Analysis Polyadenylation Signal Usage in Sus scrofa

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.

Analysis of Polyadenylation Signal Usage with Full-Length Transcriptome in Spodoptera frugiperda (Lepidoptera: Noctuidae)

“…In this process, putative novel polyadenylation sites were identified. To achieve it, we first ascertained all sequencing reads starting or ending with adenine or thymine that had a minimum length of 10 nt, which followed Zhang [2] and Tian's [11] process. Next, we removed the terminal As or Ts.…”

“…This mechanism is achieved by adding a 3 poly(A) tail to the 3 end of mRNA precursor cleavage site (CS). It not only affects the stability of mRNA, but also has great significance in post-transcriptional processes such as mRNA translation and trans-nuclear membrane transport [1][2][3][4][5]. It can be affected by a variety of factors, including self-carrying elements and abundant transacting protein factors.…”