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Identification of porcine imprinted genes involved in skeletal muscle development by high-throughput sequencing


 Background

Imprinted genes—exhibiting parent-specific transcription—play essential roles in the process of mammalian development and growth. To further understand the imprinted genes involved in skeletal muscle development, DNA-seq and RNA-seq were used to explore the characteristics of imprinted genes involved in skeletal muscle development from porcine reciprocal crosses.
Results

A total of 211 paternally and 417 maternally imprinted genes were obtained in this study. Of the candidate imprinted genes, 50 paternally and 112 maternally imprinted genes possessed cytosine and guanine dinucleotide (CpG) islands in their promoters that may have regulated the imprinted gene expression. Imprint-related motifs were predicted and PBX1 motifs may mediate the expression of imprinted genes in the process of skeletal-muscle development. Functional analysis showed that a maternally imprinted gene of EPHB1 was involved in skeletal muscle cell proliferation. Imprinted genes involved in the biological processes of cell proliferation, differentiation and fusion were also analyzed. More maternally imprinted genes, including ADRA1D, E2F1, FBXO40, GHRH and WNT5A, were involved in skeletal muscle development than paternally imprinted genes.
Conclusions

Skeletal muscle development is crucial for meat production. This study identified 628 porcine imprinted genes in skeletal muscle and revealed their functional role in skeletal muscle development. Our findings should further assist with the potential use of imprinted genes in pig breeding.