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 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 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 Prediction of Transcription Factor Binding Sites of SP1 on Human Chromosome1

2021 ◽  
Vol 11 (11) ◽  
pp. 5123
Author(s):  
Maiada M. Mahmoud ◽  
Nahla A. Belal ◽  
Aliaa Youssif
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Messenger Rna ◽  
Area Under The Curve ◽  
Noisy Data ◽  
Transcription Factor Binding Sites ◽  
Classification Problem ◽  
Transcription Factor Binding ◽  
K Nearest Neighbors ◽  
Factor Binding

Transcription factors (TFs) are proteins that control the transcription of a gene from DNA to messenger RNA (mRNA). TFs bind to a specific DNA sequence called a binding site. Transcription factor binding sites have not yet been completely identified, and this is considered to be a challenge that could be approached computationally. This challenge is considered to be a classification problem in machine learning. In this paper, the prediction of transcription factor binding sites of SP1 on human chromosome1 is presented using different classification techniques, and a model using voting is proposed. The highest Area Under the Curve (AUC) achieved is 0.97 using K-Nearest Neighbors (KNN), and 0.95 using the proposed voting technique. However, the proposed voting technique is more efficient with noisy data. This study highlights the applicability of the voting technique for the prediction of binding sites, and highlights the outperformance of KNN on this type of data. The study also highlights the significance of using voting.

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