Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Xin S

PROVIDER: S-EPMC6162446 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature

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

Xin Shijie S Wang Xiaohui X Dai Guojun G Zhang Jingjing J An Tingting T Zou Wenbin W Zhang Genxi G Xie Kaizhou K Wang Jinyu J

Genes 20180906 9

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 ...[more]

PMID: 30200658

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Dataset Information

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

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

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