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Genes 2018, 9(9), 446;

Bioinformatics Analysis of SNPs in IL-6 Gene Promoter of Jinghai Yellow Chickens

1,2,3,* , 1,2
College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
Key Lab for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou 225009, China
Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
Author to whom correspondence should be addressed.
Received: 18 July 2018 / Revised: 24 August 2018 / Accepted: 31 August 2018 / Published: 6 September 2018
(This article belongs to the Section Animal Genetics and Genomics)
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The proinflammatory cytokine, interleukin-6 (IL-6), plays a critical role in many chronic inflammatory diseases, particularly inflammatory bowel disease. To investigate the regulation of IL-6 gene expression at the molecular level, genomic DNA sequencing of Jinghai yellow chickens (Gallus gallus) was performed to detect single-nucleotide polymorphisms (SNPs) in the region −2200 base pairs (bp) upstream to 500 bp downstream of IL-6. Transcription factor binding sites and CpG islands in the IL-6 promoter region were predicted using bioinformatics software. Twenty-eight SNP sites were identified in IL-6. Four of these 28 SNPs, three [−357 (G > A), −447 (C > G), and −663 (A > G)] in the 5′ regulatory region and one in the 3′ non-coding region [3177 (C > T)] are not labelled in GenBank. Bioinformatics analysis revealed 11 SNPs within the promoter region that altered putative transcription factor binding sites. Furthermore, the C-939G mutation in the promoter region may change the number of CpG islands, and SNPs in the 5′ regulatory region may influence IL-6 gene expression by altering transcription factor binding or CpG methylation status. Genetic diversity analysis revealed that the newly discovered A-663G site significantly deviated from Hardy-Weinberg equilibrium. These results provide a basis for further exploration of the promoter function of the IL-6 gene and the relationships of these SNPs to intestinal inflammation resistance in chickens. View Full-Text
Keywords: Jinghai yellow chicken; IL-6 gene SNPs; transcription factor; CpG island; bioinformatics Jinghai yellow chicken; IL-6 gene SNPs; transcription factor; CpG island; bioinformatics

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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.

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