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| Status |
Public on Dec 15, 2021 |
| Title |
PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
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| Summary |
The objective of this study is to determine the effects of pre-conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin-like PCB (3, 3’, 4, 4’, 5-pentachlorobiphenyl; PCB126) as a model environmental chemical because the mechanism of action is well-characterized, involving activation of aryl hydrocarbon receptor, a ligand-activated transcription factor. Adult zebrafish were exposed to 3 and 10 nM PCB126 for 24 h (water-borne exposure) and testis tissue was sampled at 7 days post-exposure for histology, DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing (RRBS) and RNAseq to quantify DNA methylation and gene expression, respectively. RRBS revealed 37 and 92 differentially methylated regions (DMRs) in response to 3 and 10nM PCB126 exposures, respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated, respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing, nucleoside metabolic process, iron-sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism, oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall, the results from this study provide new understanding about the mechanisms of action of dioxin-like PCBs in affecting testicular function and potential multigenerational phenotypes.
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| Overall design |
5-6 biological replicates per treatment condition. Three treatment conditions (DMSO control, 3nM PCB126 and 10 nM PCB126)
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| Contributor(s) |
Aluru N, Engelhardt J |
| Citation(s) |
35477799 |
| Submission date |
Dec 12, 2021 |
| Last update date |
May 03, 2022 |
| Contact name |
Neelakanteswar Aluru |
| E-mail(s) |
naluru@whoi.edu
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| Phone |
508-289-3607
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| Organization name |
Woods Hole Oceanographic Institution
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| Department |
Biology
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| Lab |
Aluru Lab
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| Street address |
45 Water Street
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| City |
Woods Hole |
| State/province |
MA |
| ZIP/Postal code |
02543 |
| Country |
USA |
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| Platforms (2) |
| GPL14875 |
Illumina HiSeq 2000 (Danio rerio) |
| GPL18413 |
Illumina HiSeq 2500 (Danio rerio) |
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| Samples (34)
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| Relations |
| BioProject |
PRJNA788302 |
| SRA |
SRP350440 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE190741_P0_3-overlap-P10.txt.gz |
1.0 Kb |
(ftp)(http) |
TXT |
| GSE190741_P0_3.metilene_qval.0.05.txt.gz |
1.1 Kb |
(ftp)(http) |
TXT |
| GSE190741_P10.metilene_qval.0.05.txt.gz |
2.5 Kb |
(ftp)(http) |
TXT |
| GSE190741_RAW.tar |
2.6 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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