Genome-Wide Analysis and Functional Characterization of the Polyadenylation Site in Pigs Using RNAseq Data

Abstract

Polyadenylation, a critical step in the production of mature mRNA for translation in most eukaryotes, involves cleavage and poly(A) tail addition at the 3′ end of mRNAs at the polyadenylation site (PAS). Sometimes, one gene can have more than one PAS, which can produce the alternative polyadenylation (APA) phenomenon and affect the stability, localization and translation of the mRNA. In this study, we discovered 28,363 PASs using pig RNAseq data, with 13,033 located in 7,403 genes. Among the genes, 41% were identified to have more than one PAS. PAS distribution analysis indicated that the PAS position was highly variable in genes. Additionally, the analysis of RNAseq data from the liver and testis showed a difference in their PAS number and usage. RT-PCR and qRT-PCR were performed to confirm our findings by detecting the expression of 3′UTR isoforms for five candidate genes. The analysis of RNAseq data under a different androstenone level and salmonella inoculation indicated that the functional usage of PAS might participate in the immune response and may be related to the androstenone level in pigs. This study provides new insights into pig PAS and facilitates further functional research of PAS.

Genome-Wide Profiling of Polyadenylation Events in Maize Using High-Throughput Transcriptomic Sequences

“…Availability of large numbers of transcriptomic sequences provides an unprecedented opportunity to explore genome-wide polyadenylation profiles. The standard RNA-seq reads are commonly used to define the genome wide polyadenylation profiles in species with no available or limited polyadenylation data (Zhao et al 2014; Wang et al 2016b). Here, 9.48 billion RNA-Seq reads from the 24 high-throughput transcriptomic studies were analyzed to comprehensively characterize genome-wide polyadenylation profiles in the maize.…”

“…The reads containing eight or more A-residues at the 3′ end or T-residues at 5′ end (according to the strand specificity) were defined as the polyadenylated reads as described previously (Wang et al 2016b). Briefly, the FindTail program (Dong et al 2015) with “–endgap 2” parameter was used to select the polyadenylated reads.…”

Characterization and Functional Analysis of Polyadenylation Sites in Fast and Slow Muscles

“…e tissue specificity of PASs has been confirmed in other organisms [8,42,43]. We analyzed PASs in four tissues at two ages by using RNAseq datasets and the new modified structure annotation file.…”

“…Muscle filament sliding Actin filament organization Glucose metabolic process Glycolysis/gluconeogenesis PPAR signaling pathway ACAA1 (PAS-seq), direct RNA sequencing (DRS), poly(A)-test RNA-sequencing (PAT-seq), and whole-transcriptome termini site sequencing (WTTS-seq) [24,[49][50][51]. However, there are only limited articles comprehensively annotating porcine polyadenylation with RNA-seq datasets [43]. In general, short-read RNA sequencing techniques have the fact that alignments allow us to infer, but have limitations for directly understanding the complexity of potential isoforms [22].…”

Mammalian Cis-Acting RNA Sequence Elements

“…Immediately after cleavage, poly(A) polymerases (PAPs) promote lengthening of the poly(A) tail, completing the mRNA maturation process [98,99]. Genomewide polyadenylation site (PAS) analysis in mammalian cells identified a great diversity of PAS utilization in different tissues and organs [73,100]. Mutations can cause the loss of the canonical adenylation signal and subsequent switch to alternative PAS utilization [101].…”