Abstract
Simple SummaryRNA 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.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.
Highlights
RNA polyadenylation is an important step in the messenger RNA maturation process, and the first step is recognizing the polyadenylation signal (PAS)
After removing low quantity reads and the reads not starting or ending with at least 10 As or Ts, we obtained a total of 105,103 expressed sequence tag (EST) sequences and 352,764,416 RNA-seq reads with a poly(A) tail
By removing internally primed cleavage sites (The downstream of the cleavage site contained at least eight consecutive A in the genome) and merging closely spaced cleavage sites, we identified a total of 62,491 pA sites
Summary
RNA polyadenylation is an important step in the messenger RNA (mRNA) maturation process, and the first step is recognizing the polyadenylation signal (PAS). 1. Introduction with regard to jurisdictional claims in RNA polyadenylation, addition of a 30 poly(A) tail at the cleavage site (CS) of a pre-mRNA, is an important step of eukaryotic gene expression, affecting mRNA stability, translation, transport, and other post-transcriptional processes [1,2,3,4,5,6]. The two core cis-acting elements are a highly conserved AAUAAA hexamer motif, known as the polyadenylation signal (PAS), 10–30 bp 50 to the cleavage site, and a more variable U/UG-rich element 15–30 bp 30 of the cleavage site [7]. The PAS is the binding site for the cleavage and polyadenylation specificity factor (CPSF) [8,9], one protein complex of the polyadenylation machinery. The downstream U/UG-rich element is the binding site of the cleavage-stimulating factor (CstF) [11], another key polyadenylation machinery protein complex. In silico analysis of the poly (A) tail-containing transcripts from human, mouse, freshwater planarian (Schmidtea mediterrane) and fruit fly (Drosophila melanogaster) reveals that the canonical PAS, AAUAAA, is present only in 40–49% of the mRNAs, 25~40% of the mRNAs contain a single-nucleotide variant of the canonical AAUAAA hexamer motif, and the remaining
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