Abstract
BackgroundThe expression of genes involved in regulating adipogenesis and lipid metabolism may affect economically important fatness traits in pigs. Allele-specific expression (ASE) reflects imbalance between allelic transcript levels and can be used to identify underlying cis-regulatory elements. ASE has not yet been intensively studied in pigs. The aim of this investigation was to analyze the differential allelic expression of four genes, PPARA, PPARG, SREBF1, and PPARGC1A, which are involved in the regulation of fat deposition in porcine subcutaneous and visceral fat and longissimus dorsi muscle.ResultsQuantification of allelic proportions by pyrosequencing revealed that both alleles of PPARG and SREBF1 are expressed at similar levels. PPARGC1A showed the greatest ASE imbalance in fat deposits in Polish Large White (PLW), Polish Landrace and Pietrain pigs; and PPARA in PLW pigs. Significant deviations of mean PPARGC1A allelic transcript ratio between cDNA and genomic DNA were detected in all tissues, with the most pronounced difference (p < 0.001) in visceral fat of PLW pigs. To search for potential cis-regulatory elements affecting ASE in the PPARGC1A gene we analyzed the effects of four SNPs (rs337351686, rs340650517, rs336405906 and rs345224049) in the promoter region, but none were associated with ASE in the breeds studied. DNA methylation analysis revealed significant CpG methylation differences between samples showing balanced (allelic transcript ratio ≈1) and imbalanced allelic expression for CpG site at the genomic position in chromosome 8 (SSC8): 18527678 in visceral fat (p = 0.017) and two CpG sites (SSC8:18525215, p = 0.030; SSC8:18525237, p = 0.031) in subcutaneous fat.ConclusionsOur analysis of differential allelic expression suggests that PPARGC1A is subjected to cis-regulation in porcine fat tissues. Further studies are necessary to identify other regulatory elements localized outside the PPARGC1A proximal promoter region.
Highlights
The expression of genes involved in regulating adipogenesis and lipid metabolism may affect economically important fatness traits in pigs
One hundred forty-five pigs were genotyped (Additional file 1), and at least 10 heterozygotes found in Polish Large White (PLW) and Duroc for Peroxisome proliferator activated receptor alpha (PPARA); PLW, Polish Landrace (PL) and Duroc for Peroxisome proliferator activated receptor gamma (PPARG); PLW, PL, Duroc and Pietrain for PPARGC1A; and PL, Duroc and Pietrain breed for Sterol regulatory element binding transcription factor (SREBF1)
Our study analyzed Allele-specific expression (ASE) of four functional candidate genes encoding transcription factors (PPARA, PPARG, SREBF1) and a coactivator of multiple transcription factors (PPARGC1A) using pyrosequencing as an accurate and sensitive means of quantifying allelic transcript proportions [28]. We demonstrated that both alleles of PPARG and SREBF1 are expressed at similar levels in subcutaneous and visceral fat and l. dorsi muscle in 30 unrelated animals representing three commercial pig breeds
Summary
The expression of genes involved in regulating adipogenesis and lipid metabolism may affect economically important fatness traits in pigs. Allele-specific expression (ASE) reflects imbalance between allelic transcript levels and can be used to identify underlying cis-regulatory elements. In contrast to random (e.g. X-chromosome inactivation), or non-random (imprinting) monoallelic expression where one allele is completely silenced, ASE is associated with more subtle differences in transcript level [4, 5]. This can be a consequence of variations in cis-regulatory DNA regions involved in transcription efficiency or transcript stability, allele-specific DNA methylation, allele-specific histone modification or location of the chromosomal territory within the nucleus [6, 7]. Cases of ASE that show no such consistency (bi-directional ASE) suggest regulatory elements not in a strong linkage disequilibrium with the gene [15]
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