Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Evolution of microRNA expression at the onset of drosophila metamorphosis by mRNA

ABSTRACT: We found two lines of evidence suggesting that miRNA abundance has been shaped by different evolutionary regimes at the two developmental stages attributed to functional constraints, which points to mechanisms more subtle and diverse than previously thought. 4 genotypes and 2 developmental states were investigated in this study, each with 3 biological replicates, so a total of 24 (4x2x3) hybridizations were conducted. Differential analysis between genotypes or sexes were analyzed.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Xiao-Qin Xia

PROVIDER: E-GEOD-55398 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Histone modifications have been shown to be crucial for secondary metabolism in various filamentous fungi. Here we studied the influence of histone acetylation on secondary metabolite production in the phytopathogenic fungus Fusarium fujikuroi, a known producer of several secondary metabolites including pigments and mycotoxins. Deletion of the classical HDACs FfHdF1, FfHdF2 and FfHdF3 indicated that FfHdF1 and FfHdF2 are major regulators of secondary metabolism, whereas FfHdF3 is involved in developmental processes but dispensable for secondary metabolite production in F. fujikuroi. Microarray analysis with the major HDAC FfHdF2 revealed differential regulation of several secondary metabolite gene clusters, subsequently verified by a combination of chemical and biological approaches. These results indicate that HDACs are responsible for gene silencing but also gene activation. Chromatin immunoprecipitation assays with M-NM-^TffhdF2 revealed significant alterations regarding the acetylation state in the landscape of secondary metabolite gene clusters thereby providing insights into the regulatory mechanism. In addition, the class I HDAC FfHdF1 also has major impact on secondary metabolism in F. fujikuroi. Furthermore, deletion of both ffhdF1 and ffhdF2 resulted in de-repression of secondary metabolites under normally repressing conditions. Thus, manipulation of HDAC encoding genes might provide a powerful tool for the activation of cryptic secondary metabolites. Investigation of whole genome gene expression of the Fusarium fujikuroi wild type IMI58289, M-NM-^TffhdF2 mutant under nitrogen starvation and nitrogen sufficient conditions. In this study we hybridized in total 12 microarrays using total RNA recovered from a wild-type culture of F. fujikuroi IMI58289 and M-NM-^TffhdF2 mutant culture. All cultures were grown on a 6 mM Gln (10%) and a 60 mM Gln medium (100%). For each combination of culture and medium a biological replicate was created. Each chip measures the expression level of 14,397 genes from F. fujikuroi IMI58289 with eight 60-mer probes.

Project description:The phytopathogenic fungus Fusarium fujikuroi is the causal agent of bakanae disease on rice due to its ability to produce gibberellins. Besides these phytohormones, F. fujikuroi is able to produce a wide range of other secondary metabolites (SMs), such as mycotoxins and pigments. Although much progress has been made in the field of secondary metabolism over the last years, the transcriptional regulation of SM biosynthetic genes is complex and far from being fully understood. Environmental conditions (e.g. nitrogen availability and pH), global and pathway-specific regulators as well as chromatin remodeling were shown to play major roles in this regulation. Here, the role of FfSge1, a homolog of the morphological switch regulators Wor1 and Ryp1 in Candida albicans and Histoplasma capsulatum, respectively, is explored with emphasis on secondary metabolism. FfSge1 is not required for conidia formation and pathogenicity, but is involved in vegetative growth. Genome-wide transcriptome analysis of the M-NM-^Tffsge1 deletion mutant compared to the wild type revealed that FfSge1 is a global regulator of secondary metabolism in F. fujikuroi that activates the expression of several SMs. In addition, FfSge1 is also required for expression of a yet uncharacterized SM gene cluster containing a noncanonical non-ribosomal peptide synthetase. Investigation of whole genome gene expression of the Fusarium fujikuroi wild type IMI58289, M-NM-^Tffsge1 mutant under nitrogen starvation and nitrogen sufficient conditions. In this study we hybridized in total 8 microarrays using total RNA recovered from a wild-type culture of F. fujikuroi IMI58289 and M-NM-^Tffsge1 mutant culture. All cultures were grown on a 6 mM Gln (10%) and a 60 mM Gln medium (100%). For each combination of culture and medium a biological replicate was created. Each chip measures the expression level of 14,397 genes from F. fujikuroi IMI58289 with eight 60-mer probes. Please note that the wild type samples have been published as part of the GEO accession GSE43745, but re-analyzed with the M-NM-^Tffsge1 mutant samples in the current study.

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Evolution of microRNA expression at the onset of drosophila metamorphosis by mRNA

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