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| Status |
Public on Nov 24, 2024 |
| Title |
Whole transcriptome sequencing explored the toxic effect of cadmiun on Caenorhabditis elegans [miRNA-seq] |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
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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| Overall design |
Examination of the change of RNA and protein after cadmium exposure in Caenorhabditis elegans.
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| Contributor(s) |
Qu Z, Guo P |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Nov 27, 2021 |
| Last update date |
Nov 24, 2024 |
| Contact name |
Panpan Wang |
| E-mail(s) |
[email protected]
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| Organization name |
郑州大学
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| Department |
College of Public Health
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| Street address |
郑州市高新区科学大道100号郑州大学
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| City |
Zhengzhou |
| State/province |
1995-07-13 |
| ZIP/Postal code |
450001 |
| Country |
China |
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| Platforms (1) |
| GPL19757 |
Illumina NextSeq 500 (Caenorhabditis elegans) |
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| Samples (6)
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| GSM5705704 |
miRNA Caenorhabditis elegans-control-rep1 |
| GSM5705705 |
miRNA Caenorhabditis elegans-control-rep2 |
| GSM5705706 |
miRNA Caenorhabditis elegans-control-rep3 |
| GSM5705707 |
miRNA Caenorhabditis elegans-cadmium exposure-rep1 |
| GSM5705708 |
miRNA Caenorhabditis elegans-cadmium exposure-rep2 |
| GSM5705709 |
miRNA Caenorhabditis elegans-cadmium exposure-rep3 |
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| This SubSeries is part of SuperSeries: |
| GSE189666 |
Whole transcriptome sequencing explored the toxic effect of cadmiun on Caenorhabditis elegans |
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| Relations |
| BioProject |
PRJNA784107 |
| SRA |
SRP348174 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE189664_RAW.tar |
40.0 Kb |
(http)(custom) |
TAR (of TXT) |
| GSE189664_microRNA_CPM_matrix.txt.gz |
9.8 Kb |
(ftp)(http) |
TXT |
| GSE189664_microRNA_counts_matrix.txt.gz |
4.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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