|
|
|
| Bioinformatics Analysis of Polymorphism in the Promoter Region of IL-6 Gene in Jinghai Yellow Chickens (Gallus gallus) |
|
|
|
|
Abstract Interleukin-6 (IL-6) is also called proinflammatory cytokine interleukin-6, plays a critical role in many chronic inflammatory and autoimmune diseases, especially inflammatory bowel disease. In this study, in order to investigate the regulation of IL-6 gene expression at the molecular level, Jinghai Yellow Chickens(Gallus gallus) were used as experimental materials, genomic DNA sequencing was used to detect single nucleotide polymorphisms (SNPs) of proinflammatory cytokine IL-6 gene from the upstream -2 200 bp to downstream 500 bp region, bioinformatics softwares were used to predict the core promoter region transcription factors and CpG islands of IL-6 gene, to analyze how the single nucleotide mutation of IL-6 gene changed the transcription factors and the CpG islands. The sequencing results showed that 28 SNPs sites were found in the gene, nineteen SNPs were located in the 5' regulatory region, two were located in exon (both of them are synonymous mutation), two were located in intron and 5 SNPs were located in the 3' region. Out of 28 mutation sites, there were 4 SNPs are not labeled in GenBank, three of them (G -357 A, C -447 G and A -663 G) were located in the 5' regulatory region and one in the 3' region (C3177T). Bioinformatics analysis showed that IL-6 gene had a very distinct core promoter recognition feature, there were 11 SNPs located in this core region, causing the change of transcription factor binding sites, the new discovered G-357A mutation may generate a new transcription factor binding site (Sp1) from the beginning of -360 bp, C-447G mutation can lead to one transcription factor change (HB become C/E BPalp), A-663G mutation may lead to the formation of 3 new transcription factor binding sites (AP-2alph and two Sp1), other detected SNPs could produce 5 new transcription factor binding sites (Sp1, ISGF-3, TEC1, IRF-1, ICS BP) and lead to 7 transcription factor binding sites (MEB-1, GLO, GATA-1, C/E BPal, Sp1, GR, Sp1) disappearing; meanwhile, the prediction results suggested that the SNP of C-939G may regulate the expression of IL-6 gene by affecting the number of the CpG island. C-939G mutation in the promoter region may lead the number of CpG island to change from 3 to 2, before the mutation, the CpG islands which were located in -1 010~-908 bp, -616~-509 bp and -370~-58 bp, respectively, after the mutation, the CpG islands were located in -615~-505 bp and -370~-58 bp, respectively. It can be speculated that SNPs in 5' regulatory region may influence the expression of IL-6 gene by changing the transcription factor or the methylation region. The results of this study have great significance for further exploring the function of IL-6 gene and the relationships between these SNPs and chicken intestinal inflammation resistance, and production performance.
|
|
Received: 21 June 2017
Published: 01 January 2018
|
|
|
|
|
|
|
