Expression Profile and Regulatory Properties of m6A-Modified circRNAs in the Longissimus Dorsi of Queshan Black and Large White Pigs
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Sample Collection, Sequencing, and m6A-circRNA Prediction Analysis
2.2. Putative m6A-circRNA Sequence Analysis, Open Reading Frame (ORF) and Internal Ribosome Entry Site (IRES) Prediction
2.3. Functional Enrichment Analysis of m6A-circRNA Parent and Target Genes
2.4. Construction of the m6A-circRNA–miRNA–mRNA Network
2.5. m6A RNA Methylation Quantification (Me-RIP)
2.6. MeRIP-qPCR
2.7. Statistical Analysis
3. Results
3.1. Identification and Characterization of m6A-circRNAs in the Longissimus Dorsi of Queshan Black and Large White Pigs
3.2. Sequence Analysis and Coding Ability Prediction of Putative m6A-circRNAs
3.3. Construction of Regulatory Network of Putative m6A-circRNAs
3.4. GO and KEGG Annotation and Enrichment Analysis of Putative m6A-circRNAs
3.5. GO and KEGG Annotation and Enrichment Analysis of Target Genes
3.6. Analysis of the Expression Pattern of m6A-circRNAs in the Longissimus Dorsi of Queshan Black and Large White Pigs
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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circRNA_ID | Forward Primer (5′ to 3′) | Reverse Primer (5′ to 3′) |
---|---|---|
circZNF609 | GACAGTGGGGATGAATGGGA | TGTTCTCAGACCTGCCACAT |
circTEX9 | AAAGTGCCATGGAAGTTCGC | TTCCTCCAGTTGCCCTTCAA |
circCTIF | TGATTCCTTCAGTGGTGCCA | GCTGGGCAAATCTTCAAGGT |
circKIAA0556 | CTGAACACACATGGATGCCC | ATCCTTGGCCTTGACACTCA |
circPFKM | GGTAAGATCACAGCGGAGGA | GTTCCCGAAAGTCCTTGCAC |
circPATJ | CCTATTGGGCCCTGTATGAAG | AGTTTCTGTTTCCACTGCTCC |
circKIAA0513 | CTCATTGGCAAAGAGACCGG | TTCTCAGCCACACTAAGGGA |
circEGF | TTCCCGTGTTCTCTTAAGCG | CATCTGCCACCAATTGCTCA |
circSETBP1 | GGAGGAGGAAAGAGCCACT | TTCTCAGGAGGGTAAGGGA |
circCAMLG | CTTGCCTTTGGAGTCAGAGC | CCGAATCACCCAGCACTACT |
circRNASEH1 | GGAGGTGGTCAACAAAGAGG | CGTGTAGAGAACAGCTTGC |
circGUCY2C | TCTGGTGGAGGAAAGGACAC | TTTTGGTCATGGAAGAGGCC |
circRNA ID | Index | Score |
---|---|---|
circZNF609 | non-IRES | 0.342887 |
circTEX9 | IRES | 0.561539 |
circSETBP1 | IRES | 0.522931 |
circCTIF | IRES | 0.560397 |
circCAMLG | IRES | 0.660322 |
circRNASEH1 | non-IRES | 0.190536 |
circKIAA0556 | IRES | 0.529494 |
circGUCY2C | IRES | 0.594912 |
circPFKM | non-IRES | 0.141979 |
circPATJ | IRES | 0.582689 |
circKIAA0513 | non-IRES | 0.264454 |
circEGF | IRES | 0.804553 |
circRNA_ID | Minimal ORF Length (nt) | ||||
---|---|---|---|---|---|
30 | 75 | 150 | 300 | 600 | |
circZNF609 | 5 | 2 | 1 | 0 | 0 |
circTEX9 | 8 | 4 | 1 | 0 | 0 |
circCTIF | 5 | 3 | 3 | 0 | 0 |
circKIAA0556 | 5 | 4 | 1 | 1 | 1 |
circPFKM | 3 | 2 | 0 | 0 | 0 |
circPATJ | 3 | 1 | 0 | 0 | 0 |
circKIAA0513 | 4 | 3 | 0 | 0 | 0 |
circEGF | 5 | 2 | 1 | 1 | 0 |
circSETBP1 | 3 | 3 | 1 | 1 | 0 |
circCAMLG | 4 | 3 | 3 | 2 | 1 |
circRNASEH1 | 2 | 2 | 2 | 1 | 0 |
circGUCY2C | 2 | 1 | 1 | 0 | 0 |
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Qi, K.; Dou, Y.; Zhang, Z.; Wei, Y.; Song, C.; Qiao, R.; Li, X.; Yang, F.; Wang, K.; Li, X.; et al. Expression Profile and Regulatory Properties of m6A-Modified circRNAs in the Longissimus Dorsi of Queshan Black and Large White Pigs. Animals 2023, 13, 2190. https://doi.org/10.3390/ani13132190
Qi K, Dou Y, Zhang Z, Wei Y, Song C, Qiao R, Li X, Yang F, Wang K, Li X, et al. Expression Profile and Regulatory Properties of m6A-Modified circRNAs in the Longissimus Dorsi of Queshan Black and Large White Pigs. Animals. 2023; 13(13):2190. https://doi.org/10.3390/ani13132190
Chicago/Turabian StyleQi, Kunlong, Yaqing Dou, Zhe Zhang, Yilin Wei, Chenglei Song, Ruimin Qiao, Xiuling Li, Feng Yang, Kejun Wang, Xinjian Li, and et al. 2023. "Expression Profile and Regulatory Properties of m6A-Modified circRNAs in the Longissimus Dorsi of Queshan Black and Large White Pigs" Animals 13, no. 13: 2190. https://doi.org/10.3390/ani13132190