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ChIP-Seq and RNA-Seq analysis of the iron regulatory transcription factors in Cryptococcus neoformans in response to iron availability

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Cryptococcus neoformans var. grubii H99

PROVIDER: GSE126314 | GEO | 2020/02/16

REPOSITORIES: GEO

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ChIP-Seq analysis of the iron regulatory transcription factors in Cryptococcus neoformans in response to iron availability

Project description:Purpose: Defining the regulatory role of the transcription factors, Cir1 and HapX, in C. neoformans. Methods: Chromatin immunoprecipitation followed by high-throughput sequencing was performed using chromatin immunoprecipitated DNA from the strains Cir1-Flag and HapX-Flag grown in low- and high-iron condition. Results: Cir1 and HapX bind to the promoter region of the genes involved in iron acquisition and metabolism in C. neoformans.

2020-02-16 | GSE126312 | GEO

Transcriptome analysis of the iron regulatory transcription factors in Cryptococcus neoformans in response to iron availability

Project description:Purpose: Understanding the iron-responsive regulatory networks in Cryptococcus neoformans. Methods: The transcriptome profiles of the wild-type, cir1 mutant and hapX mutant were generated by RNA-seq using Illumina Hiseq, in triplicate. The transcriptome profiles of each mutant was compared with that of the wild-type strain. Results: The iron-responsive transcription factors, Cir1 and HapX, are major regulators for iron acquisition and metabolism in C. neoformans.

2020-02-16 | GSE126313 | GEO

ChIP-Seq analysis of the iron regulatory transcription factors in Cryptococcus neoformans in response to iron availability

Project description:ChIP-Seq analysis of the iron regulatory transcription factors in Cryptococcus neoformans in response to iron availability

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ChIP-Seq and RNA-Seq analysis of the iron regulatory transcription factors in Cryptococcus neoformans in response to iron availability

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ChIP Seq analysis of the Cu metalloregulatory transcription factor Cuf1 in Cryptococcus neoformans in response to Cu availability

Project description:The essential yet toxic nature of Cu ions in living cells requires exquisite control of Cu homeostasis. The fungal pathogen C. neoformans regulates Cu homeostasis for survival during a complex host colonization process. During pulmonary infection host innate immune cells use Cu in an attempt to toxify C. neoformans, which responds by activating expression of Cu detoxifying proteins. However, during brain colonization expression of the fungal Cu import machinery is activated and required for virulence. To achieve the genetic plasticity required for adaptation to a continuum of distinct Cu environments within the host, C. neoformans utilizes the Cu-responsive transcription factor, Cuf1. Cuf1 is unique as it senses and responds to both high and low Cu environments, activating different sets of genes dependent on environmental Cu status. Cells lacking Cuf1 are compromised for colonization of the lungs and brain, highlighting Cuf1 as an important virulence factor. A genome-wide assessment of the Cuf1 binding sites in the genome of C. neoformans driven by Cu status identified novel genes required for adaptation to high and low Cu environments. These genes and their regulation provide new insights with respect to adaptive responses to changes in host Cu availability and could reveal new targets for therapeutic intervention in cryptococcosis.

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Reconstructing the maize leaf regulatory network using ChIP-seq data of 104 transcription factors.

Project description:The transcription regulatory network inside a eukaryotic cell is defined by the combinatorial actions of transcription factors (TFs). However, TF binding studies in plants are too few in number to produce a general picture of this complex network. In this study, we use large-scale ChIP-seq to reconstruct it in the maize leaf, and train machine-learning models to predict TF binding and co-localization. The resulting network covers 77% of the expressed genes, and shows a scale-free topology and functional modularity like a real-world network. TF binding sequence preferences are conserved within family, while co-binding could be key for their binding specificity. Cross-species comparison shows that core network nodes at the top of the transmission of information being more conserved than those at the bottom. This study reveals the complex and redundant nature of the plant transcription regulatory network, and sheds light on its architecture, organizing principle and evolutionary trajectory.

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The iron-responsive, GATA-type transcription factor Cir1 influences mating in Cryptococcus neoformans.

Project description:Mating and sexual development have been associated with virulence in various fungal pathogens including Cryptococcus neoformans. This fungus is a significant pathogen of humans because it causes life-threatening cryptococcal meningitis in immunocompromised people such as AIDS patients. The virulence of C. neoformans is known to be associated with the mating type of the cells (α or a), with the α mating type being predominant among clinical isolates. However, the mechanisms by which mating and sexual development are controlled by environmental conditions and their relationship with virulence require further investigation. Cir1 is a GATA-type transcription factor that regulates the expression of genes required for utilization of essential metals such as iron and copper, and also genes required for major virulence factors including the polysaccharide capsule and melanin. Here we investigated the role of Cir1 in the mating of C. neoformans. Our results demonstrate that mutants lacking CIR1 are defective in mating, and that Cir1 contributes to copper mediated enhancement of sexual filamentation. Furthermore, we found that Cir1 influences the expression of mating pheromone genes suggesting that this protein plays a role in the early phase of sexual development on V8 mating medium.

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