Transcriptomic profiling of Aspergillus flavus in response to 5-azacytidine

Lin, Jianqing; Zhao, Xixi; Zhi, Qing-Qing; Zhao, Ming; He, Zhu‐Mei

doi:10.1016/j.fgb.2013.04.007

Cited by 71 publications

(90 citation statements)

References 49 publications

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“…Our study is part of an emerging research trend that applies the use of Next Generation Sequencing tools to the study of many relevant pathogenic fungi [75–77] with the aim of deepening the knowledge of the gene expressions that underlie their pathogenicity. Together with the work published in [27] and by Robertson et al .…”

Section: Resultsmentioning

confidence: 99%

From Glacier to Sauna: RNA-Seq of the Human Pathogen Black Fungus Exophiala dermatitidis under Varying Temperature Conditions Exhibits Common and Novel Fungal Response

et al. 2015

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Exophiala dermatitidis (Wangiella dermatitidis) belongs to the group of the so-called black yeasts. Thanks in part to its thick and strongly melanized cell walls, E. dermatitidis is extremely tolerant to various kinds of stress, including extreme pH, temperature and desiccation. E. dermatitidis is also the agent responsible for various severe illnesses in humans, such as pneumonia and keratitis, and might lead to fatal brain infections. Due to its association with the human environment, its poly-extremophilic lifestyle and its pathogenicity in humans, E. dermatitidis has become an important model organism. In this study we present the functional analysis of the transcriptional response of the fungus at 1°C and 45°C, in comparison with that at 37°C, for two different exposition times, i.e. 1 hour and 1 week. At 1°C, E. dermatitidis uses a large repertoire of tools to acclimatize, such as lipid membrane fluidization, trehalose production or cytoskeleton rearrangement, which allows the fungus to remain metabolically active. At 45°C, the fungus drifts into a replicative state and increases the activity of the Golgi apparatus. As a novel finding, our study provides evidence that, apart from the protein coding genes, non-coding RNAs, circular RNAs as well as fusion-transcripts are differentially regulated and that the function of the fusion-transcripts can be related to the corresponding temperature condition. This work establishes that E. dermatitidis adapts to its environment by modulating coding and non-coding gene transcription levels and through the regulation of chimeric and circular RNAs.

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Section: Resultsmentioning

confidence: 99%

From Glacier to Sauna: RNA-Seq of the Human Pathogen Black Fungus Exophiala dermatitidis under Varying Temperature Conditions Exhibits Common and Novel Fungal Response

et al. 2015

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“…In both N. crassa and A. immersus , DNA methylation could be reverted to varying extents by treatment with 5-azacytidine (5-aza) and other cytosine analogues [19–21]. Curiously, even in filamentous fungi lacking DNA methylation, such as Aspergillus spp., 5-aza has been shown to induce a mycelial phenotype modification, characterized by overgrowing and dispersed hyphae, designated as “fluffy” ([22,23] and references therein).…”

Section: Introductionmentioning

confidence: 99%

Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content

et al. 2014

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BackgroundWe investigated how an extremely transposon element (TE)-rich organism such as the plant-symbiotic ascomycete truffle Tuber melanosporum exploits DNA methylation to cope with the more than 45,000 repeated elements that populate its genome.ResultsWhole-genome bisulfite sequencing performed on different developmental stages reveals a high fraction of methylated cytosines with a strong preference for CpG sites. The methylation pattern is highly similar among samples and selectively targets TEs rather than genes. A marked trend toward hypomethylation is observed for TEs located within a 1 kb distance from expressed genes, rather than segregated in TE-rich regions of the genome. Approximately 300 hypomethylated or unmethylated TEs are transcriptionally active, with higher expression levels in free-living mycelium compared to fruitbody. Indeed, multiple TE-enriched, copy number variant regions bearing a significant fraction of hypomethylated and expressed TEs are found almost exclusively in free-living mycelium. A reduction of DNA methylation, restricted to non-CpG sites and accompanied by an increase in TE expression, is observed upon treatment of free-living mycelia with 5-azacytidine.ConclusionsEvidence derived from analysis of the T. melanosporum methylome indicates that a non-exhaustive, partly reversible, methylation process operates in truffles. This allows for the existence of hypomethylated, transcriptionally active TEs that are associated with copy number variant regions of the genome. Non-exhaustive TE methylation may reflect a role of active TEs in promoting genome plasticity and the ability to adapt to sudden environmental changes.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-014-0411-5) contains supplementary material, which is available to authorized users.

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“…In both N. crassa and A. immersus, DNA methylation could be reverted to varying extents by treatment with 5-azacytidine (5-aza) and other cytosine analogues [19][20][21]. Curiously, even in filamentous fungi lacking DNA methylation, such as Aspergillus spp., 5-aza has been shown to induce a mycelial phenotype modification, characterized by overgrowing and dispersed hyphae, designated as "fluffy" ( [22,23] and references therein).…”

mentioning

confidence: 99%

Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content

et al. 2014

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Transcriptomic profiling of Aspergillus flavus in response to 5-azacytidine

Cited by 71 publications

References 49 publications

From Glacier to Sauna: RNA-Seq of the Human Pathogen Black Fungus Exophiala dermatitidis under Varying Temperature Conditions Exhibits Common and Novel Fungal Response

From Glacier to Sauna: RNA-Seq of the Human Pathogen Black Fungus Exophiala dermatitidis under Varying Temperature Conditions Exhibits Common and Novel Fungal Response

Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content

Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content

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