Species-specific gene regulatory network rewiring mediated by the GATA-type regulator NsdD in Aspergillus [Ani_NsdD_ChIP_seq]
Ontology highlight
ABSTRACT:
ORGANISM(S): Aspergillus nidulans
PROVIDER: GSE219139 | GEO | 2025/05/29
REPOSITORIES: GEO
Similar Datasets
Project description:Multifunctional TFs are central in coordinating development and metabolism in filamentous fungi. In this study, we systematically dissect the regulatory functions of NsdD, a highly conserved GATA-type TF in Pezizomycotina, using network-based multi-omics approaches in two distantly related species, A. nidulans and A. flavus. Our analyses reveal that NsdD governs fungal development and metabolism through species-specific GRNs, directly targeting key upstream regulators and genes involved in core cellular processes. These regulatory distinctions underlie the morphological and metabolic differences observed between the two species. Notably, our cross-species comparison uncovers extensive GRN rewiring, demonstrating how evolutionary divergence can reshape transcriptional networks even under conserved regulatory control. The resulting GRN maps offer a valuable framework for understanding gene regulation in Aspergillus and provide a foundation for broader studies on the evolution of transcriptional networks and conserved regulatory factors in filamentous fungi.
2025-05-29 | GSE219138 | GEO
Project description:Multifunctional TFs are central in coordinating development and metabolism in filamentous fungi. In this study, we systematically dissect the regulatory functions of NsdD, a highly conserved GATA-type TF in Pezizomycotina, using network-based multi-omics approaches in two distantly related species, A. nidulans and A. flavus. Our analyses reveal that NsdD governs fungal development and metabolism through species-specific GRNs, directly targeting key upstream regulators and genes involved in core cellular processes. These regulatory distinctions underlie the morphological and metabolic differences observed between the two species. Notably, our cross-species comparison uncovers extensive GRN rewiring, demonstrating how evolutionary divergence can reshape transcriptional networks even under conserved regulatory control. The resulting GRN maps offer a valuable framework for understanding gene regulation in Aspergillus and provide a foundation for broader studies on the evolution of transcriptional networks and conserved regulatory factors in filamentous fungi.
2025-05-29 | GSE219137 | GEO
Project description:Multifunctional TFs are central in coordinating development and metabolism in filamentous fungi. In this study, we systematically dissect the regulatory functions of NsdD, a highly conserved GATA-type TF in Pezizomycotina, using network-based multi-omics approaches in two distantly related species, A. nidulans and A. flavus. Our analyses reveal that NsdD governs fungal development and metabolism through species-specific GRNs, directly targeting key upstream regulators and genes involved in core cellular processes. These regulatory distinctions underlie the morphological and metabolic differences observed between the two species. Notably, our cross-species comparison uncovers extensive GRN rewiring, demonstrating how evolutionary divergence can reshape transcriptional networks even under conserved regulatory control. The resulting GRN maps offer a valuable framework for understanding gene regulation in Aspergillus and provide a foundation for broader studies on the evolution of transcriptional networks and conserved regulatory factors in filamentous fungi.
2025-05-29 | GSE219140 | GEO
Project description:Asexual development is fundamental to the ecology and lifestyle of filamentous fungi and can facilitate both plant and human infection. In the filamentous fungal genus Aspergillus, the production of asexual spores is primarily governed by the BrlA-AbaA-WetA central regulatory cascade. The final step in this cascade, which is controlled by the WetA protein, not only governs cellular development (i.e., the morphological differentiation of spores) but also ensures its coupling with chemical development (i.e., the coordinated production and deposition of diverse secondary metabolites, such as aflatoxins, into spores). While the wetA gene is conserved across the genus Aspergillus, the structure and degree of conservation of the BrlA-AbaA-WetA regulatory cascade and the broader wetA gene regulatory network (GRN) remain largely unknown. We carried out comparative transcriptome analyses between wetA null mutant and wild type (WT) asexual spores in three representative species spanning the diversity of the genus Aspergillus: the genetic model A. nidulans, the agricultural pest A. flavus, and the human pathogen A. fumigatus. We discovered that WetA regulates asexual sporulation in all three species via a negative feedback loop that represses BrlA, the cascade’s first step. Furthermore, ChIP-seq experiments in A. nidulans asexual spores suggest that WetA is a DNA-binding protein that interacts with a novel regulatory element, which we term the WetA Response Element (WRE). Interestingly, the WRE is found completely conserved in the non-coding region upstream of the wetA translation start site of many diverse Aspergillus genomes. In contrast, several global transcriptional regulators, most notably those in the velvet complex (veA, velB, and laeA) known to regulate the coupling between asexual development and production of secondary metabolites, show species-specific regulatory patterns. These results suggest that the BrlA-AbaA-WetA cascade’s regulatory role in cellular and chemical development of asexual spores is functionally conserved, but that the WetA-associated GRN has diverged during Aspergillus evolution. This entry is for the ChIP-seq data.
2018-07-24 | GSE114141 | GEO
Project description:Asexual development is fundamental to the ecology and lifestyle of filamentous fungi and can facilitate both plant and human infection. In the filamentous fungal genus Aspergillus, the production of asexual spores is primarily governed by the BrlA-AbaA-WetA central regulatory cascade. The final step in this cascade, which is controlled by the WetA protein, not only governs cellular development (i.e., the morphological differentiation of spores) but also ensures its coupling with chemical development (i.e., the coordinated production and deposition of diverse secondary metabolites, such as aflatoxins, into spores). While the wetA gene is conserved across the genus Aspergillus, the structure and degree of conservation of the BrlA-AbaA-WetA regulatory cascade and the broader wetA gene regulatory network (GRN) remain largely unknown. We carried out comparative transcriptome analyses between wetA null mutant and wild type (WT) asexual spores in three representative species spanning the diversity of the genus Aspergillus: the genetic model A. nidulans, the agricultural pest A. flavus, and the human pathogen A. fumigatus. We discovered that WetA regulates asexual sporulation in all three species via a negative feedback loop that represses BrlA, the cascade’s first step. Furthermore, ChIP-seq experiments in A. nidulans asexual spores suggest that WetA is a DNA-binding protein that interacts with a novel regulatory element, which we term the WetA Response Element (WRE). Interestingly, the WRE is found completely conserved in the non-coding region upstream of the wetA translation start site of many diverse Aspergillus genomes. In contrast, several global transcriptional regulators, most notably those in the velvet complex (veA, velB, and laeA) known to regulate the coupling between asexual development and production of secondary metabolites, show species-specific regulatory patterns. These results suggest that the BrlA-AbaA-WetA cascade’s regulatory role in cellular and chemical development of asexual spores is functionally conserved, but that the WetA-associated GRN has diverged during Aspergillus evolution. This entry is for the RNA-seq data.
2018-07-24 | GSE114143 | GEO
Project description:Abstract BACKGROUND: Mating-type loci in yeasts and ascomycotan filamentous fungi (Pezizomycotina) encode master transcriptional factors that play a critical role in sexual development. Genome-wide analyses of mating-type-specification circuits and mating-type target genes are available in Saccharomyces cerevisiae and Schizosaccharomyces pombe; however, no such analyses have been performed in heterothallic (self-incompatible) Pezizomycotina. The heterothallic fungus Podospora anserina serves as a model for understanding the basic features of mating-type control. Its mat+ and mat- mating types are determined by dissimilar allelic sequences. The mat- sequence contains three genes, designated FMR1, SMR1 and SMR2, while the mat+ sequence contains one gene, FPR1. FMR1 and FPR1 are the major regulators of fertilization, and this study presents a genome-wide view of their target genes and analyzes their target gene regulation. METHODOLOGY/PRINCIPAL FINDINGS: The transcriptomic profiles of the mat+ and mat- strains revealed 157 differentially transcribed genes, and transcriptomic analysis of fmr1(-) and fpr1(-) mutant strains was used to determine the regulatory actions exerted by FMR1 and FPR1 on these differentially transcribed genes. All possible combinations of transcription repression and/or activation by FMR1 and/or FPR1 were observed. Furthermore, 10 additional mating-type target genes were identified that were up- or down-regulated to the same level in mat+ and mat- strains. Of the 167 genes identified, 32 genes were selected for deletion, which resulted in the identification of two genes essential for the sexual cycle. Interspecies comparisons of mating-type target genes revealed significant numbers of orthologous pairs, although transcriptional profiles were not conserved between species. CONCLUSIONS/SIGNIFICANCE: This study represents the first comprehensive genome-wide analysis of mating-type direct and indirect target genes in a heterothallic filamentous fungus. Mating-type transcription factors have many more target genes than are found in yeasts and exert a much greater diversity of regulatory actions on target genes, most of which are not directly related to mating. With GPL10116 : 4 conditions each with four biological replicates :mat+, mat-, fpr1-, fmr1-; common reference is a pool of four conditions M48h, M96h, C48h and C96h ; Conditions are labelled in Cy3 and the common reference in Cy5
2011-12-22 | E-GEOD-27297 | biostudies-arrayexpress
Project description:Aflatoxins are toxic and carcinogenic secondary metabolites produced by the fungi Aspergillus flavus and A. parasiticus. In order to better understand the molecular mechanisms that regulate aflatoxin production, the biosynthesis of the toxin in A. flavus and A. parasticus grown in yeast extract sucrose media supplemented with 50 mM tryptophan (Trp) were examined. A. flavus grown in the presence of 50 mM tryptophan was found to have significantly reduced aflatoxin B1 and B2 biosynthesis, while A. parasiticus cultures had significantly increased B1 and G1 biosynthesis. Microarray analysis of RNA extracted from fungi grown under these conditions revealed seventy seven genes that are expressed significantly different between A. flavus and A. parasiticus, including the aflatoxin biosynthetic genes aflD (nor-1), aflE (norA), and aflO (omtB). It is clear that the regulatory mechanisms of aflatoxin biosynthesis in response to Trp in A. flavus and A. parasiticus are different. These candidate genes may serve as regulatory factors of aflatoxin biosynthesis. Keywords: Aflatoxin, Aspergillus, flavus, Amnio Acids, Tryptophan
2007-06-07 | GSE6182 | GEO
Project description:Abstract BACKGROUND: Mating-type loci in yeasts and ascomycotan filamentous fungi (Pezizomycotina) encode master transcriptional factors that play a critical role in sexual development. Genome-wide analyses of mating-type-specification circuits and mating-type target genes are available in Saccharomyces cerevisiae and Schizosaccharomyces pombe; however, no such analyses have been performed in heterothallic (self-incompatible) Pezizomycotina. The heterothallic fungus Podospora anserina serves as a model for understanding the basic features of mating-type control. Its mat+ and mat- mating types are determined by dissimilar allelic sequences. The mat- sequence contains three genes, designated FMR1, SMR1 and SMR2, while the mat+ sequence contains one gene, FPR1. FMR1 and FPR1 are the major regulators of fertilization, and this study presents a genome-wide view of their target genes and analyzes their target gene regulation. METHODOLOGY/PRINCIPAL FINDINGS: The transcriptomic profiles of the mat+ and mat- strains revealed 157 differentially transcribed genes, and transcriptomic analysis of fmr1(-) and fpr1(-) mutant strains was used to determine the regulatory actions exerted by FMR1 and FPR1 on these differentially transcribed genes. All possible combinations of transcription repression and/or activation by FMR1 and/or FPR1 were observed. Furthermore, 10 additional mating-type target genes were identified that were up- or down-regulated to the same level in mat+ and mat- strains. Of the 167 genes identified, 32 genes were selected for deletion, which resulted in the identification of two genes essential for the sexual cycle. Interspecies comparisons of mating-type target genes revealed significant numbers of orthologous pairs, although transcriptional profiles were not conserved between species. CONCLUSIONS/SIGNIFICANCE: This study represents the first comprehensive genome-wide analysis of mating-type direct and indirect target genes in a heterothallic filamentous fungus. Mating-type transcription factors have many more target genes than are found in yeasts and exert a much greater diversity of regulatory actions on target genes, most of which are not directly related to mating.
2011-12-22 | GSE27297 | GEO
Project description:DNA methylation is an important epigenetic modification widespread in eukaryotes and bacteria. However, genomic methylation levels show a dramatic diversity throughout the evolution of life, varying even between closely-related species and strains. In Aspergillus, a genus of filamentous fungi, the existence of DNA methylation has been controversial with previous studies reporting different conclusions using different species and detection methods. Here, we report DNA methylation analysis of Aspergillus oryzae, an important species in the Japanese fermentation industry, and a close relative of the pathogen Aspergillus flavus whose DNA methylation has been denied by the recent previous study using bisulfite sequencing. In this study, we conduct bisulfite-seq and RNA-seq of A. oryzae using three biological replicates from each of liquid and solid culture conditions. The statistical analysis of these data reveals thousands of highly-confident methylated cytosines (mCs), while the re-analysis of data from A. flavus detects few mCs being consistent with the previous study. Based on the comparative genome analysis of A. oryzae and A. flavus, we find that a substantial fraction of mCs are observed in syntenic segments including the aflatoxin biosynthesis gene cluster. Together, our results are the first evidence of DNA methylation in A. oryzae, providing a new example of the evolutionary diversity of DNA methylation as well as a new insight into its industrial applications.
2025-04-01 | GSE130260 | GEO
Project description:DNA methylation is an important epigenetic modification widespread in eukaryotes and bacteria. However, genomic methylation levels show a dramatic diversity throughout the evolution of life, varying even between closely-related species and strains. In Aspergillus, a genus of filamentous fungi, the existence of DNA methylation has been controversial with previous studies reporting different conclusions using different species and detection methods. Here, we report DNA methylation analysis of Aspergillus oryzae, an important species in the Japanese fermentation industry, and a close relative of the pathogen Aspergillus flavus whose DNA methylation has been denied by the recent previous study using bisulfite sequencing. In this study, we conduct bisulfite-seq and RNA-seq of A. oryzae using three biological replicates from each of liquid and solid culture conditions. The statistical analysis of these data reveals thousands of highly-confident methylated cytosines (mCs), while the re-analysis of data from A. flavus detects few mCs being consistent with the previous study. Based on the comparative genome analysis of A. oryzae and A. flavus, we find that a substantial fraction of mCs are observed in syntenic segments including the aflatoxin biosynthesis gene cluster. Together, our results are the first evidence of DNA methylation in A. oryzae, providing a new example of the evolutionary diversity of DNA methylation as well as a new insight into its industrial applications.
2025-04-01 | GSE130259 | GEO