Functional Characterization of Genetic Polymorphisms Identified in the Promoter Region of the BovinePEPSGene

Abstract

Peptidase S (PEPS) is a metallopeptidase that cleaves N-terminal residues from proteins and peptides. PEPS is used as a cell maintenance enzyme with critical roles in peptide turnover. The promoter region located upstream of the initiation site plays an important role in regulating gene expression. Polymorphism in the promoter region can alter gene expression and lead to biological changes. In the current study, polymorphisms in the promoter region of the PEPS gene were investigated. Polymerase chain reaction (PCR)-restriction fragment length polymorphism and DNA sequencing methods were used to screen sequence variations in the promoter region of DNA samples from 743 Chinese Holstein cattle. Two polymorphisms (g. -534 T > C and g. -2545 G > A) were identified and eight haplotypes were classified by haplotype analysis. The two genetic polymorphisms and haplotypes were associated with fat percentage and somatic cell score in Chinese Holstein cattle. The results of real-time PCR showed that cow kidneys exhibit the highest PEPS expression level. Moreover, bioinformatics analysis predicted that the single-nucleotide polymorphism g. -534 T > C is located in the core promoter region and in the transcription factor binding sites. The promoter activities of the polymorphism of -543 T > C were measured by luciferase assay in the human kidney epithelial cell line 293T. Transcriptional activity is significantly lower in cell lines transfected with the reporter construct containing 2.5 kb upstream fragments with -543 C than in those with wild-type -543 T. The results indicated that genetic variation at locus -543 influences PEPS promoter activity. The genetic variation in the promoter region of PEPS gene may regulate PEPS gene transcription and might have consequences at a regulatory level.

PLCz Functional Haplotypes Modulating Promoter Transcriptional Activity Are Associated with Semen Quality Traits in Chinese Holstein Bulls

“…For example, a promoter haplotype of the mannan-binding lectin ( MBL ) gene was associated with the dramatic decrease in the serum concentration of the gene product [39]. Similarly, a genetic variation (g. −534 T>C) in the bovine peptidase S ( PEPS ) gene promoter was associated with fat percentage and SCS (somatic cell score) traits [40]. In this study, the g. −456 G>A locus was in a transcription factor (CAP/AP1) binding site, which was present with the G allele but lost by the presence of the A allele.…”

Searching for new loci and candidate genes for economically important traits through gene-based association analysis of Simmental cattle

“…In addition, the polymorphism in NCAPG shows significant associations with carcass weight, carcass yield estimate, and lipid deposition and has been identified as a candidate causative variant for bovine carcass weight quantitative trait locus (QTL) 23 27 29 30 31 . For LAP3 , it participates in oxytocin hydrolysis and acts as promoter polymorphism and milk production, and is highly expressed in skin and mammary and adipose tissue 23 32 33 . For LOCAL , it encodes a ligand-dependent nuclear receptor co-repressor, may affect skeletal frame size and adult height in human, horse, and cattle 34 35 36 , and has a strong correlation with the nearest gene NCAPG .…”

Functional SNPs of INCENP Affect Semen Quality by Alternative Splicing Mode and Binding Affinity with the Target Bta-miR-378 in Chinese Holstein Bulls

“…Coding region SNPs (cSNPs) may have an important significance in the structure and function of the protein and the study of hereditary diseases [ 30 ]. SNPs in the 5'flanking region, especially transcription factor binding sites, may regulate gene expression by affecting the promoter activity [ 31 ]. SNPs in the 3'UTR, especially binding sites of microRNA, regulate gene expression at either transcriptional or post-transcriptional level [ 32 ].…”