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

ABSTRACT: 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.

ORGANISM(S): Nakaseomyces glabratus CBS 138

PROVIDER: GSE182488 | GEO | 2021/09/23

REPOSITORIES: GEO

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ChIP-seq analysis of transcription factor AtrR binding across the Aspergillus fumigatus genome

Project description:To determine the genomic binding sites for the Aspergillus fumigatus transcription factor AtrR, we utilized three different strains. One was the wild-type AfS35 which contains a wild-type copy of atrR but lacks any HA tag. The other two are both derived from AfS35 but contain a 3X HA tag replacing the stop codon of atrR. These strains are SPF89 and SPF112, respectively. SPF89 uses the wild-type atrR promoter to drive expression of the epitope-tagged allele while SPF112 uses the much strong hspA promoter to drive production of the same protein.

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RNA-sequencing analysis of fluconazole-treated wild-type and upc2A null cells [Fluconazole]

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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.

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RNA-sequencing analysis of fluconazole-treated wild-type and upc2A null cells [Fluconazole]

Project description:RNA-sequencing analysis of fluconazole-treated wild-type and upc2A null cells [Fluconazole]

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2018-10-14 | E-MTAB-6926 | biostudies-arrayexpress

A defect in iron uptake enhances the susceptibility of Cryptococcus neoformans to azole antifungal drugs.

Project description:Transcriptome profiling of wild type and cfo1 mutant with fluconazole treatment in Cryptococcus neoformans var. grubii H99 Purpose: The goals of this study are to compare cfo1 mutant transcriptome profiling (RNA-seq) to wild-type with or without fluconazole treatment in Cryptococcus neoformans var. grubii H99. Methods: mRNA profiles of wild-type and cfo1 mutant with or without fluconazole treatment were generated by RNA-Seq, using Illumina GAIIx. The sequence reads that passed quality filters were mapped to reference genome and the normalized RPKM values were calculated by CLC Genomics Workbench. Results: Compared to wild-type, a number of genes were differentially expressed in the cfo1 mutant, especially genes involved in iron homeostasis and transport, ergosterol biosynthesis, mitochondrial function and respiration. Conclusions: Our data suggested reduced expression of the genes in the respiratory chain is the main reason for altered antifungal sensitivity of the cfo1 mutant. The results of our study revealed that iron uptake plays a key role in fluconazole sensitivity of C. neoformans.

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