Abstract
Simple SummaryRegulatory SNPs (rSNPs) are SNPs located within promoter regions that have a high potential to alter gene expression by changing the binding affinity of transcription factors to their binding sites. Such rSNPs are gaining importance in the life sciences due to their causality for specific traits and diseases. In this study, we present agReg-SNPdb, the first database comprising rSNP data of seven agricultural and domestic animal species: cattle, pig, chicken, sheep, horse, goat, and dog, and made it usable via a web interface.Transcription factors (TFs) govern transcriptional gene regulation by specifically binding to short DNA motifs, known as transcription factor binding sites (TFBSs), in regulatory regions, such as promoters. Today, it is well known that single nucleotide polymorphisms (SNPs) in TFBSs can dramatically affect the level of gene expression, since they can cause a change in the binding affinity of TFs. Such SNPs, referred to as regulatory SNPs (rSNPs), have gained attention in the life sciences due to their causality for specific traits or diseases. In this study, we present agReg-SNPdb, a database comprising rSNP data of seven agricultural and domestic animal species: cattle, pig, chicken, sheep, horse, goat, and dog. To identify the rSNPs, we constructed a bioinformatics pipeline and identified a total of 10,623,512 rSNPs, which are located within TFBSs and affect the binding affinity of putative TFs. Altogether, we implemented the first systematic analysis of SNPs in promoter regions and their impact on the binding affinity of TFs for livestock and made it usable via a web interface.
Highlights
The transcriptional regulation of gene expression in higher organisms is essential for various biological processes
We created the mysql database [52] agReg-SNPdb, which stores (i) general information about the single nucleotide polymorphisms (SNPs), such as the ID, chromosomal position and the alleles; (ii) general information about the genes, such as the gene name and chromosomal position; (iii) the table snp_region connecting the tables snp_info and gene_info by storing SNPs and their corresponding target genes together with their genomic position within the promoter region based on the distance to the transcription start sites (TSSs); and, most importantly, (iv) for each SNP within a promoter region, we store its consequences based on the predicted transcription factor binding sites (TFBSs) binding potential
To give a brief overview of the data stored in agReg-SNPdb, we show the distribution of SNPs, genes, and regulatory SNPs (rSNPs) in the promoter regions along the chromosomes in an exemplary manner for the species chicken
Summary
The transcriptional regulation of gene expression in higher organisms is essential for various biological processes. TFs regulate the transcription as a response to specific environmental conditions by binding to short degenerate sequence motifs known as transcription factor binding sites (TFBSs) in promoter regions of their target genes and, thereby, enhance or repress gene transcription. Genomic variations, such as single nucleotide polymorphisms (SNPs), define and characterize specific populations or phenotypes and are, used as markers in animal and plant breeding. SNPs that are located in regulatory regions can alter TFBSs leading to a change in the binding affinity of TFs and, in extreme cases, even result in the disruption of a TFBS or the creation of a new TFBS (Figure 1) and, affect gene expression. Such SNPs are referred to as regulatory SNPs (rSNPs) [10,11,12]
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