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Whole transcriptome sequencing explored the toxic effect of cadmiun on Caenorhabditis elegans [miRNA-seq]

ABSTRACT: 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.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE189664 | GEO | 2024/11/24

REPOSITORIES: GEO

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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.

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Whole transcriptome sequencing explored the toxic effect of cadmiun on Caenorhabditis elegans [miRNA-seq]

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