Promoter polymorphisms in genes involved in porcine myogenesis influence their transcriptional activity

Myocyte enhancer factor 2 upregulates expression of myostatin promoter in Yesso scallop, Patinopecten yessoensis

Myostatin (MSTN) plays an important role in muscle development in animals, especially for mammals and fishes. However, little information has been reported on the regulation of MSTN in marine invertebrates, such as bivalves. In the present study, we cloned the MSTN promoter sequence of Yesso scallop Patinopecten yessoensis, identifying 4 transcription start sites, eleven TATA boxes and one E-box. Additionally, transcription factor binding sites, including myocyte enhancer factor 2 (MEF2) and POU homeodomain protein, were identified. The interaction between the MSTN promoter and MEF2 was analyzed to reveal the transcriptional activity of different fragment sizes of promoters through the dual-luciferase reporter assays. The highest transcriptional activity was found in recombinant plasmids with the most MEF2 binding sites, indicating that this transcription factor upregulates MSTN in Yesso scallop. This study provides new insight into the regulation of muscle growth and development in this species.

Interaction of MyoD and MyoG with Myoz2 gene in bovine myoblast differentiation

This study aims to explore the functional role of Myoz2 in myoblast differentiation, and elucidate the potential factors interact with Myoz2 in promoter transcriptional regulation. The temporal-spatial expression results showed that the bovine Myoz2 gene was highest expressed in longissimus dorsi, and in individual growth stages and myoblast differentiation stages. Knockdown of Myoz2 inhibited the differentiation of myoblast, and negative effect of MyoD, MyoG, MyH and MEF2A expression on mRNA levels. Subsequently, the promoter region of bovine Myoz2 gene with 1.7 Kb sequence was extracted, and then it was set as eight series of deleted fragments, which were ligated into pGL3-basic to detect core promoter regions of Myoz2 gene in myoblasts and myotubes. Transcription factors MyoD and MyoG were identified as important cis-acting elements in the core promoter region (-159/+1). Also, it was highly conserved in different species based on dual-luciferase analysis and multiple sequence alignment analysis, respectively. Furthermore, a chromatin immunoprecipitation (ChIP) analysis combined with site-directed mutation and siRNA interference and overexpression confirmed that the combination of MyoD and MyoG occurred in region -159/+1, and played an important role in the regulation of bovine Myoz2 gene. These findings explored the regulatory network mechanism of Myoz2 gene during the development of bovine skeletal muscle.

Identification of a promoter polymorphism affecting GPAT3 gene expression that is likely related to intramuscular fat content in pigs

The intramuscular fat content (IMF) is an economically important trait in pigs and the Laiwu pig is famous for its excessively extremely high level of IMF. Our previous transcriptome study revealed that the dynamic expression of glycerol-phosphate acyltransferase 3 (GPAT3) is consistent with changes in the IMF of Laiwu pigs. In this study, we further analyzed the expression and polymorphism of GPAT3 in its promoter region. The results indicated that the expression of GPAT3 increased dramatically from 120 to 240 days and is consistent with changes in IMF deposition, and at both mRNA and protein levels, GPAT3 expression was markedly higher in the LD muscle of Laiwu pigs than that of Duroc × Landrace × Yorkshire pigs. Deletion from -1695 to -1187 of porcine GPAT3 greatly increased its transcription. Of the two SNPs identified, the transition from C to T at -1526 site increased the transcription of porcine GPAT3 and allele T mainly distributed in Laiwu pig population. These results collectively suggest that the SNP at -1526 site of GPAT3 may contribute to IMF deposition by affecting its expression in pigs.

Identification of Functional Single Nucleotide Polymorphisms in Porcine HSD17B14 Gene Associated with Estrus Behavior Difference between Large White and Mi Gilts

Steroid hormone levels are associated with estrous behavior, which affects timely mating and reproductive efficiency in pigs. 17β-hydroxysteroid dehydrogenase type 14 (HSD17B14) modulates steroid synthesis and metabolism. To identify the functional single nucleotide polymorphisms (SNPs) in the porcine HSD17B14 gene, ear tissues from Large White and Mi gilts were collected to extract genomic DNA. Variable lengths of truncated promoter of HSD17B14 gene were used to determine the promoter activity by a dual luciferase reporter system. The vector HSD17B14^Phe or HSD17B14^Val was transfected into porcine granulosa cells (GCs). The core promoter region was identified between -72bp and -218bp. Six of seven SNPs had significant differences of allele frequency between Large White and Mi gilts. The plasmids with the wild genotype AA of rs329427898 maintained a smaller fraction of promoter activity compared with the plasmids with the mutant genotype GG, while the plasmids with wild the genotype TT of rs319864566 had a greater promoter activity than the plasmids with the mutant genotype CC. A missense mutation (Phe73Val) caused changes in the structural dynamics and function of the HSD17B14 protein. The highly expressed HSD17B14^Val degraded less estradiol into estrone, while the relatively lowly expressed HSD17B14^Phe degraded more estradiol into estrone, suggesting the protein activity of HSD17B14^Phe was greater than that of HSD17B14^Val. Moreover, the HSD17B14^Phe group has a greater apoptosis rate of porcine GCs. The HSD17B14 gene could been used as a candidate molecular marker for estrus behavior in pigs.

Identification of Single Nucleotide Polymorphisms in Porcine MAOA Gene Associated with Aggressive Behavior of Weaned Pigs after Group Mixing

Simple Summary

Monoamine Oxidase A (MAOA) gene had been reported as a candidate gene of aggressive behavior in several species. In the present study, the most aggressive and docile weaned pigs in each pen after group mixing were selected to identify single nucleotide polymorphisms in porcine MAOA gene associated with aggressive behavior. Constructs containing variable lengths of truncated porcine MAOA promoter were used to determine the promoter activity by a dual luciferase reporter system. The core promoter region of porcine MAOA was located at −679 bp to −400 bp. A total of nine single nucleotide polymorphisms (SNPs) in the MAOA gene were genotyped, of which six SNPs had significant differences in allele frequency between the aggressive and docile pigs. Four linked SNPs in porcine MAOA gene were associated with aggressive behavior in weaned pigs after mixing, which can be used as candidate molecular markers for aggressive behavior in pigs.

Abstract

Understanding the genetic background underlying the expression of behavioral traits has the potential to fasten the genetic progress for reduced aggressive behavior of pigs. The monoamine oxidase A (MAOA) gene is known as the “warrior” gene, as it has been previously linked to aggressive behavior in humans and livestock animals. To identify single nucleotide polymorphisms in porcine MAOA gene associated with aggressive behavior of pigs, a total of 500 weaned pigs were selected and mixed in 51 pens. In each pen, two aggressive and two docile pigs (a total of 204 pigs) were selected based on their composite aggressive score (CAS). Ear tissue was sampled to extract genomic DNA. Constructs containing variable lengths of truncated porcine MAOA promoter were used to determine the promoter activity by a dual luciferase reporter system. The core promoter region was located at −679 bp to −400 bp. A total of nine single nucleotide polymorphisms (SNPs) in MAOA gene were genotyped, of which six SNPs had significant differences (p < 0.05) in allele frequency between the aggressive and docile pigs. Linkage disequilibrium and association analyses showed that the pigs inherited the wild genotypes showed more aggressive behavior (p < 0.05) than pigs with the mutant genotypes of the four linked SNPs, rs321936011, rs331624976, rs346245147, and rs346324437. In addition, pigs of GCAA haplotype were more (p < 0.05) aggressive than the pigs with GCGA or ATGG haplotype. The construct containing the wild genotype GG of rs321936011 had lower (p = 0.031) promoter activity compared to the mutant genotype AA. These results suggest that the four linked SNPs in MAOA gene could be considered as a molecular marker for behavioral trait selection in pigs.

LncRNA HULC Polymorphism Is Associated With Recurrent Spontaneous Abortion Susceptibility in the Southern Chinese Population

Previous studies have revealed that genetic variation in genes that regulate cell migration might be associated with susceptibility to recurrent spontaneous abortion. HULC regulates the migration of a variety of cells, and genetic polymorphisms of HULC are associated with susceptibility to a variety of diseases, but their association with susceptibility to recurrent spontaneous abortion has not been reported. This study included 610 cases of recurrent spontaneous abortion and 817 normal controls, and the polymorphisms of the four SNPs were genotyped using the TaqMan method. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to assess the associations between selected SNPs and susceptibility to recurrent spontaneous abortion. Our results showed that three SNPs were significantly associated with a reduced risk of recurrent spontaneous abortion: rs1041279 (GG vs. GC/CC: adjusted OR = 0.745, 95% CI = 0.559–0.993, P = 0.0445), rs7770772 (GC/CC vs. GG: adjusted OR = 0.757, 95% CI = 0.606–0.946, P = 0.0143), and rs17144343 (AA/GA vs GG adjusted OR = 0.526, 95% CI = 0.366–0.755, P = 0.0005). Individuals with one to four genotypes showed a reduced risk of recurrent spontaneous abortion (adjusted OR = 0.749, 95% CI = 0.598–0.939, P = 0.0123). This cumulative effect on protection increased with increases in the observed number of genotypes (adjusted OR = 0.727, 95% CI = 0.625–0.846, ptrend < 0.0001). Our study suggests that HULC might be a biomarker for risk for recurrent spontaneous abortion, but larger sample studies are needed to verify this result.

Myostatin gene promoter: structure, conservation and importance as a target for muscle modulation

Myostatin (MSTN) is one of the key factors regulating myogenesis. Because of its role as a negative regulator of muscle mass deposition, much interest has been given to its protein and, in recent years, several studies have analysed MSTN gene regulation. This review discusses the MSTN gene promoter, focusing on its structure in several animal species, both vertebrate and invertebrate. We report the important binding sites considering their degree of phylogenetic conservation and roles they play in the promoter activity. Finally, we discuss recent studies focusing on MSTN gene regulation via promoter manipulation and the potential applications they have both in medicine and agriculture.

The association of lncRNA-HULC polymorphisms with hepatocellular cancer risk and prognosis

BACKGROUND

Genetic polymorphisms in lncRNA HULC may affect the susceptibility and clinical outcome of cancer. We aimed to investigate the association of HULC tagSNPs with the risk and prognosis of hepatocellular cancer, as well as the influence of the SNPs on lncRNA expression level.

METHODS

A total of 1338 samples were recruited in the risk study. Among them, 351 HCC patients were involved in the prognosis study. SNP genotyping was performed using KASP method and lncRNA expression was detected by Real-time PCR.

RESULTS

We found a promoter SNP, rs1041279, was associated with a 1.41-fold increased HCC risk (P = 0.032). In the stratified analysis, rs1041279 had greater ORs for the increased HCC risk in the male subgroup (P = 0.014, OR = 1.54). Furthermore, multi-logistic regression analysis revealed a two-way interaction effect of smoking-rs2038540 SNP on HCC risk (OR = 4.20). And MDR analysis consistently demonstrated a SNP-environmental interaction among smoking-drinking-rs2038540 SNP as the best model for predicting HCC risk (P = 0.0107). In our study, no significant association was found between HULC SNPs and the overall survival (P > 0.05), and no significant effect was observed of rs1041279 SNP on lncRNA-HULC expression (P > 0.05).

CONCLUSION

lncRNA-HULC rs1041279 SNP and the interaction of rs2038540 SNP with environmental factors could enhance HCC risk.

Efficient SNP Discovery by Combining Microarray and Lab-on-a-Chip Data for Animal Breeding and Selection

The genetic markers associated with economic traits have been widely explored for animal breeding. Among these markers, single-nucleotide polymorphism (SNPs) are gradually becoming a prevalent and effective evaluation tool. Since SNPs only focus on the genetic sequences of interest, it thereby reduces the evaluation time and cost. Compared to traditional approaches, SNP genotyping techniques incorporate informative genetic background, improve the breeding prediction accuracy and acquiesce breeding quality on the farm. This article therefore reviews the typical procedures of animal breeding using SNPs and the current status of related techniques. The associated SNP information and genotyping techniques, including microarray and Lab-on-a-Chip based platforms, along with their potential are highlighted. Examples in pig and poultry with different SNP loci linked to high economic trait values are given. The recommendations for utilizing SNP genotyping in nimal breeding are summarized.

Dopamine D1 receptor (DRD1) 5' region haplotypes significantly affect transcriptional activity in vitro

The role of dopamine D1 receptor (DRD1) gene promoter polymorphisms in schizophrenia remains controversial. We aimed to characterize the polymorphisms in the promoter region because little is known about the extent of variance in this region and potential roles in gene transcription activity. In a previous case-control study, we amplified and genotyped the polymorphisms of DRD1 gene. According to its haplotype estimation, we identified eight SNPs and confirmed ten different haplotypes by cloning and sequencing the fragment spanning -1990 to +10. The promoter activity of these haplotypes was analyzed using dual luciferase assays in SH-SY5Y and HEK293 cells. Compared with the reference haplotype, the constructed haplotypes containing different variation sites could significantly alter the luciferase activity. Additionally, the prediction of the transcription factor binding sites was performed. Our examination could provide the informative reference for the role of DRD1 gene promoter in schizophrenia.