Dataset Information

Polymorphisms in the Promoter Region of the Chinese Bovine PPARGC1A Gene.

ABSTRACT: The peroxisome proliferator-activated receptor gamma coactivator-1 alpha protein, encoded by the PPARGC1A gene, plays an important role in energy homeostasis. The genetic variations within the PPARGC1A gene promoter region were scanned in 808 Chinese native bovines belonging to three cattle breeds and yaks. A total of 6 SNPs and one 4 bp insertion variation in the promoter region of the bovine PPARGC1A gene were identified: SNP -259 T>A, -301_-298insCTTT, -915 A>G, -1175 T>G, -1590 C>T, -1665 C>T and -1690 G>A, which are in the binding sites of some important transcription factors: sex-determining region Y (SRY), myeloid-specific zinc finger-1 (MZF-1) and octamer factor 1(Oct-1). It is expected that these polymorphisms may regulate PPARGC1A gene transcription and might have consequences at a regulatory level.

SUBMITTER: Li MJ

PROVIDER: S-EPMC4093395 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature

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Polymorphisms in the Promoter Region of the Chinese Bovine PPARGC1A Gene.

Li M J MJ Liu M M Liu D D Lan X Y XY Lei C Z CZ Yang D Y DY Chen H H

Asian-Australasian journal of animal sciences. 20130401 4

The peroxisome proliferator-activated receptor gamma coactivator-1 alpha protein, encoded by the PPARGC1A gene, plays an important role in energy homeostasis. The genetic variations within the PPARGC1A gene promoter region were scanned in 808 Chinese native bovines belonging to three cattle breeds and yaks. A total of 6 SNPs and one 4 bp insertion variation in the promoter region of the bovine PPARGC1A gene were identified: SNP -259 T>A, -301_-298insCTTT, -915 A>G, -1175 T>G, -1590 C>T, -1665 C> ...[more]

PMID: 25049813

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Project description:PPARGC1A exerts important functions in activating many nuclear receptors and transcription factors that are related to energy balance. Previous studies have shown that PPARGC1A gene is associated with lactation traits of dairy cattle. However, the functional role of the buffalo PPARGC1A gene is still unknown. In this work, the complete coding sequence (CDS) of buffalo PPARGC1A was isolated and characterized for swamp and river buffalo. The CDS length of PPARGC1A for both types of buffalo was the same, which was composed of 2394 nucleotides and encoded a peptide composed of 797 amino acid residues. This protein belonged to a hydrophilic protein and contained one RRM_PPARGC1A domain (AA 674-764) without a signal peptide or a transmembrane domain. The differential expressions of this gene in 10 buffalo tissues in lactation and non-lactation displayed that the PPARGC1A was highly expressed in the muscle, heart, liver, brain and kidney of both non-lactating and lactating periods, but its expression was significantly different in the muscle, heart, liver, small intestine, mammary gland, rumen, spleen and lung between the two periods. Eight single nucleotide polymorphisms (SNPs) were found in buffalo, in which the c.778C > T, c.1257G > A and c.1311G > A were shared by two types of buffalo with similar allele frequencies, while the c.419C > T, c.759A > G, c.920C > A, c.926G > A and c.1509A > T were only observed in river buffalo. The SNP419, SNP920 and SNP926 were non-synonymous, which led to the amino acid changes of p.Ser140Phe, p.Pro307His and p.Arg309Lys. Seven nucleotide differential sites were identified in the PPARGC1A gene between buffalo and other Bovidae species. Phylogenetic analysis indicated that buffaloes were independently clustered into one branch, but they were closely related to the species of the Bos genus. The results indicate that buffalo PPARGC1A is an inducible transcriptional coactivator involved in regulating carbohydrate and fat metabolism. It can exert a functional role in a variety of buffalo tissues and may participate in milk fat synthesis and development in the mammary gland.

Project description:BackgroundBRM (Brahma homologue) is well known for its critical role in tumor suppression and cancer development. Genetic variations in the promoter region of BRM have been suggested to be associated with loss of BRM expression and lung cancer risk. To the authors' knowledge, no study on the role of BRM genetic polymorphisms in hepatocellular carcinoma (HCC) risk has been performed.Methodology/principal findingsIn two independent case-control studies containing 796 HCC cases and 806 cancer-free individuals, we genotyped two putative functional insertion/deletion (indel) polymorphisms [BRM-1321 (rs3832613) and BRM-741 (rs34480940)] within promoter region of BRM in Chinese populations using a PCR-based method. Real-time RT-PCR analysis was used to explore the genotype-phenotype correlation between these polymorphisms and BRM expression in both tissue samples and HCC cell lines. Logistic regression analysis showed that compared to BRM-1321del/del genotype, the ins/del and ins/ins variant genotypes had an increased HCC risk [adjusted odds ratio (OR) = 1.47, 95% confidence interval (CI) = 1.19-1.82; adjusted OR = 2.55, 95% CI = 1.75-3.72, respectively]. No significant association between BRM-741 and HCC incidence was observed. However, stratification analysis revealed a significant association between ins/ins genotype of BRM-741 and increased HCC susceptibility in smokers (adjusted OR = 2.07, 95% CI = 1.33-3.22). Quantitative PCR analyses demonstrated that the genotypes of BRM-1321 and the corresponding haplotypes were significantly correlated with BRM expression in vivo. Compared with ins/ins genotype, subjects carrying ins/del and del/del genotype had 2.30 and 4.99 fold higher BRM expression in HCC tissue samples, respectively. Similar trends were observed in western blot analysis at protein level.Conclusions/significanceOur findings suggest that BRM promoter polymorphism (BRM-1321) could regulate BRM expression and may serve as a potential marker for genetic susceptibility to HCC.

Dataset Information

Polymorphisms in the Promoter Region of the Chinese Bovine PPARGC1A Gene.

Publications

Polymorphisms in the Promoter Region of the Chinese Bovine PPARGC1A Gene.

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