Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1208920 | ENA |
REPOSITORIES: ENA
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Project description:In spite of many reports on the toxicity of silver nanoparticles (AgNPs), the mechanisms underlying the toxicity are far from clear. The present study conducted transcriptome and microRNAome sequencing for Euplotes vannus to understand the molecular mechanisms by which this protist copes with AgNPs exposure. By transcriptome profiling, 1884 and 5834 differentially expressed genes (DEGs) were identified after one hour and 12 hours exposure to 15 mg/L AgNPs, respectively. From microRNAsome profiling, totally 16 differentially expressed microRNAs were identified under AgNPs stress.In spite of many reports on the toxicity of silver nanoparticles (AgNPs), the mechanisms underlying the toxicity are far from clear. The present study conducted transcriptome and microRNAome sequencing for Euplotes vannus to understand the molecular mechanisms by which this protist copes with AgNPs exposure. By transcriptome profiling, 1884 and 5834 differentially expressed genes (DEGs) were identified after one hour and 12 hours exposure to 15 mg/L AgNPs, respectively. The DEGs were significantly enriched in macropinocytosis and phagocytic vesicles suggesting that the uptake of AgNPs may be mediated by endocytic pathways, while the differential expression of ABC transporters and copper-transporting ATPase implicates active efflux transport of Ag. Several DNA repair pathways were also significantly enriched with differentially expressed cell cycle control genes implying that exposure to AgNPs might have caused DNA damage and G2/M cell cycle arrest. The damage might have resulted from increased ROS production, as evidenced by elevated expression of several antioxidants genes to combat oxidative stress. From microRNAsome profiling, totally 16 differentially expressed microRNAs were identified under AgNPs stress. Integrated analysis of the microRNA and mRNA expression profiles found that the differentially expressed microRNAs target a series of genes involved in many important biological processes, suggesting that E. vannus exposure elicited a broad post-transcriptional regulatory mechanism through microRNAs–mRNAs–biological functions network to cope with the toxicity of AgNPs.
2019-08-10 | GSE118417 | GEO
Project description:In spite of many reports on the toxicity of silver nanoparticles (AgNPs), the mechanisms underlying the toxicity are far from clear. The present study conducted transcriptome and microRNAome sequencing for Euplotes vannus to understand the molecular mechanisms by which this protist copes with AgNPs exposure. By transcriptome profiling, 1884 and 5834 differentially expressed genes (DEGs) were identified after one hour and 12 hours exposure to 15 mg/L AgNPs, respectively. From microRNAsome profiling, totally 16 differentially expressed microRNAs were identified under AgNPs stress.In spite of many reports on the toxicity of silver nanoparticles (AgNPs), the mechanisms underlying the toxicity are far from clear. The present study conducted transcriptome and microRNAome sequencing for Euplotes vannus to understand the molecular mechanisms by which this protist copes with AgNPs exposure. By transcriptome profiling, 1884 and 5834 differentially expressed genes (DEGs) were identified after one hour and 12 hours exposure to 15 mg/L AgNPs, respectively. The DEGs were significantly enriched in macropinocytosis and phagocytic vesicles suggesting that the uptake of AgNPs may be mediated by endocytic pathways, while the differential expression of ABC transporters and copper-transporting ATPase implicates active efflux transport of Ag. Several DNA repair pathways were also significantly enriched with differentially expressed cell cycle control genes implying that exposure to AgNPs might have caused DNA damage and G2/M cell cycle arrest. The damage might have resulted from increased ROS production, as evidenced by elevated expression of several antioxidants genes to combat oxidative stress. From microRNAsome profiling, totally 16 differentially expressed microRNAs were identified under AgNPs stress. Integrated analysis of the microRNA and mRNA expression profiles found that the differentially expressed microRNAs target a series of genes involved in many important biological processes, suggesting that E. vannus exposure elicited a broad post-transcriptional regulatory mechanism through microRNAs–mRNAs–biological functions network to cope with the toxicity of AgNPs.
2019-08-10 | GSE118415 | GEO
Project description:Euplotes vannus and Strombidium sulcatum Raw sequence reads
| PRJNA593678 | ENA
Project description:Euplotes woodruffi strain:Iz01 MIC Genome sequencing and assembly
| PRJNA694926 | ENA
Project description:Ciliates undergo developmentally programmed genome elimination, in which small RNAs direct the removal of target DNA segments, including transposable elements. At each sexual generation, the development of the macronucleus (MAC) requires massive and reproducible elimination of a large proportion of the germline micronuclear (MIC) genome, leading to a highly streamlined somatic MAC genome. 25-nt long scnRNAs are produced from the entire germline MIC genome during meiosis, and this initial complex small RNA population is then transported to the maternal MAC, where selection of scnRNAs corresponding to germline (MIC)-specific sequences is thought to take place. Selected scnRNAs, loaded onto the PIWI protein Ptiwi09, guide the deposition of histone H3 post-translational modifications (H3K9me3 and H3K27me3) onto transposable elements in the developing macronucleus, ultimately triggering their specific elimination. How germline-specific MIC scnRNAs are selected remains to be determined. Here, we provide important mechanistic insights into the scnRNA selection pathway by identifying a Paramecium homolog of Gametocyte specific factor 1 (Gtsf1) as essential for the selective degradation of scnRNAs corresponding to retained somatic MAC sequences. Consistently, we also show that Gstf1 is exclusively localized in the maternal macronucleus, where scnRNA selection is presumed to occur, and associates with the scnRNA-binding protein Ptiwi09. Furthermore, Gtsf1 is necessary for DNA elimination and correct H3K9me3 and H3K27me3 localization in the new developing macronucleus, demonstrating that the scnRNA selection process is important for genome elimination. We propose that Gtsf1 is required for the coordinated degradation of Ptiwi09-scnRNA complexes that pair with nascent RNA transcribed from the maternal MAC genome, similarly to the mechanism suggested for microRNA target-directed degradation in metazoans.
2024-10-17 | PXD045214 | Pride