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Background  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. 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.    Results  Quantification 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.    Conclusions  Our 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.    Electronic supplementary material  The online version of this article (10.1186/s12863-018-0696-6) contains supplementary material, which is available to authorized users.

bmc genomic data

Investigation of allele-specific expression of genes involved in adipogenesis and lipid metabolism suggests complex regulatory mechanisms of PPARGC1A expression in porcine fat tissues