Similar Datasets
Project description:Purpose: Cadmium (Cd) is detrimental to environment and human health, but the specific mechanism of the regulatory network is still remained unclear. Caenorhabditis elegans (C. elegans) is selected as the ideal model organism to investigate the effect of Cd exposure. Methods: We employed the phosphoproteomic technologies, high-throughput sequencing method and bioinformatic tools (RNAhybrid, Risearch2 and Targetscan) to investigate the phosphorylated change and the regulatory networks of circRNA, lncRNA, microRNA (miRNA) and mRNA after Cd exposure in C. elegans. The Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene set enrichment analysis (GSEA) were also employed. The relationship between transcriptional factors (TFs) and kinases, and the kinase-substrate were predicted using Jaspar database and iGPS, respectively. Results:26 differentially expressed circRNAs (DEcircRNAs), 143 lncRNAs (DElncRNAs), 69 miRNAs (DEmiRNAs) and 6209 mRNAs (DEmRNAs) were identified. According to qRCR, four DEcircRNAs and three DElncRNAs were found and confirmed the different expression levels between the treated and control group. 23 miRNAs and six miRNAs were the potential targets of the confirmed circRNAs and lncRNAs respectively using the predictive tools of RNAhybrid, RIsearch and Targetscan. Similarly, the target mRNAs of miRNAs were identified. Next, the regulatory network of lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA were established. Furthermore, five protein-coding genes might be regulated by DElnRNAs through cis-acting and 114 by trans-acting. The GO and KEGG analysis were performing on the parents’ genes of the mRNAs. GSEA was performed on all protein-coding genes, and the correlation between these genes and validated lncRNAs were used for pre-ranking. For the phosphopromotics, 42 differentially regulative phosphopeptides were identified. In this work, four novel pairs of TFs-kinases-substrate which might be influenced by Cd exposure were firstly constructed. Conclusions: Cd might mainly influence the reproductive function and aging of C. elegans through regulating the circRNAs and lncRNAs. Also, it might inhibit the expression of TFs to reduce the phosphorylated level of corresponding protein.
2024-11-24 | GSE189660 | GEO
Project description:Purpose: Cadmium (Cd) is detrimental to environment and human health, but the specific mechanism of the regulatory network is still remained unclear. Caenorhabditis elegans (C. elegans) is selected as the ideal model organism to investigate the effect of Cd exposure. Methods: We employed the phosphoproteomic technologies, high-throughput sequencing method and bioinformatic tools (RNAhybrid, Risearch2 and Targetscan) to investigate the phosphorylated change and the regulatory networks of circRNA, lncRNA, microRNA (miRNA) and mRNA after Cd exposure in C. elegans. The Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene set enrichment analysis (GSEA) were also employed. The relationship between transcriptional factors (TFs) and kinases, and the kinase-substrate were predicted using Jaspar database and iGPS, respectively. Results:26 differentially expressed circRNAs (DEcircRNAs), 143 lncRNAs (DElncRNAs), 69 miRNAs (DEmiRNAs) and 6209 mRNAs (DEmRNAs) were identified. According to qRCR, four DEcircRNAs and three DElncRNAs were found and confirmed the different expression levels between the treated and control group. 23 miRNAs and six miRNAs were the potential targets of the confirmed circRNAs and lncRNAs respectively using the predictive tools of RNAhybrid, RIsearch and Targetscan. Similarly, the target mRNAs of miRNAs were identified. Next, the regulatory network of lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA were established. Furthermore, five protein-coding genes might be regulated by DElnRNAs through cis-acting and 114 by trans-acting. The GO and KEGG analysis were performing on the parents’ genes of the mRNAs. GSEA was performed on all protein-coding genes, and the correlation between these genes and validated lncRNAs were used for pre-ranking. For the phosphopromotics, 42 differentially regulative phosphopeptides were identified. In this work, four novel pairs of TFs-kinases-substrate which might be influenced by Cd exposure were firstly constructed. Conclusions: Cd might mainly influence the reproductive function and aging of C. elegans through regulating the circRNAs and lncRNAs. Also, it might inhibit the expression of TFs to reduce the phosphorylated level of corresponding protein.
2024-11-24 | GSE189664 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2023-03-01 | GSE222361 | GEO
Project description:Whole transcriptome sequencing explored the toxic effect of cadmiun on Caenorhabditis elegans
| PRJNA784104 | ENA
Project description:Whole transcriptome sequencing explored the toxic effect of cadmiun on Caenorhabditis elegans [miRNA-seq]
| PRJNA784107 | ENA
Project description:Whole transcriptome sequencing explored the toxic effect of cadmiun on Caenorhabditis elegans [RNA-seq]
| PRJNA784101 | ENA
Project description:Purpose: Naringin (Nar) is a dihydroflavonoid compound, which is widely found in Chinese herbal medicine and citrus fruit. As one of the phytochemicals, it acts as a dietary supplement and can delay aging and prevent aging-related disease, such as obesity and diabetes. However, the exact mechanism still partially remained unclear. Methods: In this study, the high-glucose induced (HGI) Caenorhabditis elegans model was used to evaluate the anti-aging and anti-obesity effects of Nar. Results: It indicated that the mean lifespan and fast movement span of HGI worms were extended roughly 24% and 11% by Nar treatment, respectively. Oil red O staining revealed the significant reduction of fat accumulation (P<0.05) and the dFP::LGG labeled worms showed the promotion of autophagy. Additionally, the whole transcript sequencing and gene set variation analysis algorithm suggested that Nar improved the lipid biosynthesis and metabolism pathways, as well as the TGF-β, Wnt and longevity signaling pathway. The PPI network was applied to screen out hub genes in the above-mentioned pathways for further analysis. The expression levels of hub genes fat-7 and ech-6 were down-regulated, as well as aak-2, nhr-49, acs-2, hlh-30, lgg-1, unc-51, pha-4, skn-1 and yap-1 were up-regulated. Then, mutant worms and RNA interference were used to study the mechanism. It revealed that suppression of the expression of autophagy related genes including hlh-30, lgg-1, unc-51, pha-4, skn-1 and yap-1 could disable the fat-lowering, lifespan-prolonging, and health-promoting properties of Nar. Finally, a competing endogenous RNAs network was constructed to profoundly understand the beneficial mechanism caused by Nar. Conclusions: our findings elucidate that Nar plays the important role to alleviate HGI aging and anti-obesity effects by reducing fat accumulation and promoting autophagy.
2023-03-01 | GSE222360 | GEO
Project description:Purpose: Naringin (Nar) is a dihydroflavonoid compound, which is widely found in Chinese herbal medicine and citrus fruit. As one of the phytochemicals, it acts as a dietary supplement and can delay aging and prevent aging-related disease, such as obesity and diabetes. However, the exact mechanism still partially remained unclear. Methods: In this study, the high-glucose induced (HGI) Caenorhabditis elegans model was used to evaluate the anti-aging and anti-obesity effects of Nar. Results: It indicated that the mean lifespan and fast movement span of HGI worms were extended roughly 24% and 11% by Nar treatment, respectively. Oil red O staining revealed the significant reduction of fat accumulation (P<0.05) and the dFP::LGG labeled worms showed the promotion of autophagy. Additionally, the whole transcript sequencing and gene set variation analysis algorithm suggested that Nar improved the lipid biosynthesis and metabolism pathways, as well as the TGF-β, Wnt and longevity signaling pathway. The PPI network was applied to screen out hub genes in the above-mentioned pathways for further analysis. The expression levels of hub genes fat-7 and ech-6 were down-regulated, as well as aak-2, nhr-49, acs-2, hlh-30, lgg-1, unc-51, pha-4, skn-1 and yap-1 were up-regulated. Then, mutant worms and RNA interference were used to study the mechanism. It revealed that suppression of the expression of autophagy related genes including hlh-30, lgg-1, unc-51, pha-4, skn-1 and yap-1 could disable the fat-lowering, lifespan-prolonging, and health-promoting properties of Nar. Finally, a competing endogenous RNAs network was constructed to profoundly understand the beneficial mechanism caused by Nar. Conclusions: our findings elucidate that Nar plays the important role to alleviate HGI aging and anti-obesity effects by reducing fat accumulation and promoting autophagy.
2023-03-01 | GSE222359 | GEO
Project description:Identification of the molecular lesion in Caenorhabditis elegans mutants isolated through forward genetic screens usually involves time-consuming genetic mapping. We used Illumina deep sequencing technology to sequence a complete, mutant C. elegans genome and thus pinpointed a single-nucleotide mutation in the genome that affects a neuronal cell fate decision. This constitutes a proof-of-principle for using whole-genome sequencing to analyze C. elegans mutants.
| S-EPMC2574580 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2008-06-16 | GSE11738 | GEO