Landscape of alternative splicing and polyadenylation during growth and development of muscles in pigs

• Published in: Communications biology 2024-12, Vol.7 (1), p.1607-14
• Main Authors: Sun, Yuanlu, Pang, Yu, Wu, Xiaoxu, Zhu, Rongru, Wang, Liang, Tian, Ming, He, Xinmiao, Liu, Di, Yang, Xiuqin
• Format: Article
• Language: English
• Subjects: 38; 38/109; 45; 45/91; 631/136; 631/337; 64; Alternative Splicing; Animals; Biomedical and Life Sciences; Developmental stages; Gene Expression Regulation, Developmental; Gene mapping; Gene regulation; Genes; Life Sciences; Muscle Development - genetics; Muscle, Skeletal - growth & development; Muscle, Skeletal - metabolism; Muscles; Polyadenylation; Post-transcription; Proteomes; Swine - genetics; Swine - growth & development; Transcriptome; Transcriptomes
• ISSN: 2399-3642; 2399-3642
• DOI: 10.1038/s42003-024-07332-w

Alternative polyadenylation (APA) is emerging as a post-transcriptional regulatory mechanism, similar as that of alternative splicing (AS), and plays a prominent role in regulating gene expression and increasing the complexity of the transcriptome and proteome. We use polyadenylation selected long-read isoform sequencing to obtain full-length transcript sequences in porcine muscles at five developmental stages. We identify numerous novel transcripts unannotated in the existing pig genome, including transcripts mapping to known and unknown gene loci, and widespread transcript diversity in porcine muscles. The top 100 most isoformic genes are mainly enriched in Gene Ontology terms related to muscle growth and development. It is revealed that intron retention/exon inclusion and the usage of distal polyadenylation site (PAS) are associated with ageing through analyzing changes of AS and PAS during muscle development. We also identify developmental changes in major transcripts and major PASs. Furthermore, genes/transcripts important for muscle development are identified. The results confirm the importance of AS and APA in pig muscles, substantially increasing transcriptional diversity and showing an important mechanism underlying gene regulation in muscles. The integrative analysis of Iso-Seq and RNA-Seq reveals changes in alternative splicing and polyadenylation at five developmental stages of muscles in pigs.