Genome-Wide ChIPseq Analysis of AhR, COUP-TF, and HNF4 Enrichment in TCDD-Treated Mouse Liver
Abstract
:1. Introduction
2. Results
2.1. Evaluation of ChIPseq Datasets
2.2. Evaluation of Transcription Factor Gene Targets
2.3. Evaluation of Gene Transcriptional Changes
2.4. Functional Enrichment of Putatively AhR, COUP-TFII and HNF4α Co-Regulated Genes in Mice Treated with 30 µg/kg for 28 Days
2.5. Identification of AhR, COUP-TFII and HNF4α Binding Patterns in the Liver Secretome
2.6. Identification of AhR, COUP-TFII and HNF4α Binding Patterns in HNF4α-Dependent Genes
3. Discussion
4. Materials and Methods
4.1. Animal Treatment
4.2. ChIP-Sequencing
4.3. RNA Sequencing
4.4. Functional and Motif Enrichment Analyses
4.5. ChIPseq Transcription Factor Overrepresentation Analysis
4.6. Gene Set Enrichment Analysis
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Conflicts of Interest
References
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TermID | DEGs | All Genes in Term | Adj. p-Value |
---|---|---|---|
TZ_DIURNAL_GENES | 1222 | 5613 | 0 |
TZ_SCS_PORTALHEP | 326 | 581 | 6.91 × 10−269 |
TZ_SCS_MIDCENTRALHEP | 292 | 563 | 1.76 × 10−226 |
TZ_SCS_CENTRALHEP | 203 | 466 | 3.59 × 10−136 |
GO_CC_MM_MITOCHONDRION | 308 | 1328 | 6.80 × 10−120 |
KEGG_MM_METABOLIC_PATHWAYS | 290 | 1180 | 1.59 × 10−119 |
HEPG2_SECRETOME | 216 | 757 | 1.53 × 10−101 |
PHH_SECRETOME | 211 | 726 | 7.27 × 10−101 |
TZ_LIVER | 103 | 181 | 3.77 × 10−83 |
GO_CC_MM_CYTOSOL | 210 | 927 | 3.02 × 10−78 |
TZ_SCS_MIDPORTALHEP | 81 | 149 | 8.88 × 10−63 |
GO_MF_MM_ATP_BINDING | 240 | 1454 | 3.22 × 10−61 |
TZ_MALE_ENRICHED | 113 | 367 | 1.08 × 10−55 |
GO_BP_MM_METABOLIC_PROCESS | 131 | 521 | 2.05 × 10−53 |
GO_MF_MM_METAL_ION_BINDING | 168 | 871 | 1.64 × 10−51 |
TZ_SCS_MACROPHAGES | 171 | 904 | 2.96 × 10−51 |
GO_MF_MM_PROTEIN_HOMODIMERIZATION_ACTIVITY | 125 | 509 | 9.79 × 10−50 |
TZ_SCS_ENDOTHELIALCELLS | 119 | 461 | 9.79 × 10−50 |
GO_BP_MM_OXIDATION-REDUCTION_PROCESS | 128 | 535 | 1.25 × 10−49 |
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Cholico, G.N.; Nault, R.; Zacharewski, T.R. Genome-Wide ChIPseq Analysis of AhR, COUP-TF, and HNF4 Enrichment in TCDD-Treated Mouse Liver. Int. J. Mol. Sci. 2022, 23, 1558. https://doi.org/10.3390/ijms23031558
Cholico GN, Nault R, Zacharewski TR. Genome-Wide ChIPseq Analysis of AhR, COUP-TF, and HNF4 Enrichment in TCDD-Treated Mouse Liver. International Journal of Molecular Sciences. 2022; 23(3):1558. https://doi.org/10.3390/ijms23031558
Chicago/Turabian StyleCholico, Giovan N., Rance Nault, and Tim R. Zacharewski. 2022. "Genome-Wide ChIPseq Analysis of AhR, COUP-TF, and HNF4 Enrichment in TCDD-Treated Mouse Liver" International Journal of Molecular Sciences 23, no. 3: 1558. https://doi.org/10.3390/ijms23031558