Unveiling the Impact of ApoF Deficiency on Liver and Lipid Metabolism: Insights from Transcriptome-Wide m6A Methylome Analysis in Mice
Abstract
:1. Introduction
2. Materials and Methods
2.1. Lipid Metabolism Disorder Mice with ApoF Gene Knockout
2.2. Histopathological Examination of Liver Tissue
2.3. CT Image Acquisition
2.4. Measurement of Serum Transaminase Enzymes and Blood Lipids
2.5. RNA Isolation and Extraction
2.6. High-Throughput m6A MeRIP-seq and mRNA-seq
2.7. RT-qPCR
2.8. Bioinformatic Analysis
2.9. Western Blotting
2.10. Statistical Analysis
3. Results
3.1. Genotype Identification
3.2. Histopathological Observation and Detection of Enzyme Activity and Dyslipidemia in ApoF Knockout Mice
3.3. Description of the m6A-Modified Genes and Peaks
3.4. DEG Annotations
3.5. The Annotations of Differential m6A Genes
3.6. The Annotations for Overlapping Genes between the DEGs and Differential m6A Genes
3.7. The Expression Levels of mRNA and Protein of m6A Regulators
3.8. The Role of m6A Regulators in Lipid Metabolism
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Gene | Accession Number | Primer Sequence (5′ → 3′) | |
---|---|---|---|
ApoF | NM_133997 | Forward | CACTTCACACGGAGAGGCAACC |
Reverse | GAGCAGCATCTGGCAGGACAAG | ||
IGF2BP3 | NM_023670 | Forward | CATCTGTTTATTCCCGCCCTGTC |
Reverse | AGCCTTGAACTGAGCCTCTGG | ||
ZC3H13 | NM_026083 | Forward | GGCAAAGAGAGTGGGAAGATAA |
Reverse | CCTGTCCTCTCGAACATGAATA | ||
HNRNPC | NM_001170981 | Forward | TTAATGAAAGAAATGCCCGAGC |
Reverse | CTCTGCAGCCAGGTTAATATCT | ||
GAPDH | NM_001289726 | Forward | ACTCCACTCACGGCAAATTCAAC |
Reverse | ACACCAGTAGACTCCACGACATAC |
Genes | Regulators | 8-Week-Old WT vs. 8-Week-Old KO | 28-Week-Old WT vs. 28-Week-Old KO | ||
---|---|---|---|---|---|
log2(Fold Change) | p Value | log2(Fold Change) | p Value | ||
IGF2BP3 | reader | 5.6676 | 8.96 × 10−58 | 0.3463 | 5.66 × 10−1 |
METTL5 | writer | 0.3457 | 6.68 × 10−2 | 0.0420 | 7.95 × 10−1 |
ZC3H13 | writer | 0.2689 | 8.20 × 10−2 | −0.0542 | 7.69 × 10−1 |
ALKBH5 | eraser | −0.2811 | 1.03 × 10−1 | −0.0004 | 9.98 × 10−1 |
HNRNPA2B1 | reader | 0.2657 | 1.15 × 10−1 | −0.0270 | 8.63 × 10−1 |
VIRMA | writer | 0.2376 | 1.84 × 10−1 | −0.1127 | 4.81 × 10−1 |
METTL14 | writer | 0.2085 | 2.03 × 10−1 | −0.0975 | 6.00 × 10−1 |
IGF2BP2 | reader | 0.5964 | 2.35 × 10−1 | −0.4649 | 2.78 × 10−1 |
FTO | eraser | −0.1363 | 3.62 × 10−1 | −0.1105 | 4.17 × 10−1 |
WTAP | writer | 0.1078 | 4.37 × 10−1 | 0.1507 | 3.54 × 10−1 |
METTL3 | writer | −0.1495 | 4.54 × 10−1 | −0.0561 | 7.57 × 10−1 |
YTHDF1 | reader | 0.1498 | 4.73 × 10−1 | −0.0304 | 8.99 × 10−1 |
YTHDF2 | reader | 0.1664 | 5.16 × 10−1 | 0.0396 | 8.67 × 10−1 |
RBM15B | writer | −0.1015 | 6.50 × 10−1 | 0.1865 | 5.26 × 10−1 |
FMR1 | reader | −0.0769 | 6.66 × 10−1 | −0.0056 | 9.76 × 10−1 |
YTHDC2 | reader | −0.0711 | 7.36 × 10−1 | −0.2400 | 2.33 × 10−1 |
RBM15 | writer | −0.0473 | 7.91 × 10−1 | 0.1011 | 5.50 × 10−1 |
HNRNPC | reader | 0.0240 | 8.64 × 10−1 | 0.4048 | 6.86 × 10−4 |
CBLL1 | writer | −0.0065 | 9.77 × 10−1 | 0.1255 | 5.85 × 10−1 |
IGF2BP1 | reader | Not detected | Not detected | −2.1825 | 5.87 × 10−1 |
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Shen, X.; Chen, M.; Zhang, J.; Lin, Y.; Gao, X.; Tu, J.; Chen, K.; Zhu, A.; Xu, S. Unveiling the Impact of ApoF Deficiency on Liver and Lipid Metabolism: Insights from Transcriptome-Wide m6A Methylome Analysis in Mice. Genes 2024, 15, 347. https://doi.org/10.3390/genes15030347
Shen X, Chen M, Zhang J, Lin Y, Gao X, Tu J, Chen K, Zhu A, Xu S. Unveiling the Impact of ApoF Deficiency on Liver and Lipid Metabolism: Insights from Transcriptome-Wide m6A Methylome Analysis in Mice. Genes. 2024; 15(3):347. https://doi.org/10.3390/genes15030347
Chicago/Turabian StyleShen, Xuebin, Mengting Chen, Jian Zhang, Yifan Lin, Xinyue Gao, Jionghong Tu, Kunqi Chen, An Zhu, and Shanghua Xu. 2024. "Unveiling the Impact of ApoF Deficiency on Liver and Lipid Metabolism: Insights from Transcriptome-Wide m6A Methylome Analysis in Mice" Genes 15, no. 3: 347. https://doi.org/10.3390/genes15030347
APA StyleShen, X., Chen, M., Zhang, J., Lin, Y., Gao, X., Tu, J., Chen, K., Zhu, A., & Xu, S. (2024). Unveiling the Impact of ApoF Deficiency on Liver and Lipid Metabolism: Insights from Transcriptome-Wide m6A Methylome Analysis in Mice. Genes, 15(3), 347. https://doi.org/10.3390/genes15030347