agReg-SNPdb: A Database of Regulatory SNPs for Agricultural Animal Species

SIMPLE SUMMARY: Regulatory 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. ABSTRACT: 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.