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

Lulu Deng,Chengchi Fang,Cheng Zou,Changchun Li,Long Li

doi:10.1155/2020/2626584

Lulu Deng, Chengchi Fang + Show 3 more

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https://doi.org/10.1155/2020/2626584

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Abstract

Many increasing documents have proved that alternative polyadenylation (APA) events with different polyadenylation sites (PAS) contribute to posttranscriptional regulation. However, little is known about the detailed molecular features of PASs and its role in porcine fast and slow skeletal muscles through microRNAs (miRNAs) and RNA binding proteins (RBPs). In this study, we combined single-molecule real-time sequencing and Illumina RNA-seq datasets to comprehensively analyze polyadenylation in pigs. We identified a total of 10,334 PASs, of which 8734 were characterized by reference genome annotation. 32.86% of PAS-associated genes were determined to have more than one PAS. Further analysis demonstrated that tissue-specific PASs between fast and slow muscles were enriched in skeletal muscle development pathways. In addition, we obtained 1407 target genes regulated by APA events through potential binding 69 miRNAs and 28 RBPs in variable 3′ UTR regions and some are involved in myofiber transformation. Furthermore, the de novo motif search confirmed that the most common usage of canonical motif AAUAAA and three types of PASs may be related to the strength of motifs. In summary, our results provide a useful annotation of PASs for pig transcriptome and suggest that APA may serve as a role in fast and slow muscle development under the regulation of miRNAs and RBPs.

Highlights

Polyadenylation involving in the cleavage of 3′ signaling region of precursor mRNA and the addition of a poly(A) tail is the final core step of mRNA maturation [1, 2]. e upstream and downstream cis elements constantly regulate the cleavage of polyadenylation sites (PASs). ese elements mainly consist of an upstream canonical poly(A) signal AAUAAA and a less defined downstream U/GU-rich region [3, 4]
Comparing with the Ensembl reference annotation, 84.52% of PASs were aligned to the annotated genes, and the remaining 1600 PASs were mapped to the intergenic regions (Figure 1(b) and Table S2), which might represent unknown genes or novel distal sites in the downstream 3′ untranslated region (3′ UTR) regions of the known genes. ese PASs which were located in annotated genes mainly corresponded to two modes based on the annotated genomic features: 3′ most exon and upstream region (Figure 1(a))
Major (83.52%, 7295) PASs were in the type of 3′ UTR regions, and a small part of PASs was in introns (9.61%, 839), CDS (1.59%, 139), and 5′ UTR regions (0.29%, 25)

Summary

Introduction

Polyadenylation involving in the cleavage of 3′ signaling region of precursor mRNA (pre-mRNA) and the addition of a poly(A) tail is the final core step of mRNA maturation [1, 2]. e upstream and downstream cis elements constantly regulate the cleavage of polyadenylation sites (PASs). ese elements mainly consist of an upstream canonical poly(A) signal AAUAAA and a less defined downstream U/GU-rich region (typically GUGU) [3, 4]. Polyadenylation involving in the cleavage of 3′ signaling region of precursor mRNA (pre-mRNA) and the addition of a poly(A) tail is the final core step of mRNA maturation [1, 2]. E upstream and downstream cis elements constantly regulate the cleavage of polyadenylation sites (PASs). Ese elements mainly consist of an upstream canonical poly(A) signal AAUAAA and a less defined downstream U/GU-rich region (typically GUGU) [3, 4]. PASs located in internal exons or introns named coding region-APA (CR-APA). In another case, PASs located in the 3′ untranslated region (3′ UTR) (UTR-APA) result in the production of transcripts with diverse 3′ UTRs [9]

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