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ChIP-seq analysis of transcription factor Upc2A binding across the Candida glabrata genome [Upc2A ChIP-seq]

ABSTRACT: ChIP-seq analysis of transcription factor Upc2A binding across the Candida glabrata genome [Upc2A ChIP-seq]

PROVIDER: PRJNA756362 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15532638_1.fastq.gz	Fastqsanger.gz
	SRR15532638_2.fastq.gz	Fastqsanger.gz
	SRR15532639_1.fastq.gz	Fastqsanger.gz
	SRR15532639_2.fastq.gz	Fastqsanger.gz
	SRR15532640_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

ChIP-seq analysis of transcription factor Upc2A binding across the Candida glabrata genome [Upc2A ChIP-seq]

Project description:To determine the genomic binding sites for the Candida glabrata transcription factor Upc2A, we utilized three different strains. One was the wild-type KKY2001 which contains a wild-type copy of UPC2A but lacks any HA tag. The other two are both derived from KKY2001 but contain a 3X HA tag immediately after the start codon of UPC2A. These strains are BVGC82 and BVGC84, respectively. Both contain a single copy of a loxP element located 252 bp downstream from the UPC2A stop codon. BVGC82 contains a wild-type copy of the UPC2A gene while BVGC84 contains a mutant form of UPC2A (G898D) that confers elevated resistance to fluconazole. ChIP was performed with anti-HA antibodies in all cases. Strains containing the wild-type UPC2A gene (no HA tag) are referred to as C1 and C2. Strains containing the 3X HA epitope tag at the N-terminus of the wild-type UPC2A gene are referred to as wt1 and wt2. These same strains challenged with fluconazole prior to ChIP are referred to as wtf1 and wtf2. The strain containing the G898D UPC2A allele are referred to as M1 and M2 (no fluconazole challenge) and MF1 and MF2 (with fluconazole challenge.

2021-09-23 | GSE182488 | GEO

Loss-of-function ROX1 mutations suppress the fluconazole susceptibility of upc2A∆ mutation in Candida glabrata, implicating additional positive regulators of ergosterol biosynthesis

Project description:Two of the major classes of antifungal drugs in clinical use target ergosterol biosynthesis. Despite its importance, our understanding of the transcriptional regulation of ergosterol biosynthesis genes in pathogenic fungi is essentially limited to the role of hypoxia and sterol-stress induced transcription factors such as Upc2 and Upc2A as well as homologs of Sterol Response Element Binding (SREB) factors. To identify additional regulators of ergosterol biosynthesis in Candida glabrata, an important human fungal pathogen with reduced susceptibility to ergosterol biosynthesis inhibitors relative to other Candida spp., we used a serial passaging strategy to isolate suppressors of the fluconazole hypersusceptibility of a upc2A∆ deletion mutant. This led to the identification of loss of function mutants in two genes: ROX1, the homolog of a hypoxia gene transcriptional suppressor in Saccharomyces cerevisiae, and CST6, a transcription factor that is involved in the regulation of carbon dioxide response in C. glabrata. Here, we describe a detailed analysis of the genetic interaction of ROX1 and UPC2A. In the presence of fluconazole, loss of Rox1 function restores ERG11 expression to the upc2A∆ mutant and inhibits the expression of ERG3 and ERG6, leading to increased levels or ergosterol and decreased levels of the toxic sterol, 14α methyl-ergosta-8,24(28)-dien-3β, 6α-diol, relative to upc2A∆. Our observations establish that Rox1 is a negative regulator of ERG gene biosynthesis and indicate that a least one additional positive transcriptional regulator of ERG gene biosynthesis must be present in C. glabrata.

2021-12-20 | GSE191145 | GEO

RNA-seq Analysis of Wild-Type and G898D UPC2A Transcriptomes [G898D UPC2A transcriptome]

Project description:Purpose: Determine the number of genes that respond to the presence of a gain-of-function mutant form of the UPC2A transcription factor in Candida glabrata. Methods: Prepare total RNA from wild-type and gain-of-function G898D UPC2A cells. Use standard RNA-seq to evaluate and compare the transcriptomic changes caused by this allele of UPC2A. Results: Although a clear increase was seen in fluconazole resistance conferred by the G898D UPC2A allele, elevated transcription was only observed for 11 genes with 9 of these involved in ergosterol biosynthesis. Conclusions: The presence of the G898D UPC2A allele led to elevated constitutive transcription for genes involved in ergosterol biosynthesis.

2021-09-23 | GSE182490 | GEO

Genomic level analysis of Upc2A-regulated transcription in Candida glabrata

Project description:Genomic level analysis of Upc2A-regulated transcription in Candida glabrata

| PRJNA756551 | ENA

Candida glabrata haploid and diploid

Project description:The different expression of Candida glabrata haploid and diploid.

2021-04-30 | GSE173617 | GEO

Homo sapiens whole blood infected with Candida spp. (here: Candida glabrata)

Project description:Homo sapiens fresh whole blood was infected with Candida glabrata. RNA-pool of both species extracted at 0min (control), 15, 30, 60, 120, 240 min. Samples are rRNA depleted. Measurement of Candida glabrata gene expression.

2018-12-26 | GSE114175 | GEO

Limosilactobacillus fermentum Limits Candida glabrata Growth by Ergosterol Depletion

Project description:Candida glabrata is a human-associated opportunistic fungal pathogen. It shares its niche with Lactobacillus spp. in the gastrointestinal and vaginal tract. In fact, Lactobacillus species are thought to competitively prevent Candida overgrowth. We investigated the molecular aspects of this antifungal effect by analyzing the interaction of C. glabrata strains with Limosilactobacillus fermentum. From a collection of clinical C. glabrata isolates, we identified strains with different sensitivities to L. fermentum in coculture. We analyzed the variation of their expression pattern to isolate the specific response to L. fermentum. C. glabrata-L. fermentum coculture induced genes associated with ergosterol biosynthesis, weak acid stress, and drug/chemical stress. L. fermentum coculture depleted C. glabrata ergosterol. The reduction of ergosterol was dependent on the Lactobacillus species, even in coculture with different Candida species. We found a similar ergosterol-depleting effect with other lactobacillus strains (Lactobacillus crispatus and Lactobacillus rhamosus) on Candida albicans, Candida tropicalis, and Candida krusei. The addition of ergosterol improved C. glabrata growth in the coculture. Blocking ergosterol synthesis with fluconazole increased the susceptibility against L. fermentum, which was again mitigated by the addition of ergosterol. In accordance, a C. glabrata Derg11 mutant, defective in ergosterol biosynthesis, was highly sensitive to L. fermentum. In conclusion, our analysis indicates an unexpected direct function of ergosterol for C. glabrata proliferation in coculture with L. fermentum.

2023-02-08 | GSE202656 | GEO

Absolute expression level of Candida glabrata genes

Project description:Total RNA versus genomic DNA hybridization on custom arrays designed for all Candida glabrata genes

2010-07-06 | GSE22194 | GEO

Genes upregulated in old Candida glabrata

Project description:Comparison of young and old Candida glabrata cells reveals regulation of genes involved in cell wall remodeling, sterol biogenesis, stress pathways

2017-04-24 | GSE85985 | GEO

Absolute expression level of Candida glabrata genes

Project description:Total RNA versus genomic DNA hybridization on custom arrays designed for all Candida glabrata genes Total RNA was collected in mid-log phase from Candida glabrata cells grown in rich medium (abbreviated CM, in house recipe). RNA was then converted to cDNA, Cy3-labeled and hybridized competitively against Cy5 labeled genomic DNA from Candida glabrata

2010-07-06 | E-GEOD-22194 | biostudies-arrayexpress

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