Transcriptome-wide N6-methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern

Background: N-6-methyladenosine (m(6)A) is the most prevalent internal form of modification in messenger RNA in higher eukaryotes and potential regulatory functions of reversible m(6)A methylation on mRNA have been revealed by mapping of m(6)A methylomes in several species. m(6)A modification in active gene regulation manifests itself as altered methylation profiles in a tissue-specific manner or in response to changing cellular or species living environment. However, up to date, there has no data on m(6)A porcine transcriptome-wide map and its potential biological roles in adipose deposition and muscle growth. Methods: In this work, we used methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-Seq) technique to acquire the first ever m(6)A porcine transcriptome-wide map. Transcriptomes of muscle and adipose tissues from three different pig breeds, the wild boar, Landrace, and Rongchang pig, were used to generate these maps. Results: Our findings show that there were 5,872 and 2,826 m(6)A peaks respectively, in the porcine muscle and adipose tissue transcriptomes. Stop codons, 3'-untranslated regions, and coding regions were found to be mainly enriched for m(6)A peaks. Gene ontology analysis revealed that common m(6)A peaks in nuclear genes are associated with transcriptional factors, suggestive of a relationship between m(6)A mRNA methylation and nuclear genome transcription. Some genes showed tissue- and breed-differential methylation, and have novel biological functions. We also found a relationship between the m(6)A methylation extent and the transcript level, suggesting a regulatory role for m(6)A in gene expression. Conclusion: This comprehensive map provides a solid basis for the determination of potential functional roles for RNA m(6)A modification in adipose deposition and muscle growth.