utilize more IP6 to synthesize IP7 functioning in low-Pi signaling. Since Kcs1 also can phosphorylate these IP7 species to synthesize IP8, reduction in the Kcs1 activity can ensure accumulation of the IP7 species, leading to further stimulation of low Pi-signaling, i.e., forming a positive feedback loop. We also report that genes apparently not involved in the PHO system are regulated by Pho4 either dependent upon or independently of the Pi conditions, and many of the latter genes are involved in stress-response. In S. cerevisiae, a large-scale cDNA analysis and mapping of RNA polymerase II binding using a high-resolution tiling array have identified a large number of antisense RNA species whose functions are yet to be clarified. Here we have shown that nutrient-regulated antisense and intragenic RNAs, as well as direct regulation of structural gene transcription, function in the response to nutrient availability. Our findings also imply that Pho4 is present in the nucleus even under high-Pi condition to activate or repress transcription, which challenges our current understanding of Pho4 regulation.
2008-12-23 | GSE13350 | GEO
Project description:Ras/cAMP signal transduction, perturbations
| PRJNA92621 | ENA
Project description:In oligotrophic ocean waters where bacteria are often subjected to chronic nutrient limitation, community transcriptome sequencing has pointed to the presence of highly abundant small RNAs (sRNAs). The role of sRNAs in regulating response to nutrient stress was investigated in a model heterotrophic marine bacterium Ruegeria pomeroyi grown in continuous culture under carbon and nitrogen limitation. RNAseq analysis identified 98 sRNAs, of which 69 were cis-encoded and located antisense to their target genes, and 30 were trans-encoded and linked to predicted target genes through complementarity analysis. The most prevalent functional roles of target genes were transport, cell-cell interactions, signal transduction, and transcriptional regulation. Thirty-two percent of the sRNAs had been identified in a previous study of R. pomeroyi growth on organic sulfur compounds, and may be constitutively expressed, while 69% were not identified in previous studies. Eighty-six percent and were transcribed equally under both carbon and nutrient limitation, and may be involved in a general stress response; 14% were differentially regulated under carbon versus nitrogen stress, and may respond to specific nutrient limitations. A network analysis of the predicted target genes of the R. pomeroyi sRNAs indicated that they average fewer connections than typical protein-encoding genes, and appear to be more important in peripheral or niche-defining functions encoded in the pan genome rather than central metabolism encoded in the core genome.
2016-02-27 | E-MTAB-4468 | biostudies-arrayexpress
Project description:Identification of E2F1-regulated genes that modulate the transition from quiescence into DNA synthesis, or have roles in apoptosis, signal transduction, membrane biology, and transcription repression. Keywords: other
2003-07-16 | GSE498 | GEO
Project description:Identification of E2F1-regulated genes that modulate the transition from quiescence into DNA synthesis, or have roles in apoptosis, signal transduction, membrane biology, and transcription repression.
2008-06-13 | E-GEOD-498 | biostudies-arrayexpress
Project description:IMPACT: Unraveling intracellular signal transduction and pathway crosstalk by exploring pathway landscape
| PRJNA218218 | ENA
Project description:Set2-mediated methylation of H3K36 (H3K36me) regulates a diverse number of activities including DNA repair, mRNA splicing and the suppression of inappropriate or ‘cryptic’ transcription. Here, we describe an unexpected connection between Set2-mediated H3K36me and the regulation of nutrient stress response. We find cells deleted for SET2 (set2∆) are sensitive to inhibitors of Tor1, Tor2 and MAP kinase pathways that regulate the nutrient response pathway. Further genetic and biochemical analyses confirm a role for Set2-mediated H3K36me in nutrient stress response. At the molecular level, set2∆ cells demonstrate a dysregulated genome-wide transcriptional response to nutrient stress. Remarkably, newly initiated and bi-directional transcription events within the bodies of genes develop in set2∆ cells during nutrient stress. Importantly, these antisense transcripts extend into the promoters of the genes they arise from, resulting in pervasive transcriptional interference. Our results suggest that Set2-enforced transcriptional fidelity is critical to the proper regulation highly-tuned transcription programs.
2017-06-05 | GSE89265 | GEO
Project description:The study was done to determine the effect of Tocotrienol rich fraction (TRF) on the expression of RNAs in C. elegans under oxidative stress. Apart from its antioxidant properties, tocotrienols are beneficial to health due to its neuroprotective effect, anti-carcinogenic as well as cholesterol-lowering property. It has also been demonstrated that tocotrienols play a role in regulating signal transduction of cell death pathway. However, the molecular mechanism of how tocotrienols modulate the aging pathway is still scarce. To elucidate the molecular mechanism of lifespan extension by this antioxidant, the microarray technology is further used to analyze the changes in gene expression with TRF treatment in the present study.
2017-07-06 | GSE100814 | GEO
Project description:Free fatty acid β oxidation and akt signal pathway processes were up-regulated in liver of Balb/cBy mice after 12 week HFD-fed, which can conrtibute to up-regulate free fatty acid β oxidation and improved insulin signal transduction We used microarrays to detail the global genes expression underlying free fatty acid β oxidation, unfolded protein response and akt signal pathway, and then identified up-regulated and down-regulated genes during there processes.
2020-03-31 | GSE128670 | GEO