| DNA methylation,which belongs to a stable and heritable epigenetic modification,is able to regulate gene transcription without altering the gene sequences.Retrotransposition is a special RNA-based duplication mechanism in which transcribed and spliced m RNA are occasionally reverse transcribed and integrated into a new DNA locus to form a retrogene.However,the roles of DNA methylation on origin,evolution and survival of newly originated retrogenesare largely unknown.For this purpose,we used reduced representation bisulfite sequencing(RRBS)and corresponding RNA-seq data of eight diverse Sus scrofa tissues to investigate processes and mechanisms of DNA methylation modification in retrogenes.The main results are as follows:1.We have identified 964 retrocopies,of which 560 significantly contribute to the origin of new retrogenes in pigs.2.By GO and KEGG pathway analysis,these new genes are available for the storage of glycans and lipids as a source of proteins and fats.3.Parental genes display diverse average DNA methylation levels in different genome regions,but retrogenes are generally hyper-methylated.Intriguingly,with hypo-methylation in gene body,parental genes have more opportunities to be retroposed and form more retrocopies.However,hyper-methylation in retrogenes is probably for the sake of protecting retrogenes themselves from being deleted by the deleterious mutations.Or,it might accelerate the mutation chances to promote survival of retrogenes.4.Gene body DNA methylation divergence between parental-retrogene pair is influenced by selective pressure.5.DNA methylation of retrogenes in promoter changes along evolutionary time and plays an important role in regulating retrogene expression levels.In summary,these results suggest that retroposition is an important mechanism which contributes to the formation of new pig genes,and DNA methylation modification drives origination,evolution,and survival of retrogenes. |
PDF Full Text Request