Identification of the Bovine CSN3 Core Promoter Region and the Relationships Between CSN3 Promoter Polymorphisms and the CSN3 A and B Alleles
Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Animals, Samples, and Promoter Analysis
2.2. Construction of a Progressively Shortened pGL3-Basic Recombinant Vector
2.3. Cell Transfection and the Dual-Luciferase Reporter Assay
2.4. Sequencing the Core Promoter Region of Bovine CSN3
2.5. Promoter Mutations Outside the CSN3 Core Promoter Region
2.6. Identification of the CSN3 A and B Alleles and Their Relationships with CSN3 Promoter Polymorphisms
2.7. Construction of the Promoter Mutation Recombinant Vector and the Dual-Luciferase Reporter Assay
2.8. Statistical Analysis
3. Results
3.1. Identification of the Bovine CSN3 Core Promoter
3.2. Sequence Variations in the Bovine CSN3 Core Promoter Region
3.3. CSN3 Promoter Polymorphisms
3.4. Identification of CSN3*A and CSN3*B Variants and Their Relationships with CSN3 Promoter Polymorphisms
3.5. Differences in the Promoter Activities of CSN3
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Primer Name | Primer Sequences (5′-3′) | Size (bp) | Positions Relative to the TSS |
---|---|---|---|
CSN3-P1F | atctgcgatctaagtaagcttACCAGAGCAACAATTTTTGCCT | 2059 | −2000/+59 |
CSN3-P2F | atctgcgatctaagtaagcttCTCCTGCCCCACTGTAGAA | 1677 | −1618/+59 |
CSN3-P3F | atctgcgatctaagtaagcttCATGACCATCACTCTGAACATTC | 1231 | −1172/+59 |
CSN3-P4F | atctgcgatctaagtaagcttTGTGAAGAAAGGGGAATCCTC | 803 | −744/+59 |
CSN3-P5F | atctgcgatctaagtaagcttCAACCACAGCCCATAATATATGTAG | 485 | −426/+59 |
CSN3-P6F | atctgcgatctaagtaagcttCTGCATTCCATTAACCGAGAC | 221 | −162/+59 |
CSN3-P-R | cagtaccggaatgccaagcttTTCCTTGTGACCGTCAGCT |
Primer Name | Primer Sequences (5′-3′) | Size (bp) | Positions Relative to the TSS |
---|---|---|---|
CSN3-P6F | atctgcgatctaagtaagcttCTGCATTCCATTAACCGAGACTG | 221 | −162/+9 |
CSN3-P7F | atctgcgatctaagtaagcttCTATCGTCAGATCTTTCCTTTCTGTC | 181 | −122/+59 |
CSN3-P8F | atctgcgatctaagtaagcttGCAATGTAAAAGGAAGATAAATCTCATG | 141 | −82/+59 |
CSN3-P9F | atctgcgatctaagtaagcttAACACCCTTTAATTAGTCTCTGGTTATT | 101 | −42/+59 |
CSN3-P10F | atctgcgatctaagtaagcttTCCTTACAGTGGAAAGGCCAAC | 61 | −2/+59 |
CSN3-P-R | cagtaccggaatgccaagcttTTCCTTGTGACCGTCAGCTCTT |
Allele Position Before The TSS and SNP ID | −66 A>G No SNP ID | −394 T>A No SNP ID | −641 A>− rs134762502(AT>−) | −982 A>T No SNP ID | −1002 T>− rs136772334 | −1269 T>C No SNP ID | −1654 T>A rs110303451 | −1867 T>A No SNP ID | −2039 T>G rs109870556 | |
---|---|---|---|---|---|---|---|---|---|---|
Number of Mutant Bases (Sample Number) and Mutation Frequencies | ||||||||||
No base mutation (Nos. 2, 3, 9, 11, 12, 16, 20, 25, 26, 27, 28, 31, 33, 34, and 39) | ||||||||||
One base mutation (no. 5) | C | |||||||||
One base mutation (no. 10) | A | |||||||||
One base mutation (no. 19) | G | |||||||||
One base mutation (no. 37) | — | |||||||||
Two base mutations (no. 15) | T | — | ||||||||
Two base mutations (no. 18) | T | A | ||||||||
Two base mutations (no. 35) | A | G | ||||||||
Two base mutations (no. 40) | — | G | ||||||||
Three base mutations (nos. 1, 4, 6, 7, 8, 17, 22, 23, 24, 29, 30, 32, 36, and 38) | — | A | G | |||||||
Three base mutations (no. 14) | G | A | A | |||||||
Four base mutations (no. 13) | G | — | A | G | ||||||
Five base mutations (no. 21) | — | — | C | A | G | |||||
Mutation frequencies | 5% | 5% | 5% | 5% | 45% | 5% | 42.5% | 5% | 47.5% |
Allele | CSN3*A | CSN3*B |
---|---|---|
Sample numbers | 4, 5, 7, 8, 10, 13, 14, 17, 20, 21, 22, 24, 27, 28, 29, 30, 34, 37, 40 | 1, 2, 3, 6, 9, 11, 12, 15, 16, 18, 19, 23, 25, 26, 31, 32, 33, 35, 36, 38, 39 |
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Li, W.; Wang, X.; Xu, X.; Wu, P.; Fu, T.; Zhang, L.; Gao, T. Identification of the Bovine CSN3 Core Promoter Region and the Relationships Between CSN3 Promoter Polymorphisms and the CSN3 A and B Alleles. Animals 2025, 15, 134. https://doi.org/10.3390/ani15020134
Li W, Wang X, Xu X, Wu P, Fu T, Zhang L, Gao T. Identification of the Bovine CSN3 Core Promoter Region and the Relationships Between CSN3 Promoter Polymorphisms and the CSN3 A and B Alleles. Animals. 2025; 15(2):134. https://doi.org/10.3390/ani15020134
Chicago/Turabian StyleLi, Wenqing, Xiaoyang Wang, Xiuyang Xu, Pinhui Wu, Tong Fu, Liyang Zhang, and Tengyun Gao. 2025. "Identification of the Bovine CSN3 Core Promoter Region and the Relationships Between CSN3 Promoter Polymorphisms and the CSN3 A and B Alleles" Animals 15, no. 2: 134. https://doi.org/10.3390/ani15020134
APA StyleLi, W., Wang, X., Xu, X., Wu, P., Fu, T., Zhang, L., & Gao, T. (2025). Identification of the Bovine CSN3 Core Promoter Region and the Relationships Between CSN3 Promoter Polymorphisms and the CSN3 A and B Alleles. Animals, 15(2), 134. https://doi.org/10.3390/ani15020134