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. 2015 Mar 25;47(1):20.
doi: 10.1186/s12711-015-0111-y.

Epigenetic regulation of the ELOVL6 gene is associated with a major QTL effect on fatty acid composition in pigs

Jordi Corominas  1   2 , Jorge A P Marchesi  3 , Anna Puig-Oliveras  4   5 , Manuel Revilla  6   7 , Jordi Estellé  8   9   10 , Estefânia Alves  11 , Josep M Folch  12   13 , Maria Ballester  14   15
Affiliations

Epigenetic regulation of the ELOVL6 gene is associated with a major QTL effect on fatty acid composition in pigs

Jordi Corominas et al. Genet Sel Evol. .

Abstract

Background: In previous studies on an Iberian x Landrace cross, we have provided evidence that supported the porcine ELOVL6 gene as the major causative gene of the QTL on pig chromosome 8 for palmitic and palmitoleic acid contents in muscle and backfat. The single nucleotide polymorphism (SNP) ELOVL6:c.-533C > T located in the promoter region of ELOVL6 was found to be highly associated with ELOVL6 expression and, accordingly, with the percentages of palmitic and palmitoleic acids in longissimus dorsi and adipose tissue. The main goal of the current work was to further study the role of ELOVL6 on these traits by analyzing the regulation of the expression of ELOVL6 and the implication of ELOVL6 polymorphisms on meat quality traits in pigs.

Results: High-throughput sequencing of BAC clones that contain the porcine ELOVL6 gene coupled to RNAseq data re-analysis showed that two isoforms of this gene are expressed in liver and adipose tissue and that they differ in number of exons and 3'UTR length. Although several SNPs in the 3'UTR of ELOVL6 were associated with palmitic and palmitoleic acid contents, this association was lower than that previously observed with SNP ELOVL6:c.-533C > T. This SNP is in full linkage disequilibrium with SNP ELOVL6:c.-394G > A that was identified in the binding site for estrogen receptor alpha (ERα). Interestingly, the ELOVL6:c.-394G allele is associated with an increase in methylation levels of the ELOVL6 promoter and with a decrease of ELOVL6 expression. Therefore, ERα is clearly a good candidate to explain the regulation of ELOVL6 expression through dynamic epigenetic changes in the binding site of known regulators of ELOVL6 gene, such as SREBF1 and SP1.

Conclusions: Our results strongly suggest the ELOVL6:c.-394G > A polymorphism as the causal mutation for the QTL on pig chromosome 8 that affects fatty acid composition in pigs.

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Figures

Figure 1
Figure 1
Genetic architecture of the porcine ELOVL6 gene, with the two transcribed variants identified by BAC sequencing and RNAseq analysis. Exons are indicated by blue boxes with dark blue corresponding to sequences that code for ELOVL6 protein and pale blue to 5’UTR and 3’UTR regions.
Figure 2
Figure 2
Association analysis between SNP genotypes for SSC8 and the percentages of: palmitic (A) and palmitoleic (B) acid in muscle and palmitic (C) and palmitoleic (D) acid in backfat. ELOVL6 polymorphisms are included and labeled with a red circle. Positions in Mb are relative to the Sscrofa 10.2 assembly of the pig genome. The vertical dashed line indicates the position of ELOVL6 gene and the horizontal dashed line marks the chromosome-wide significance level (FDR-based q-value ≤ 0.05).
Figure 3
Figure 3
Characterization of the methylation patterns on the ELOVL6 gene promoter. (A) Schematic representation of the transcription factor binding elements studied, together with the CpG-sites analyzed in the methylation study. (B) Plot showing the percentages of methylation observed for each CpG-site in four porcine tissues: liver, backfat, muscle and spleen. Data represent means ± SEM. Values with different superscript letters (a, b, c and d) indicate significant differences between groups (p-value < 0.05), as determined by a linear model in R.
Figure 4
Figure 4
Tissue-specific differences in ELOVL6 gene expression among liver, adipose tissue, muscle and spleen. Gene expression quantification was performed by real-time quantitative PCR (RT-qPCR), according to the procedure described in [2]. Gene expression was compared using the 2ΔCt data obtained from quantitative PCR analyses. Data represent mean ± SEM.
Figure 5
Figure 5
Effect of the ELOVL6:c.-394G > A polymorphism on ELOVL6 gene expression regulation. (A) Plot showing the percentage of methylation observed for each CpG-site according to ELOVL6:c.-394G > A genotypes. (B) Plot showing ELOVL6 expression levels in backfat according to ELOVL6:c.-394G > A genotypes. Data represents means ± SEM. Values with different superscript letter (a, b and c) indicate significant differences between groups (p-value < 0.05) as determined by a linear model in R.
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