Analysis Polyadenylation Signal Usage in Sus scrofa

SIMPLE SUMMARY: RNA polyadenylation is an important step of eukaryotic gene expression and the progress depends on a highly conserved AAUAAA hexamer motif, known as the polyadenylation signal (PAS). We identified polyadenylation signals in Sus scrofa, the PAS motif similar with other mammalians. APA (alternative polyadenylation) analysis show that most gene was affect by the alternative polyadenlation in Sus scrofa. The PAS data presented in this manuscript will be useful for Sus scrofa research by facilitating the improved annotation of the Sus scrofa genome and post-transcriptionally regulation mode. ABSTRACT: RNA polyadenylation is an important step in the messenger RNA (mRNA) maturation process, and the first step is recognizing the polyadenylation signal (PAS). The PAS type and distribution is a key determinant of post-transcriptional mRNA modification and gene expression. However, little is known about PAS usage and alternative polyadenylation (APA) regulation in livestock species. Recently, sequencing technology has enabled the generation of a large amount of sequencing data revealing variation in poly(A) signals and APA regulation in Sus scrofa. We identified 62,491 polyadenylation signals in Sus scrofa using expressed sequence tag (EST) sequences combined with RNA-seq analysis. The composition and usage frequency of polyadenylation signal in Sus scrofa is similar with that of human and mouse. The most highly conserved polyadenylation signals are AAUAAA and AUUAAA, used for over 63.35% of genes. In addition, we also analyzed the U/GU-rich downstream sequence (DSE) element, located downstream of the cleavage site. Our results indicate that APA regulation was widely occurred in Sus scrofa, as in other organisms. Our result was useful for the accurate annotation of RNA 3′ ends in Sus scrofa and the analysis of polyadenylation signal usage in Sus scrofa would give the new insights into the mechanisms of transcriptional regulation.