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Genome-wide analysis of a transcriptional network of the Sterol Regulatory Element Binding Protein, Sre1, in the human fungal pathogen Cryptococcus neoformans (ChIP-seq)

ABSTRACT: Purpose: Defining the regulatory role of the transcription factor Sre1 in C. neoformans. Methods: Chromatin immunoprecipitation followed by high-throughput sequencing was performed using chromatin immunoprecipitated DNA from the strain Flag-Sre1 grown in low- and high-iron media under normoxia and hypoxia condition. Results: Sre1 directly bind to the promoter region of the genes involved in ergosterol biosynthetic pathway and iron acquisition in C. neoformans.

ORGANISM(S): Cryptococcus neoformans var. grubii H99

PROVIDER: GSE135038 | GEO | 2020/09/01

REPOSITORIES: GEO

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Project description:Regulation of iron acquisition genes is critical for microbial survival under both iron-limiting conditions (to acquire essential iron) and iron-replete conditions (to limit iron toxicity). In fungi, iron acquisition genes are repressed under iron-replete conditions by a conserved GATA transcriptional regulator. Here we investigate the role of this transcription factor, Sre1, in the cellular responses of the fungal pathogen Histoplasma capsulatum to iron. We showed that cells in which SRE1 levels were diminished by RNA interference were unable to repress siderophore biosynthesis and utilization genes in the presence of abundant iron, and thus produced siderophores even under iron-replete conditions. Mutation of a GATA-containing consensus site found in the promoters of these genes also resulted in inappropriate gene expression under iron-replete conditions. Microarray analysis comparing control and SRE1-depleted strains under conditions of iron limitation or abundance revealed both iron-responsive genes and Sre1-dependent genes, which comprised distinct but overlapping sets. Iron-responsive genes included putative oxidoreductases, metabolic and mitochondrial enzymes, superoxide dismutase, and nitrosative-stress response genes; Sre1-dependent genes were of diverse function. Genes regulated by iron levels and Sre1 included all of the siderophore biosynthetic genes, a gene involved in reductive iron acquisition, an iron-responsive transcription factor, and two catalases. Based on transcriptional profiling and phenotypic analyses, we conclude that Sre1 plays a critical role in the regulation of both traditional iron-responsive genes and iron-independent pathways such as regulation of cell morphology. These data highlight the evolving realization that the effect of Sre1 orthologs on fungal biology extends beyond the iron regulon. For microarray studies, initial cultures of HcLH120 (Control RNAi-1) or 123 (SRE1 RNAi-2) yeast cells were grown in 5 mL HMM, and then passaged 1:25 into 100 mL HMM. After 2 days of growth, the cultures were pelleted, washed in 100 mL of PBS, resuspended in 100 mL of mRPMI pH 6.5 and diluted to an OD600~2 in 1 L of mRPMI. After 24 hours of growth, 200 mL of culture was harvested for each of the three zero time points. Then the cultures were split into 2 X 400 mL, and 10 uM FeSO4 (final concentration) was added to one set of cultures. At each time point (.5, 1, 4, or 8 hours), 100 mL of culture was harvested for RNA extraction.

Dataset Information

Genome-wide analysis of a transcriptional network of the Sterol Regulatory Element Binding Protein, Sre1, in the human fungal pathogen Cryptococcus neoformans (ChIP-seq)

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