Comprehensive Atlas of Alternative Splicing Reveals NSRP1 Promoting Adipogenesis through CCDC18
Abstract
:1. Introduction
2. Results
2.1. Genome-Wide Identification of Alternative Splicing Events (ASEs) in Different Tissues
2.2. Tissue-Specific Differentially Alternative Splicing Genes (DASGs) and Differentially Expressed Genes (DEGs)
2.3. Functional Analysis of DEGs Association with ASEs
2.4. Effects of Transcription Factors (TFs) on Alternative Splicing (AS)
2.5. The Impact of Genes under Potential Selection on Alternative Splicing
2.6. Effects of Splicing Factors (SFs) on Alternative Splicing
2.7. Splicing Factor NSRP1 and Correlated Genes Impact Adipose-Deposition Traits
2.8. Splicing Factor NSRP1 Regulates Adipogenesis
2.9. NSRP1 Promotes Adipogenesis by Regulating AS and Expression of CCDC18
3. Discussion
3.1. ASEs Identification and Gene Functional Enrichment Analysis
3.2. Associations between TFs and AS
3.3. ASGs under Potential Selection
3.4. SF NSRP1 Promotes Adipose Deposition
3.5. Limitations of the Study
3.6. Commercial Prospects of Marker Genes
4. Materials and Methods
4.1. Data Collection
4.2. Transcriptome Data Quality Control and Alignment
4.3. Identification and Differential Analysis of Alternative Splicing Events
4.4. Identification of Differentially Expressed Genes
4.5. Gene Functional Enrichment Analysis
4.6. Protein-Protein Interaction Network Analysis
4.7. Integrated Analysis of Transcription Factors, Selection Signals, Splicing Factors, and QTLs
4.8. Adipocyte Culture and Induced Differentiation
4.9. RNA Extraction and RT-qPCR
4.10. Western Blot Analysis
4.11. Cell Counting Kit-8 Proliferation Assay
4.12. 5-Ethynyl-2′-Deoxyuridine (EdU) Staining
4.13. Oil Red O Staining
4.14. Semiquantitative RT-PCR Analysis of Alternative Splicing Events
4.15. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Adipose | Blood | Heart | Kidney | Lung | Muscle | Ovary | Spleen | |
---|---|---|---|---|---|---|---|---|
DASGs | 4187 | 2898 | 173 | 242 | 315 | 244 | 584 | 1721 |
SDASGs | 1740 | 909 | 41 | 63 | 80 | 56 | 101 | 280 |
SDASGs/DASGs | 41.56% | 31.37% | 23.70% | 26.03% | 25.40% | 22.95% | 17.29% | 16.27% |
DEGs | 840 | 960 | 178 | 218 | 358 | 310 | 1348 | 620 |
SDEGs | 504 | 604 | 69 | 109 | 210 | 161 | 880 | 311 |
SDEGs/DEGs | 60% | 62.92% | 38.76% | 50% | 58.66% | 51.94% | 65.28% | 50.16% |
coDASG_DEGs | 83 | 164 | 0 | 4 | 4 | 2 | 15 | 65 |
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Liu, L.; Wang, W.; Liu, W.; Li, X.; Yi, G.; Adetula, A.A.; Huang, H.; Tang, Z. Comprehensive Atlas of Alternative Splicing Reveals NSRP1 Promoting Adipogenesis through CCDC18. Int. J. Mol. Sci. 2024, 25, 2874. https://doi.org/10.3390/ijms25052874
Liu L, Wang W, Liu W, Li X, Yi G, Adetula AA, Huang H, Tang Z. Comprehensive Atlas of Alternative Splicing Reveals NSRP1 Promoting Adipogenesis through CCDC18. International Journal of Molecular Sciences. 2024; 25(5):2874. https://doi.org/10.3390/ijms25052874
Chicago/Turabian StyleLiu, Lei, Wei Wang, Weiwei Liu, Xingzheng Li, Guoqiang Yi, Adeyinka Abiola Adetula, Haibo Huang, and Zhonglin Tang. 2024. "Comprehensive Atlas of Alternative Splicing Reveals NSRP1 Promoting Adipogenesis through CCDC18" International Journal of Molecular Sciences 25, no. 5: 2874. https://doi.org/10.3390/ijms25052874