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Background <p>Alternative polyadenylation (APA) is one of the important post-transcriptional regulatory mechanisms in eukaryotes. It can regulate gene expression by altering the length of the 3’ untranslated region (3’UTR), thus influencing the presence of cis-elements. The growth and development of skeletal muscle is a process which is regulated by multiple factors in an orderly manner, but the role of APA in this process remains unclear.</p> Methods <p>In this study, RNA-Seq data from the longissimus dorsi muscles of Jinfen White pigs, Large White pigs and Mashen pigs at day1, day90 and day180 of age were analysed to explore the dynamic changes of APA during growth and development of skeletal muscle in pigs. The DaPars and APAtrap algorithms were utilized to identify APA events during the muscle development process in three pig breeds at multiple developmental stages. Subsequent analysis focused on investigating the trends of 3’UTR changes, and in conjunction with differential expression results, exploring the variations in 3’UTR abundance and length. In addition, differences in cytoplasmic polyadenylation elements (CPEs), polyadenylation signals (PASs), and microRNA sites were characterized in 3’UTRs corresponding to different observed lengths.</p> Results <p>By comparing the differentially expressed and differentially alternatively-polyadenylated transcripts (DE-DaPTs) across the three breeds, four common genes were identified: <i>CMYA</i>5, <i>GPD</i>1, <i>TWF</i>2 and <i>PPP</i>1R3B. Furthermore, the 3’ rapid amplification of cDNA ends (3’RACE) experiment confirmed that <i>GPD</i>1 has two distinct UTR-APA isoforms in various tissues and cells, with 3’UTR lengths of 567&#xa0;bp and 1764&#xa0;bp, respectively.</p> Conclusions <p>The present results provide further evidence that APA might have a role in muscle development in pigs. <i>GPD</i>1 was confirmed to have two APA isoforms exhibiting different 3′UTR lengths in multiple tissues and cells of pigs. This research seeks to elucidate the post-transcriptional mRNA regulation mediated by APA, thereby laying the groundwork for a deeper understanding of the molecular mechanisms of selective polyadenylation in myogenesis.</p>

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Global landscape of alternative polyadenylation during the growth and development of skeletal muscle in pigs

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年5月13日

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  • Linyu Jin,
  • Lei Yao,
  • Haonan Xu,
  • Cheng Peng,
  • Yang Yang,
  • Bugao Li,
  • Guoqing Cao,
  • Chang Lu

摘要

Background

Alternative polyadenylation (APA) is one of the important post-transcriptional regulatory mechanisms in eukaryotes. It can regulate gene expression by altering the length of the 3’ untranslated region (3’UTR), thus influencing the presence of cis-elements. The growth and development of skeletal muscle is a process which is regulated by multiple factors in an orderly manner, but the role of APA in this process remains unclear.

Methods

In this study, RNA-Seq data from the longissimus dorsi muscles of Jinfen White pigs, Large White pigs and Mashen pigs at day1, day90 and day180 of age were analysed to explore the dynamic changes of APA during growth and development of skeletal muscle in pigs. The DaPars and APAtrap algorithms were utilized to identify APA events during the muscle development process in three pig breeds at multiple developmental stages. Subsequent analysis focused on investigating the trends of 3’UTR changes, and in conjunction with differential expression results, exploring the variations in 3’UTR abundance and length. In addition, differences in cytoplasmic polyadenylation elements (CPEs), polyadenylation signals (PASs), and microRNA sites were characterized in 3’UTRs corresponding to different observed lengths.

Results

By comparing the differentially expressed and differentially alternatively-polyadenylated transcripts (DE-DaPTs) across the three breeds, four common genes were identified: CMYA5, GPD1, TWF2 and PPP1R3B. Furthermore, the 3’ rapid amplification of cDNA ends (3’RACE) experiment confirmed that GPD1 has two distinct UTR-APA isoforms in various tissues and cells, with 3’UTR lengths of 567 bp and 1764 bp, respectively.

Conclusions

The present results provide further evidence that APA might have a role in muscle development in pigs. GPD1 was confirmed to have two APA isoforms exhibiting different 3′UTR lengths in multiple tissues and cells of pigs. This research seeks to elucidate the post-transcriptional mRNA regulation mediated by APA, thereby laying the groundwork for a deeper understanding of the molecular mechanisms of selective polyadenylation in myogenesis.