Regulation of DNA methylation on EEF1D and RPL8 expression in cattle

Xuan Liu,Qin Zhang,Li Jiang,Jie Yang

doi:10.1007/s10709-017-9974-x

Xuan Liu, Qin Zhang + Show 2 more

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https://doi.org/10.1007/s10709-017-9974-x

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Abstract

Dynamic changes to the epigenome play a critical role in a variety of biology processes and complex traits. Many important candidate genes have been identified through our previous genome wide association study (GWAS) on milk production traits in dairy cattle. However, the underlying mechanism of candidate genes have not yet been clearly understood. In this study, we analyzed the methylation variation of the candidate genes, EEF1D and RPL8, which were identified to be strongly associated with milk production traits in dairy cattle in our previous studies, and its effect on protein and mRNA expression. We compared DNA methylation profiles and gene expression levels of EEF1D and RPL8 in five different tissues (heart, liver, mammary gland, ovary and muscle) of three cows. Both genes showed the highest expression level in mammary gland. For RPL8, there was no difference in the DNA methylation pattern in the five tissues, suggesting no effect of DNA methylation on gene expression. For EEF1D, the DNA methylation levels of its first CpG island differed in the five tissues and were negatively correlated with the gene expression levels. To further investigate the function of DNA methylation on the expression of EEF1D, we collected blood samples of three cows at early stage of lactation and in dry period and analyzed its expression and the methylation status of the first CpG island in blood. As a result, the mRNA expression of EEF1D in the dry period was higher than that at the early stage of lactation, while the DNA methylation level in the dry period was lower than that at the early stage of lactation. Our result suggests that the DNA methylation of EEF1D plays an important role in the spatial and temporal regulation of its expression and possibly have an effect on the milk production traits.

Highlights

Milk production traits are the most important traits in dairy cattle
The results showed about two- to three-fold higher expression level in mammary gland than in other tissues (Fig. 1a), which is well in accordance with the mRNA expression of EEF1D in these tissues in our previous study (Jiang et al 2014)
Since no significant SNPs were found in the coding region of EEF1D in our previous association studies, we paid our attention to the promoter region

Summary

Introduction

Milk production traits are the most important traits in dairy cattle. In the past decades, many studies have been carried out to reveal the genetic basis of milk production traits (Zhang et al 1998; Farnir et al 2002; Ashwell et al 2004; Jiang et al 2010; Mai et al 2010) and a lot of candidate genes or QTL affecting milk yield and milk components have been reported (Viitala et al 2006; Winter et al 2002; Wang et al 2013). Genetica (2017) 145:387–395 expression profiles (Wickramasinghe et al 2012; Connor et al 2013; Singh et al 2013; Cui et al 2014) These findings provide new insights into genetic basis of milk production traits, the underlying mechanism of potential candidate genes have not yet been clearly understood. One SNP located in the promoter region of EEF1D showed strong association with milk yield, fat percentage and protein percentage with P values of 9.23E-06, 2.07E-15 and 1.26E-07, respectively (Jiang et al 2014). We investigated the mRNA expression of 20 significant candidate genes in different tissues in dairy cattle and most of them showed higher expression in mammary gland than in other tissues Both EEF1D and RPL8 had the highest expression in mammary gland among the 20 genes. EEF1D and RPL8 were considered as two promising candidate genes for milk production traits in dairy cattle

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