scholarly journals SNP Diversity in CD14 Gene Promoter Suggests Adaptation Footprints in Trypanosome Tolerant N’Dama (Bos taurus) but not in Susceptible White Fulani (Bos indicus) Cattle

Genes ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 112 ◽  
Author(s):  
Olanrewaju B. Morenikeji ◽  
Anna L. Capria ◽  
Olusola Ojurongbe ◽  
Bolaji N. Thomas
Keyword(s):  
Genetic Diversity ◽  
Immune Response ◽  
Transcription Factor ◽  
Binding Sites ◽  
Promoter Region ◽  
Gene Promoter ◽  
Transcription Factor Binding Sites ◽  
Factor Binding ◽  
White Fulani ◽  
Cd14 Gene

Immune response to infections has been shown to be mediated by genetic diversity in pattern recognition receptors, leading to disease tolerance or susceptibility. We elucidated naturally occurring variations within the bovine CD14 gene promoter in trypanosome-tolerant (N’Dama) and susceptible (White Fulani) cattle, with genomic and computational approaches. Blood samples were collected from White Fulani and N’Dama cattle, genomic DNA extracted and the entire promoter region of the CD14 gene amplified by PCR. We sequenced this region and performed in silico computation to identify SNP variants, transcription factor binding sites, as well as micro RNAs in the region. CD14 promoter sequences were compared with the reference bovine genome from the Ensembl database to identify various SNPs. Furthermore, we validated three selected N’Dama specific SNPs using custom Taqman SNP genotyping assay for genetic diversity. In all, we identified a total of 54 and 41 SNPs at the CD14 promoter for N’Dama and White Fulani respectively, including 13 unique SNPs present in N’Dama only. The significantly higher SNP density at the CD14 gene promoter region in N’Dama may be responsible for disease tolerance, possibly an evolutionary adaptation. Our genotype analysis of the three loci selected for validation show that mutant alleles (A/A, C/C, and A/A) were adaptation profiles within disease tolerant N’Dama. A similar observation was made for our haplotype analysis revealing that haplotypes H1 (ACA) and H2 (ACG) were significant combinations within the population. The SNP effect prediction revealed 101 and 89 new transcription factor binding sites in N’Dama and White Fulani, respectively. We conclude that disease tolerant N’Dama possessing higher SNP density at the CD14 gene promoter and the preponderance of mutant alleles potentially confirms the significance of this promoter in immune response, which is lacking in susceptible White Fulani. We, therefore, recommend further in vitro and in vivo study of this observation in infected animals, as the next step for understanding genetic diversity relating to varying disease phenotypes in both breeds.

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

Genes ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 446 ◽  
Author(s):  
Shijie Xin ◽  
Xiaohui Wang ◽  
Guojun Dai ◽  
Jingjing Zhang ◽  
Tingting An ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Binding Sites ◽  
Promoter Region ◽  
Bioinformatics Analysis ◽  
Cpg Islands ◽  
Regulatory Region ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Factor Binding

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.

scholarly journals Genetic Diversity in HIV-1 Subtype C LTR from Brazil and Mozambique Generates New Transcription Factor-Binding Sites

Viruses ◽  
2014 ◽  
Vol 6 (6) ◽  
pp. 2495-2504 ◽  
Author(s):  
José Boullosa ◽  
Mahesh Bachu ◽  
Dulce Bila ◽  
Udaykumar Ranga ◽  
Theodoro Süffert ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Transcription Factor ◽  
Binding Sites ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Subtype C ◽  
Factor Binding ◽  
Hiv 1

scholarly journals Regulation of chicken vanin1 gene expression by peroxisome proliferators activated receptor α and miRNA-181a-5p

2021 ◽  
Vol 34 (2) ◽  
pp. 172-184
Author(s):  
Zhongliang Wang ◽  
Jianfeng Yu ◽  
Nan Hua ◽  
Jie Li ◽  
Lu Xu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Binding Sites ◽  
Promoter Region ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Expression Level ◽  
Luciferase Reporter ◽  
Peroxisome Proliferators ◽  
Factor Binding

Objective: Vanin1 (VNN1) is a pantetheinase that can catalyze the hydrolysis of pantetheine to produce pantothenic acid and cysteamine. Our previous studies showed that <i>VNN1</i> is specifically expressed in chicken liver. In this study, we aimed to investigate the roles of peroxisome proliferators activated receptor α (PPARα) and miRNA-181a-5p in regulating <i>VNN1</i> gene expression in chicken liver.Methods: 5′-RACE was performed to identify the transcription start site of chicken <i>VNN1</i>. JASPAR and TFSEARCH were used to analyze the potential transcription factor binding sites in the promoter region of chicken <i>VNN1</i> and miRanda was used to search miRNA binding sites in 3′ untranslated region (3′UTR) of chicken <i>VNN1</i>. We used a knock-down strategy to manipulate PPARα (or miRNA-181a-5p) expression levels <i>in vitro</i> to further investigate its effect on <i>VNN1</i> gene transcription. Luciferase reporter assays were used to explore the specific regions of VNN1 targeted by PPARα and miRNA-181a-5p.Results: Sequence analysis of the VNN1 promoter region revealed several transcription factor-binding sites, including hepatocyte nuclear factor 1α (HNF1α), PPARα, and CCAAT/enhancer binding protein α. GW7647 (a specific agonist of PPARα) increased the expression level of <i>VNN1</i> mRNA in chicken primary hepatocytes, whereas knockdown of PPARα with siRNA increased VNN1 mRNA expression. Moreover, the predicted PPARα-binding site was confirmed to be necessary for PPARα regulation of <i>VNN1</i> gene expression. In addition, the <i>VNN1</i> 3′UTR contains a sequence that is completely complementary to nucleotides 1 to 7 of miRNA-181a-5p. Overexpression of miR-181a-5p significantly decreased the expression level of <i>VNN1</i> mRNA.Conclusion: This study demonstrates that PPARα is an important transcriptional activator of <i>VNN1</i> gene expression and that miRNA-181a-5p acts as a negative regulator of <i>VNN1</i> expression in chicken hepatocytes.

scholarly journals Verification and Analysis of Sheep Tail Type-Associated PDGF-D Gene Polymorphisms

Animals ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 89 ◽  
Author(s):  
Qing Li ◽  
Zengkui Lu ◽  
Meilin Jin ◽  
Xiaojuan Fei ◽  
Kai Quan ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Promoter Region ◽  
Adipogenic Differentiation ◽  
Tail Length ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Peroxisome Proliferator ◽  
Peroxisome Proliferator Activated Receptor ◽  
Factor Binding

The aim of this study was to examine the correlation between the platelet-derived growth factor-D (PDGF-D) gene and sheep tail type character and explore the potential underlying mechanism. A total of 533 sheep were included in this study. Polymorphic sites were examined by Pool-seq, and individual genotype identification and correlation analysis between tail type data were conducted using the matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-TOF-MS) method. JASPART website was used to predict transcription factor binding sites in the promoter region with and without PDGF-D gene mutation. The effect of PDGF-D on adipogenic differentiation of sheep preadipocytes was investigated. Two single nucleotide polymorphism sites were identified: g.4122606 C > G site was significantly correlated with tail length, and g.3852134 C > T site was significantly correlated with tail width. g.3852134 C > T was located in the promoter region. Six transcription factor binding sites were eliminated after promoter mutation, and three new transcription factor binding sites appeared. Expression levels of peroxisome proliferator-activated receptor gamma (PPARγ) and lipoproteinlipase (LPL) were significantly up-regulated upon PDGF-D overexpression. Oil red O staining showed increased small and large oil drops in the PDGF-D overexpression group. Together these results indicate the PDGF-D gene is an important gene controlling sheep tail shape and regulating sheep tail fat deposition to a certain degree.

scholarly journals Unique distance- and DNA-turn-dependent interactions in the human protein C gene promoter confer submaximal transcriptional activity

1999 ◽  
Vol 340 (2) ◽  
pp. 513-518 ◽  
Author(s):  
C. Arnold SPEK ◽  
Rogier M. BERTINA ◽  
Pieter H. REITSMA
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Transcription Initiation ◽  
Protein C ◽  
Gene Promoter ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Initiation Site ◽  
Transcription Start ◽  
Factor Binding

Recent studies on the regulation of protein C gene transcription revealed the presence of three transcription-factor binding sites in the close proximity to the transcription start site. The proximal 40 bp upstream of the transcription-initiation site contain two, partly overlapping, binding sites for the liver-enriched hepatocyte nuclear factor (HNF)-3 and one binding site to which HNF-1 and HNF-6 bind in a mutually exclusive manner. In order to examine the functionality of the tight alignment of transcription-factor binding sites around the transcription-initiation site, we performed insertional mutagenesis experiments. Sequences were inserted at position -21, separating both HNF-3 binding sites from the HNF-1-HNF-6 binding site, and position -5, separating the HNF-3-HNF-1-HNF-6 complex from the transcription start site. All insertions were made in the context of the protein C gene -386/+107 promoter region and tested for activity by transient transfection experiments. Insertions at position -21 resulted in a combined distance- and DNA-turn-dependent increase in protein C gene expression. Insertions of variable length at position -5 decreased protein C gene expression in a DNA-turn-dependent manner. However, this turn-dependent decrease was accompanied by a distance-dependent increase in promoter activity. This is the first report in which changing the spacing between adjacent transcription-factor binding sites results in enhanced transcription, indicating the submaximal alignment of promoter elements in the wild-type protein C gene promoter region.

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