Novel SNPs and InDels discovered in two promoter regions of porcine pregnancy-associated glycoprotein 2-like subfamily (pPAG2-Ls) in crossbreed pigs

Abstract

This is a pioneer study of single nucleotide polymorphisms (SNPs) within the entire promoter region (1204 bp) of the dominant pPAG2-L subfamily in the pig. The pPAG2-L subfamily was sequenced/examined using genomic deoxyribonucleic acid (gDNA) templates of crossbreed pigs (Landrace x Large White), and compared to two bacterial artificial chromosome (BAC) clones containing gDNA of the Duroc breed (as the positive controls). Our analysis of the pPAG2-L promoter identified 31 SNPs and one InDel mutation in crossbreed pigs. Among 42 SNPs identified in two BAC clones, 24 SNPs had not been previously detected in crossbreed pigs. The sequence alignment of pPAG2-L promoter, performed with Lasagne-Search 2.0, Cluster Bluster and MatInspector software, revealed a total of 28 transcription factor binding sites (TFBS) and 10 TFBS (AP-1, CCAAT, CHOP:C, FOXP1, LSF, MRF-2, Myc, NF1, NF-Y, TGIF) within SNPs in the core sequences. It was noted that TFBS (NF1) was found to be unique to the pPAG2 promoter sequence containing SNPs: g.-1100G>A(R), g.-1101T>C(Y), represented by GA and TC genotypes (p x = 0.12). Our broad-based novel database thus provides an SNP PAG2-L pattern for modern genotyping of female and male progenitors. This is required for further studies of various potential correlations between guiding SNP genotypes of the pPAG2-L subfamily in the sows of many breeds, in which the most economically important reproductive traits are properly documented on each farm.

Gene structure of the pregnancy-associated glycoprotein-like (PAG-L) in the Eurasian beaver (Castor fiber L.)

“…The identified lengths of the introns A, B, D, E, and F are relatively comparable with the predicted ones, according to the pPAG2 structure (Szafranska et al 2001 ). The final length of the pPAG2 with promoter region is equal to 8755 bp (Bieniek-Kobuszewska et al 2016 ). The second known exon-intron organization concerns the bPAG1 gene (8095 bp) which is similar to other APs and whose intron sizes vary from 87 bp to 1.8 kbp and exon-intron boundaries conform to the standard GT-AG rule for 5′ donor and 3′ acceptor sites (Xie et al 1995 ).…”

“…Presently, since our SNV data of the CfPAG-L cannot be compared in the beavers because such data are unavailable, we will therefore discuss the data in relation to the PAGs in other species. Previously, 32 SNPs/InDel and 42 SNPs/InDels have been identified within proximal and flanking distal regions of the pPAG2-L promoter in cross-breed pigs and in the Duroc breed, respectively (Bieniek-Kobuszewska et al 2016 ). Many of those SNPs have been identified within transcription factor binding sites, which suggests the importance of allelic diversity and the significant influence on regulation of the pPAG2-L expression.…”

“…The mammalian PAGs and many alternatively named PAG-Like ( PAG-Ls ) are the most closely related to the pepsin family. The identified PAGs possess a conserved structure that includes nine exons and eight introns (A–H), among which the intron F is the longest in pPAG2 , bPAG1 and 2 (Wallace et al 2015 ; Bieniek-Kobuszewska et al 2016 ). However, the organizational structures of the PAGs have not been studied and, therefore, remain completely unknown in the genomes of the Rodentia taxa.…”

Neglected Functions of TFCP2/TFCP2L1/UBP1 Transcription Factors May Offer Valuable Insights into Their Mechanisms of Action

“…Examination of the proximal promoter regions of selected upregulated genes revealed MYC-associated zinc finger protein (MAZ) and TFCP2 as two pivotal transcription factors responsible for the regulation of transcriptional activity of these genes [ 9 ]. Moreover, the sequence alignment (with Lasagne-Search 2.0, Cluster Bluster, and MatInspector software) of pregnancy-associated glycoprotein family (PAGs) pPAG2-L promoter in pigs detected a TFCP2 binding site, which may emphasize a regulatory role of this factor in mammalian reproduction [ 10 ]. The study on LH-β (luteinizing hormone β subunit) promoter activity among three breeds of Moroccan sheep, D’man, Sardi, and Timahdite, showed higher promoter activity in D’man compared to the other breeds [ 11 ].…”

Identification of 1093-bp intron A, SNPS and indels discovered in the porcine pregnancy-associated glycoprotein 2-like (pPAG2-L) gene subfamily in pigs

“…: U39199, U39762, U39763 and U39198, respectively). More recently, SNPs/InDels within pPAG2-L promoter region have been identified in the crossbreed pigs (BIENIEK-KOBUSZEWSKA et al, 2016). However, the entire sequences from five introns (A, B, D, E and F) of the pPAG2-L subfamily are still unknown.…”