A genome-wide analysis of carbon catabolite repression in Schizosaccharomyces pombe [ChIP-seq]
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ABSTRACT:
PROVIDER: PRJNA509382 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8311190_1.fastq.gz | Fastqsanger.gz | |||
| SRR8311190_2.fastq.gz | Fastqsanger.gz | |||
| SRR8311200_1.fastq.gz | Fastqsanger.gz | |||
| SRR8311200_2.fastq.gz | Fastqsanger.gz | |||
| SRR8311210_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:A genome-wide analysis of carbon catabolite repression in Schizosaccharomyces pombe
| PRJNA509428 | ENA
Project description:A genome-wide analysis of carbon catabolite repression in Schizosaccharomyces pombe [RNA-seq]
| PRJNA509427 | ENA
Project description:Optimal glucose metabolism is central to the growth and development of cells. In microbial eukaryotes, carbon catabolite repression (CCR) mediates the preferential utilization of glucose, primarily by repressing alternate carbon source utilization. In fission yeast, CCR is mediated by transcriptional repressors Scr1 and the Tup/Ssn6 complex, with the Rst2 transcription factor important for activation of gluconeogenesis and sexual differentiation genes upon derepression. Through genetic and genome-wide methods, this study aimed to comprehensively characterize CCR in fission yeast by identifying the genes and biological processes that are regulated by Scr1, Tup/Ssn6 and Rst2, the core CCR machinery. The transcriptional response of S. pombe to glucose-sufficient or glucose-deficient growth conditions in wild type and CCR mutant cells was determined by RNA-seq and ChIP-seq. Scr1 was found to regulate genes involved in carbon metabolism, hexose uptake, gluconeogenesis and the TCA cycle. Surprisingly, a role for Scr1 in the suppression of sexual differentiation was also identified, as homothallic scr1 deletion mutants showed ectopic meiosis in carbon and nitrogen rich conditions. ChIP-seq characterised the targets of Tup/Ssn6 and Rst2 identifying regulatory roles within and independent of CCR. Finally, a subset of genes bound by all three factors was identified, implying that regulation of certain loci may be modulated in a competitive fashion between the Scr1, Tup/Ssn6 repressors and the Rst2 activator. By identifying the genes directly and indirectly regulated by Scr1, Tup/Ssn6 and Rst2, this study comprehensively defined the gene regulatory networks of CCR in fission yeast and revealed the transcriptional complexities which govern this system.
2018-12-12 | GSE123617 | GEO
Project description:Optimal glucose metabolism is central to the growth and development of cells. In microbial eukaryotes, carbon catabolite repression (CCR) mediates the preferential utilization of glucose, primarily by repressing alternate carbon source utilization. In fission yeast, CCR is mediated by transcriptional repressors Scr1 and the Tup/Ssn6 complex, with the Rst2 transcription factor important for activation of gluconeogenesis and sexual differentiation genes upon derepression. Through genetic and genome-wide methods, this study aimed to comprehensively characterize CCR in fission yeast by identifying the genes and biological processes that are regulated by Scr1, Tup/Ssn6 and Rst2, the core CCR machinery. The transcriptional response of S. pombe to glucose-sufficient or glucose-deficient growth conditions in wild type and CCR mutant cells was determined by RNA-seq and ChIP-seq. Scr1 was found to regulate genes involved in carbon metabolism, hexose uptake, gluconeogenesis and the TCA cycle. Surprisingly, a role for Scr1 in the suppression of sexual differentiation was also identified, as homothallic scr1 deletion mutants showed ectopic meiosis in carbon and nitrogen rich conditions. ChIP-seq characterised the targets of Tup/Ssn6 and Rst2 identifying regulatory roles within and independent of CCR. Finally, a subset of genes bound by all three factors was identified, implying that regulation of certain loci may be modulated in a competitive fashion between the Scr1, Tup/Ssn6 repressors and the Rst2 activator. By identifying the genes directly and indirectly regulated by Scr1, Tup/Ssn6 and Rst2, this study comprehensively defined the gene regulatory networks of CCR in fission yeast and revealed the transcriptional complexities which govern this system.
2018-12-12 | GSE123614 | GEO
Project description:CrcA, a novel player in Pseudomonas aeruginosa carbon catabolite repression
| PRJEB60904 | ENA
Project description:BackgroundOptimal glucose metabolism is central to the growth and development of cells. In microbial eukaryotes, carbon catabolite repression (CCR) mediates the preferential utilization of glucose, primarily by repressing alternate carbon source utilization. In fission yeast, CCR is mediated by transcriptional repressors Scr1 and the Tup/Ssn6 complex, with the Rst2 transcription factor important for activation of gluconeogenesis and sexual differentiation genes upon derepression. Through genetic and genome-wide methods, this study aimed to comprehensively characterize CCR in fission yeast by identifying the genes and biological processes that are regulated by Scr1, Tup/Ssn6 and Rst2, the core CCR machinery.ResultsThe transcriptional response of fission yeast to glucose-sufficient or glucose-deficient growth conditions in wild type and CCR mutant cells was determined by RNA-seq and ChIP-seq. Scr1 was found to regulate genes involved in carbon metabolism, hexose uptake, gluconeogenesis and the TCA cycle. Surprisingly, a role for Scr1 in the suppression of sexual differentiation was also identified, as homothallic scr1 deletion mutants showed ectopic meiosis in carbon and nitrogen rich conditions. ChIP-seq characterised the targets of Tup/Ssn6 and Rst2 identifying regulatory roles within and independent of CCR. Finally, a subset of genes bound by all three factors was identified, implying that regulation of certain loci may be modulated in a competitive fashion between the Scr1, Tup/Ssn6 repressors and the Rst2 activator.ConclusionsBy identifying the genes directly and indirectly regulated by Scr1, Tup/Ssn6 and Rst2, this study comprehensively defined the gene regulatory networks of CCR in fission yeast and revealed the transcriptional complexities governing this system.
| S-EPMC6440086 | biostudies-literature
Project description:Cells must sense and respond to available nutrients to utilize available resources and establish fungal colonies. Saprophytic microbes harvest carbon from plant biomass, which contain insoluble, complex carbohydrates that must be degraded extracellularly prior to import into the cell. Filamentous fungi can degrade these complex carbohydrates. However, while many single cellular microbes can utilize the building blocks of these insoluble polysaccharides, they frequently are unable to degrade insoluble carbohydrates. Cellobiose is a disaccharide breakdown product of cellulose, the most abundant component of plant biomass. We investigated the genetic regulation of cellobiose utilization in the oleaginous, basidiomycete yeast Rhodotorula (Rhodosporidium) toruloides using a combination of phylogenetic, genetic, and genomic approaches. We tested the closest R. toruloides homolog of the cellulose degradation regulator CLR-2/ClrB for a role in cellobiose utilization. Deletion of this transcription factor, which we named Cbr1, eliminated the ability of cells to grow on media containing cellobiose as the sole carbon source. Although, the role of CLR-2/ClrB is limited to regulating the expression of genes involved in the utilization of cellulose and hemicellulose, Cbr1 plays a role not only in cellobiose utilization, but also utilization of tricarboxylic acid (TCA) cycle intermediates. Transcriptional profiling revealed that the genes activated by Cbr1 included genes encoding beta-glucosidases and transporters. These beta-glucosidases are secreted and are necessary and sufficient for cellobiose utilization, while one of the transporters is required for utilization of the TCA cycle intermediate, citrate. Additionally, Cbr1 inhibits carbon catabolite repression, specifically during utilization of disaccharides, which may have evolved to limit the repression of genes encoding secreted proteins that cleave disaccharides into glucose extracellularly. The co-regulation of cellobiose and TCA cycle utilization with carbon catabolite repression may shed light on alternative methods of the regulation of carbon catabolite repression in fungi.
2025-04-10 | GSE293943 | GEO
Project description:Schizosaccharomyces pombe Epigenomics
| PRJNA239195 | ENA