Sun Yuanlu, Pang Yu, Wu Xiaoxu, Zhu Rongru, Wang Liang, Tian Ming, He Xinmiao, Liu Di, Yang Xiuqin
College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China.
Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China.
Commun Biol. 2024 Dec 3;7(1):1607. 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.
可变聚腺苷酸化（APA）正作为一种转录后调控机制出现，类似于可变剪接（AS），并在调节基因表达以及增加转录组和蛋白质组的复杂性方面发挥着重要作用。我们使用聚腺苷酸化选择的长读长异构体测序来获取猪肌肉在五个发育阶段的全长转录本序列。我们鉴定出许多在现有猪基因组中未注释的新型转录本，包括映射到已知和未知基因座的转录本，以及猪肌肉中广泛的转录本多样性。异构体数量最多的前100个基因主要富集在与肌肉生长和发育相关的基因本体论术语中。通过分析肌肉发育过程中AS和PAS的变化，发现内含子保留/外显子包含以及远端聚腺苷酸化位点（PAS）的使用与衰老相关。我们还鉴定了主要转录本和主要PAS的发育变化。此外，鉴定出了对肌肉发育重要的基因/转录本。结果证实了AS和APA在猪肌肉中的重要性，极大地增加了转录多样性，并展示了肌肉中基因调控的重要机制。
