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

Overview

Journal Biology (Basel)

Publisher MDPI

Specialty Biology

Date 2021 Aug 27

PMID 34440019

Citations 5

Authors

Selina Klees

Felix Heinrich

Armin Otto Schmitt

Mehmet Gultas

Affiliations

Soon will be listed here.

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.

Citing Articles

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Deciphering the Molecular Mechanism Underlying African Animal Trypanosomiasis by Means of the 1000 Bull Genomes Project Genomic Dataset.

Rajavel A, Klees S, Hui Y, Schmitt A, Gultas M Biology (Basel). 2022; 11(5).

PMID: 35625470 PMC: 9138820. DOI: 10.3390/biology11050742.

agReg-SNPdb-Plants: A Database of Regulatory SNPs for Agricultural Plant Species.

Klees S, Heinrich F, Schmitt A, Gultas M Biology (Basel). 2022; 11(5).

PMID: 35625412 PMC: 9138521. DOI: 10.3390/biology11050684.

Deciphering Pleiotropic Signatures of Regulatory SNPs in L. Using Multi-Omics Data and Machine Learning Algorithms.

Haleem A, Klees S, Schmitt A, Gultas M Int J Mol Sci. 2022; 23(9).

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