GM liver Probes.zip (82.03 MB)
About the existence of common determinants of gene expression in the porcine liver and skeletal muscle
dataset
posted on 2019-04-04, 13:36 authored by Rayner Gonzalez-PrendesRayner Gonzalez-Prendes, Marcel Amills, Emilio Mármol-Sánchez, Quintanilla, Raquel, Anna Castelló, Ali Zidi, Yuliaxis Ramayo-Caldas, Taina Figueiredo CardosoTaina Figueiredo Cardoso, Arianna Manunza, Ángela CánovasBackground
The comparison of expression QTL (eQTL) maps obtained in different tissues is an essential step to understand how gene expression is genetically regulated in a context-dependent manner. In the current work, we have compared the transcriptomic and eQTL profiles of two porcine tissues (skeletal muscle and liver) with highly divergent expression profiles by using a data set of 103 Duroc pigs genotyped with the Porcine SNP60 BeadChip (Illumina) and with available microarray measurements of hepatic and muscle mRNA levels. Since structural variation could have effects on gene expression, we have also investigated the co-localization of cis-eQTL with copy number variant regions (CNVR) segregating in the Duroc population under study.
Results
The analysis of differential expresssion revealed the existence of 1,204 and 1,490 probes that were overexpressed and underexpressed in the gluteus medius muscle when compared to liver, respectively (|fold-change| > 1.5, q-value < 0.05). By performing genome scans in 103 Duroc pigs with available expression and genotypic data, we identified 76 and 28 genome-wide significant cis-eQTL regulating gene expression in the gluteus medius muscle and liver, respectively, and 12 of them (APH1A, ARL2BP, BSDC1, CTSF, LZIC, MARC2, PNPO, POLR3D, RABEP1, TAPT1, TMEM97 and Y1PF1) were shared by both tissues (i.e. 42.8 % of the cis-eQTL identified in the liver were replicated in the gluteus medius muscle). These results are consistent with previous studies performed in humans, where 50% of eQTL were shared across tissues. Moreover, we have identified 41 CNVRs in 350 Duroc pigs typed with the Porcine SNP60 BeadChip by using the PennCNV and GADA softwares, but only a few of these CNVRs co-localized with cis-eQTL signals.
Conclusion
Despite the fact that there are considerable differences in the gene expression patterns of the porcine liver and skeletal muscle, we have identified a substantial proportion of common cis-eQTL regulating gene expression in both tissues. Several of these cis-eQTL influence the mRNA levels of genes with important roles in meat (CTSF) and carcass quality (TAPT1), lipid metabolism (TMEM97) and obesity (MARC2), thus evidencing the practical importance of dissecting the genetic mechanisms involved in their expression.
The comparison of expression QTL (eQTL) maps obtained in different tissues is an essential step to understand how gene expression is genetically regulated in a context-dependent manner. In the current work, we have compared the transcriptomic and eQTL profiles of two porcine tissues (skeletal muscle and liver) with highly divergent expression profiles by using a data set of 103 Duroc pigs genotyped with the Porcine SNP60 BeadChip (Illumina) and with available microarray measurements of hepatic and muscle mRNA levels. Since structural variation could have effects on gene expression, we have also investigated the co-localization of cis-eQTL with copy number variant regions (CNVR) segregating in the Duroc population under study.
Results
The analysis of differential expresssion revealed the existence of 1,204 and 1,490 probes that were overexpressed and underexpressed in the gluteus medius muscle when compared to liver, respectively (|fold-change| > 1.5, q-value < 0.05). By performing genome scans in 103 Duroc pigs with available expression and genotypic data, we identified 76 and 28 genome-wide significant cis-eQTL regulating gene expression in the gluteus medius muscle and liver, respectively, and 12 of them (APH1A, ARL2BP, BSDC1, CTSF, LZIC, MARC2, PNPO, POLR3D, RABEP1, TAPT1, TMEM97 and Y1PF1) were shared by both tissues (i.e. 42.8 % of the cis-eQTL identified in the liver were replicated in the gluteus medius muscle). These results are consistent with previous studies performed in humans, where 50% of eQTL were shared across tissues. Moreover, we have identified 41 CNVRs in 350 Duroc pigs typed with the Porcine SNP60 BeadChip by using the PennCNV and GADA softwares, but only a few of these CNVRs co-localized with cis-eQTL signals.
Conclusion
Despite the fact that there are considerable differences in the gene expression patterns of the porcine liver and skeletal muscle, we have identified a substantial proportion of common cis-eQTL regulating gene expression in both tissues. Several of these cis-eQTL influence the mRNA levels of genes with important roles in meat (CTSF) and carcass quality (TAPT1), lipid metabolism (TMEM97) and obesity (MARC2), thus evidencing the practical importance of dissecting the genetic mechanisms involved in their expression.
