Transcriptome-wide N 6 -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.