Mating-type specific gene expression in the filamentous ascomycete Neurospora tetrasperma
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ABSTRACT:
ORGANISM(S): Neurospora crassa Neurospora tetrasperma
PROVIDER: GSE26798 | GEO | 2011/01/26
SECONDARY ACCESSION(S): PRJNA136275
REPOSITORIES: GEO
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Project description:Neurospora tetrasperma is a pseudohomothallic filamentous ascomycete with a large (~ 7 Mbp) region of suppressed recombination surrounding its mating-type (mat) locus. The suppressed recombination has lead to sequence divergence between the two mating-type chromosomes of wild-type heterokaryotic strains, while the remaining genome is largely homoallelic. In this study, we use microarray technology to manifest expression divergence linked to mating type in N. tetrasperma. N. tetrasperma and N. crassa, were grown on agar regimes inducing sexual growth (Synthetic Crossing medium) and vegetative growth (Vogel's Medium), respectively. [SC]: Neurospora tetrasperma mat-A FGSC#1270; mat-a FGSC#1271; Mat-A FGSC#9033; mat-a FGSC#9034; N. crassa mat-A FGSC#2489 and mat-a FGSC 4200: Synthetic Crossing medium was used as a nutrient regime before sampling and processing [Veg]: Neurospora tetrasperma mat-A FGSC#1270; mat-a FGSC#1271; Mat-A FGSC#9033; mat-a FGSC#9034; N. crassa mat-A FGSC#2489 and mat-a FGSC 4200: Vogel's Medium (Vegetative Medium) was used as a nutrient regime before sampling and processing
2011-01-26 | E-GEOD-26798 | biostudies-arrayexpress
Project description:Mating-type specific gene expression in the filamentous ascomycete Neurospora tetrasperma
| PRJNA136275 | ENA
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:Neurospora intermedia is a heterothallic filamentous ascomycete. In this study we use microarray technology to study the difference in gene expression between vegetative growth and early reproductive development. Neurospora intermedia FGSC#8882 mat-A and FGSC#8782 mat-a. Solid synthetic crossing medium (SCM) was used as a nutrient regime before sampling and processing. Two different conditions were sampled: vegetative mycelial tissue and young reproductive mycelial tissue.
2012-04-04 | E-GEOD-37034 | biostudies-arrayexpress
Project description:Yeast chromosome III contains the mating type loci that provide a paradigm for long-range interactions between distant loci. Yeast switch mating type by gene conversion between the MAT locus and either of two silent loci (HML or HMR) on opposite ends of the chromosome. This long-range process is mating type-specific so that MATa cells choose HML as template, while MATα cells use HMR. The Recombination Enhancer (RE), located on the left arm regulates this process. One long-standing hypothesis is that switching is guided by mating type-specific, and possibly RE-dependent three-dimensional folding of chromosome III. Here we used Hi-C, 5C, and live cell imaging to characterize the conformation of chromosome III in both mating types in non-switching strains. We discovered a mating type-specific difference in the folding of the left arm: in MATa cells the left arm is located closely to the centromere-proximal portion of the chromosome as well as to MAT, whereas it is more extended away in MATα cells. Deletion analysis showed that a 1 kb subregion within the RE, which is not necessary during switching, abolished mating type-dependent chromosome folding. In this mutant the conformation of chromosome III is the same in both mating types, but distinct from the wild type MATa or MATα conformations, indicating that the RE induces conformational changes in both mating types. The RE is therefore a composite element with one subregion essential for selecting the appropriate donor during switching, and a separate region involved in modulating chromosome conformation prior to switching.
2015-11-20 | GSE73890 | 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:we identified a cytochrome c-peroxidase encoding gene SsCCP1 that is essential for oxidative stress resistance. We further found that absence of SsCcp1 leads to defects in mating/filamentation and imbalance of intracellular ROS homeostasis. To further elucidate the effect of SsCcp1 on intracellular ROS homeostasis, we performed comparative transcriptome analysis with the ssccp1Δ-1 and the wild-type MAT-1 sporidia grown in YePSA medium.
2023-08-19 | GSE240666 | GEO
Project description:Yeast chromosome III contains the mating type loci that provide a paradigm for long-range interactions between distant loci. Yeast switch mating type by gene conversion between the MAT locus and either of two silent loci (HML or HMR) on opposite ends of the chromosome. This long-range process is mating type-specific so that MATa cells choose HML as template, while MATα cells use HMR. The Recombination Enhancer (RE), located on the left arm regulates this process. One long-standing hypothesis is that switching is guided by mating type-specific, and possibly RE-dependent three-dimensional folding of chromosome III. Here we used Hi-C, 5C, and live cell imaging to characterize the conformation of chromosome III in both mating types in non-switching strains. We discovered a mating type-specific difference in the folding of the left arm: in MATa cells the left arm is located closely to the centromere-proximal portion of the chromosome as well as to MAT, whereas it is more extended away in MATα cells. Deletion analysis showed that a 1 kb subregion within the RE, which is not necessary during switching, abolished mating type-dependent chromosome folding. In this mutant the conformation of chromosome III is the same in both mating types, but distinct from the wild type MATa or MATα conformations, indicating that the RE induces conformational changes in both mating types. The RE is therefore a composite element with one subregion essential for selecting the appropriate donor during switching, and a separate region involved in modulating chromosome conformation prior to switching. This submission contain 2 biological replicates of Hi-C experiments done in MATa and MATalpha cells in Saccharamycese cerevisiae. It also contains 3 biological replicates of 13 5C experiments in various mutants in MATa and MATalpha cells.
2015-11-20 | E-GEOD-73890 | biostudies-arrayexpress
Project description:Species within the human pathogenic Cryptococcus species complex are major threats to public health, causing about one million infections globally each year. Cryptococcus amylolentus is the most closely known related species of the pathogenic Cryptococcus species complex, and it is non-pathogenic. Additionally, while pathogenic Cryptococcus species have bipolar mating systems with a single large MAT locus that represents a derived state in Basidiomycetes, C. amylolentus has a tetrapolar mating system with two MAT loci (P/R and HD) located on different chromosomes. Thus, studying C. amylolentus will shed light on the origin and evolution of pathogenesis, as well as the transition from tetrapolar to bipolar mating systems in the pathogenic Cryptococcus species. In this study, we sequenced, assembled, and annotated the genomes of two C. amylolentus isolates, CBS6039 and CBS6273, which are sexual and interfertile. Genome comparison between the two C. amylolentus isolates identified the boundaries and the complete gene contents of the P/R and HD MAT loci. Also, bioinformatics and ChIP-seq analyses showed that C. amylolentus has regional centromeres that are enriched with species-specific transposable and repetitive elements, similar to the centromeric structures in the pathogenic Cryptococcus species. Additionally, we found that while neither of the P/R and HD loci in C. amylolentus is physically linked to its centromere, both MAT loci exhibit centromere linkage in meiosis, suggesting the presence of recombinational suppressors and/or epistatic gene interactions in the inter MAT-CEN regions. Furthermore, genomic comparison between C. amylolentus and pathogenic Cryptococcus species provides evidence that chromosomal rearrangements mediated by intercentromeric recombination have occurred after the two lineages split from their common ancestor. We propose a model in which the evolution of the bipolar mating system was initiated by an ectopic recombination event mediated by repetitive elements located within the centromeric regions and shared between chromosomes. This translocation brought the P/R and HD loci onto the same chromosome, and was followed by chromosomal rearrangements that resulted in the two MAT loci becoming physically linked and eventually fused to form the single contiguous MAT locus that is now extant in the pathogenic Cryptococcus species.
2018-04-08 | GSE95128 | GEO
Project description:It is widely assumed that sex-determination loci have little impact upon dominant stage in the life history of filamentous fungi, asexual development. However, this hypothesis has not been thoroughly investigated. To investigate differences between mating types during asexual development, total RNA was sampled from otherwise largely isogenic Mat-A and Mat-a N. crassa strains at early, middle, and late clonal stages of development under a condition of constant light. Mating-type loci, pheromone precursor and receptor genes were assayed with real-time PCR. Mating loci were increasingly expressed during asexual development, and expression of pheromone precursors ccg-4 and mfa-1 and receptors pre-1 and pre-2 were detected in both mating types in all development stages. A circuit of microarray hybridizations of cDNA samples from all developmental stages was also performed. Gene expression for both mating types throughout vegetative development were characterized for developmental markers such as transcription factors, for genes related to conidiation, internal clock, cell division cycle, heat shock, and for light responsive genes. We observed significant differences in overall gene expression between the mating types across clonal development, especially at late development stages. The Mat-A genotype showed a higher expression level than Mat-a for many genes, and demonstrated greater transcriptional regulatory activity. Significant up-regulation of expression was observed for many late light responsive genes at late asexual development stages in both mating types. Further investigation of the impact of light and the roles of light response genes in asexual development in this fungus are warranted. Neurospora crassa mat A FGSC#2489 and mat-a FGSC 4200: Three developmental stages, 36hr, 60hr, 96 hr were sampled and compared
2011-06-06 | E-GEOD-26209 | biostudies-arrayexpress