Next Article in Journal
Role of Homologous Recombination Genes in Repair of Alkylation Base Damage by Candida albicans
Previous Article in Journal
Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard
Article Menu

Export Article

Open AccessArticle
Genes 2018, 9(9), 446; https://doi.org/10.3390/genes9090446

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

1,2
,
1,2
,
1,2,3,* , 1,2
,
1,2
,
1,2
,
1,2,3
,
1,2,3
and
1,2,3
1
College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
2
Key Lab for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou 225009, China
3
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)
Full-Text   |   PDF [722 KB, uploaded 6 September 2018]   |  

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. 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
Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Supplementary material

SciFeed

Share & Cite This Article

MDPI and ACS Style

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.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Genes EISSN 2073-4425 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top