Bioinformatics Analysis of SNPs in IL-6 Gene Promoter of Jinghai Yellow Chickens
Abstract
:1. Introduction
2. Materials and Methods
2.1. Experimental Animals
2.2. Genomic DNA Extraction
2.3. Primer Design and Polymerase Chain Reaction Conditions
2.4. Gene Polymorphism Analysis
2.5. Bioinformatics Analysis of Interleukin-6 in Jinghai Yellow Chickens
2.5.1. Prediction of the Promoter Region
2.5.2. Transcription Factor Binding Site Prediction
2.5.3. Prediction of CpG Islands
2.5.4. Genetic Diversity Analysis
3. Results
3.1. Single-Nucleotide Polymorphisms of Interleukin-6 in Jinghai Yellow Chickens
3.2. Population Genetic Variation of Newly Discovered Interleukin-6 Single-Nucleotide Polymorphisms
3.3. Results of Prediction of the Interleukin-6 Promoter Region and Screening of Promoter Region Single-Nucleotide Polymorphisms
3.4. Prediction of Putative Transcription Factor Binding in the Interleukin-6 Promoter by Single-Nucleotide Polymorphisms
3.5. Prediction Results for CpG Islands in the Promoter Region
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Primer | Starting Position | Primer Sequence (5′ → 3′) | Annealing Temperature (°C) | Length (bp) |
---|---|---|---|---|
P1 | −2210 | F: AGAGAGGACTAACCCACAGAG | 58.5 | 698 |
R: CCAGCTTCTCCAGTCTTGTC | ||||
P2 | −1628 | F: AGGGACAGCAATGGCAGAAG | 60.5 | 717 |
R: AAGAGCTGATCCTGGTTCTGG | ||||
P3 | −994 | F: CAGAGGACGTCCTACCTCAA | 56.5 | 690 |
R: GGTGAGCCTGGCAGCC | ||||
P4 | −367 | F: AAGATAAGACGCGCCACACC | 58.5 | 803 |
R: TTGAGGTTGTTCCGGACGAG | ||||
P5 | 391 | F: CGTGTGCGAGAACAGCAT | 59.0 | 565 |
R: AAATAGAAAGTTGGAAGGAGAGTACA | ||||
P6 | 797 | F: GGTGTGCAGTCGGCAATAG | 57.5 | 803 |
R: CTCATCATTCCACACAAGG | ||||
P7 | 1388 | F: ACTGTGTGCTCCTAATGCCT | 60.5 | 770 |
R: CTTCAGATTGGCGAGGAGGG | ||||
P8 | 1989 | F: CGTACCTCAAAACCTACCTCAG | 59.0 | 768 |
R: AGTGGAGTTCTTCAGCCTTATTTAA | ||||
P9 | 2702 | F: CAAAACCAACCTGTCTAAGCTG | 59.5 | 773 |
R: TTTTAAGAACTGTATGTTGATTGTGC |
Mutation Site 1 | Chromosome Position | Serial Number | SNP Locus |
---|---|---|---|
1 | 30947851 | rs315131240 | −1534 (T > C) |
2 | 30948105 | rs731482590 | −1280 (C > T) |
3 | 30948162 | rs15937151 | −1223 (G > A) |
4 | 30948165 | rs15937152 | −1220 (G > T) |
5 | 30948177 | rs15937153 | −1208 (A > G) |
6 | 30948446 | rs316873841 | −939 (C > G) |
7 | 30948496 | rs316713313 | −889 (G > A) |
8 | 30948520 | rs15937155 | −865 (G > A) |
9 | 30948594 | rs732353671 | −791 (G > C) |
10 | 30948651 | rs732784937 | −734 (G > A) |
11 | 30948722 | −663 (A > G) | |
12 | 30948751 | rs317547243 | −634 (A > G) |
13 | 30948775 | rs317511948 | −610 (G > A) |
14 | 30948874 | rs740913355 | −511 (C > T) |
15 | 30948902 | rs314710056 | −483 (A > G) |
16 | 30948927 | rs794072580 | −458 (T > G) |
17 | 30948938 | −447 (C > G) | |
18 | 30948985 | rs317677898 | −400 (A > G) |
19 | 30949028 | −357 (G > A) | |
20 | 30951133 | rs737499962 | 1749 (C > T) |
21 | 30951150 | rs736574918 | 1766 (G > A) |
22 | 30951621 | rs315658915 | 2237 (A > G) |
23 | 30951826 | rs794520257 | 2442 (T > C) |
24 | 30952410 | rs317567286 | 3026 (G > A) |
25 | 30952457 | rs794365857 | 3073 (C > T) |
26 | 30952561 | 3177 (C > T) | |
27 | 30952578 | rs316333207 | 3194 (C > T) |
28 | 30952600 | rs740039941 | 3216 (C > G) |
No | Mutation Site | Sample Size | Genotype Frequency 1 | Gene Frequency | χ2 | p-Value | PIC | H | Ne | |||
---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | A-663G | 220 | AA: 0.000 (0) | GG: 1.000 (220) | AG: 0.000 (0) | A: 0.000 | G: 1.000 | 0.000 | 0.000 | 1.000 | ||
2 | C-447G | 220 | CC: 0.455 (100) | GG: 0.090 (20) | GC: 0.455 (100) | C: 0.680 | G: 0.320 | 0.500 | 0.799 | 0.340 | 0.434 | 1.766 |
3 | G-357A | 220 | GG: 0.290 (64) | AA: 0.255 (56) | GA: 0.455 (100) | G: 0.518 | A: 0.482 | 1.770 | 0.413 | 0.375 | 0.499 | 1.997 |
4 | C3177T | 220 | CC: 0.400 (88) | TT: 0.145 (32) | CT: 0.455 (100) | C: 0.627 | T: 0.373 | 0.170 | 0.918 | 0.358 | 0.468 | 1.878 |
Prediction Software 1 | Start Site (bp) | Termination Site (bp) | Score |
---|---|---|---|
Promoter Scan [19] | −402 | −652 | 73.12 |
−74 | −324 | 74.33 | |
Promoter 2.0 Prediction Server [21] | −900 | - | 1.092 |
Neural Network Promoter Prediction (NNPP version 2.2) [20] | −330 | −380 | 0.87 |
−339 | −389 | 0.97 | |
−519 | −569 | 0.99 | |
−659 | −709 | 0.99 | |
−1049 | −1099 | 0.92 | |
−1192 | −1242 | 0.97 | |
−1404 | −1454 | 0.91 | |
−2179 | −2229 | 0.87 |
Mutation Site | Base Group | Transcription Factor | Transcription Factor Binding Site Base Sequence | Transcription Factor Position |
---|---|---|---|---|
−357 | G | Sp1 | gacacgccacacc | −360–(−348) |
A | ||||
−447 | C | HB | cttaaaaacg | −447–(−438) |
G | C/EBPα | aaacggttaa | −452–(−443) | |
−458 | T | MEB-1 GLO | ttttttaaac ttttttaaac | −458(−449) −458–(−449) |
G | Sp1 | ccgaggaggg | −467–(−458) | |
−483 | A | PU.1 GATA-1 C/EBPα | aaaagagaac aaatgaaaag acaaatgaaa | −483–(−474) −488–(−479) −490–(−481) |
G | PU.1 ISGF-3 TEC1 IRF-1 | gaaagagaac ggaaagagaa ggaaagagaa ggaaagagaa | −483–(−474) −484–(−475) −484–(−475) −484–(−475) | |
−511 | C | TBP | tgcttataag | −513–(−504) |
T | TBP ICS BP | atgtttataa agtttcatgt | −514–(−505) −520–(−511) | |
−610 | G | Sp1 | ggagcgatgg | −615–(−606) |
A | ||||
−634 | A | GR Sp1 | cactgtgtgc cctccaccact | −635–(−626) −642–(−632) |
G | ||||
−663 | A | |||
G | AP-2α Sp1 Sp1 | cccggggagc gccccggggag cctgctgccccggg | −668–(−659) −670–(−660) −676–(−663) | |
−1208 | A | Sp1 | ggctcggggagccag | −1221–(−1207) |
G | Sp1 | ggggagccgggc | −1216–(−1205) | |
−1220 | G | Sp1 C/EBPβ | ggctcggggagccag gctgtggctc | −1221–(−1207) −1226–(−1217) |
T | ||||
−1223 | G | C/EBPβ C/EBPα | gctgtggctc ataattgctg | −1226–(−1217) −1232–(−1223) |
A |
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Xin, S.; Wang, X.; Dai, G.; Zhang, J.; An, T.; Zou, W.; Zhang, G.; Xie, K.; Wang, J. Bioinformatics Analysis of SNPs in IL-6 Gene Promoter of Jinghai Yellow Chickens. Genes 2018, 9, 446. https://doi.org/10.3390/genes9090446
Xin S, Wang X, Dai G, Zhang J, An T, Zou W, Zhang G, Xie K, Wang J. Bioinformatics Analysis of SNPs in IL-6 Gene Promoter of Jinghai Yellow Chickens. Genes. 2018; 9(9):446. https://doi.org/10.3390/genes9090446
Chicago/Turabian StyleXin, Shijie, Xiaohui Wang, Guojun Dai, Jingjing Zhang, Tingting An, Wenbin Zou, Genxi Zhang, Kaizhou Xie, and Jinyu Wang. 2018. "Bioinformatics Analysis of SNPs in IL-6 Gene Promoter of Jinghai Yellow Chickens" Genes 9, no. 9: 446. https://doi.org/10.3390/genes9090446