RNA-Seq Analysis of Glycolysis Regulation of Avian Leukosis Virus Subgroup J Replication
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Cell Culture
2.2. ALV-J-Infected Treatment
2.3. 2-Deoxy-d-Glucose Treatment
2.4. Glucose Uptake Assay
2.5. Pyruvate Content Assay
2.6. Lactate Content Assay
2.7. Total RNA Extraction, cDNA Synthesis, and Real-Time Quantitative PCR (qRT-PCR)
2.8. CCK-8 Assay
2.9. Western Blot Assay
2.10. RNA Extraction, Library Construction, Sequencing, and Data Quality Control
2.11. Identification and Differential Expression Analysis of circRNAs
2.12. Target Gene Prediction and Functional Enrichment Analysis of Differential circRNAs
2.13. Validation of DE circRNAs
2.14. Statistical Analysis
3. Results
3.1. ALV-J Elevates Glucose Uptake and Glycolysis in DF1 Cells
3.2. Inhibition of DF1 Cell Glycolysis Reduces ALV-J Replication
3.3. Overview of RNA Sequencing Data and Identification of Circular RNAs
3.4. Identification of Differentially Expressed Circular RNAs
3.5. Validation of Differentially Expressed Circular RNAs
3.6. Functional Enrichment Analysis of DE circRNA Source Genes
3.7. Functional Enrichment Analysis of DE circRNA Target Genes
4. Discussion
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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Gene | Primer Sequence (5′-3′) | Product Size (bp) | Annealing Temperature (°C) |
---|---|---|---|
PKM2 | F: GGCACCCACGAGTATCAT | 205 | 60 |
R: CATTGTCCAGCGTCACTTT | |||
HK1 | F: CCTCTTGGCTTCACATTC | 231 | 60 |
R: TTCACAGTTTGGGTCTTCAT | |||
HIF1A | F: TTGACAAGGCATCCATTA | 157 | 60 |
R: TCCTCAGAAAGCACCATA | |||
LDHA | F: TGGGCATCCATCCTCTGA | 168 | 60 |
R: CCTGCTTGTGAACCTCCT | |||
GLUT1 | F: TGTTTGGCTTGGACTTGAT | 171 | 60 |
R: TCTTGAGGACGCTCTTGG | |||
PFKP | F: GCCACAACAAACCTATAACA | 241 | 60 |
R: ATCAAAGGCAGACGAACA | |||
β-actin | F: GAACCCCAAAGCCAACAGAGAG | 142 | 60 |
R: ATCACCAGAGTCCATCACAATACCA |
circRNAs | Source Gene | Primer Sequence (5′-3′) | Product Size (bp) |
---|---|---|---|
CircRNA116 | SPPL3 | F: TGCTTTCCTTTTGCTCCCGA | 199 |
R: GACTGGAATCCACGAGGGAA | |||
CircRNA429 | MICAL2 | F: ACCCCCACTAGAAATCCTTGC | 195 |
R: CGTAGGACAGCAAATTGCCC | |||
CircRNA436 | DENND5A | F: CCAGAGGCCAAGCACCAATG | 185 |
R: GGCTGGCACCATCTCGG | |||
CircRNA898 | C2CD3 | F: CAGGGACCTGCTGAGAAGAC | 166 |
R: GATCAGCTGAGCCCATTGCC | |||
CircRNA1056 | ENO1 | F: CCTTGTCAGAGTAGCCAGCC | 136 |
R: CTGGGGTGTGATGGTGAGTC | |||
CircRNA1135 | SLC9A6 | F: GAGCACGAAGGCAGAAAGCG | 194 |
R: GCAAATGCCATGGCTCCTCG | |||
CircRNA3765 | FAF1 | F: CCCATCGAGAAGTCCAGCGG | 155 |
R: TGTGGGGCCATATGCTGGTC | |||
CircRNA3869 | DOCK1 | F: GGAGTCTTTGCTGCAGCTCT | 162 |
R: GCATCAAACACCAACGTGTCA | |||
β-actin | / | F: GAACCCCAAAGCCAACAGAGAG | 142 |
R: ATCACCAGAGTCCATCACAATACCA |
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Yang, T.; Qiu, L.; Chen, S.; Wang, Z.; Jiang, Y.; Bai, H.; Bi, Y.; Chang, G. RNA-Seq Analysis of Glycolysis Regulation of Avian Leukosis Virus Subgroup J Replication. Animals 2024, 14, 2500. https://doi.org/10.3390/ani14172500
Yang T, Qiu L, Chen S, Wang Z, Jiang Y, Bai H, Bi Y, Chang G. RNA-Seq Analysis of Glycolysis Regulation of Avian Leukosis Virus Subgroup J Replication. Animals. 2024; 14(17):2500. https://doi.org/10.3390/ani14172500
Chicago/Turabian StyleYang, Ting, Lingling Qiu, Shihao Chen, Zhixiu Wang, Yong Jiang, Hao Bai, Yulin Bi, and Guobin Chang. 2024. "RNA-Seq Analysis of Glycolysis Regulation of Avian Leukosis Virus Subgroup J Replication" Animals 14, no. 17: 2500. https://doi.org/10.3390/ani14172500