College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China.
Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China.
Cell Prolif. 2024 Feb;57(2):e13545. doi: 10.1111/cpr.13545. Epub 2023 Sep 13.
Alternative splicing (AS) disruption has been linked to disorders of muscle development, as well as muscular atrophy. However, the precise changes in AS patterns that occur during myogenesis are not well understood. Here, we employed isoform long-reads RNA-seq (Iso-seq) and single-cell RNA-seq (scRNA-seq) to investigate the AS landscape during myogenesis. Our Iso-seq data identified 61,146 full-length isoforms representing 11,682 expressed genes, of which over 52% were novel. We identified 38,022 AS events, with most of these events altering coding sequences and exhibiting stage-specific splicing patterns. We identified AS dynamics in different types of muscle cells through scRNA-seq analysis, revealing genes essential for the contractile muscle system and cytoskeleton that undergo differential splicing across cell types. Gene-splicing analysis demonstrated that AS acts as a regulator, independent of changes in overall gene expression. Two isoforms of splicing factor TRA2B play distinct roles in myogenic differentiation by triggering AS of TGFBR2 to regulate canonical TGF-β signalling cascades differently. Our study provides a valuable transcriptome resource for myogenesis and reveals the complexity of AS and its regulation during myogenesis.
选择性剪接 (AS) 紊乱与肌肉发育障碍以及肌肉萎缩有关。然而，在肌发生过程中发生的 AS 模式的精确变化还不是很清楚。在这里，我们采用了异构体长读 RNA-seq (Iso-seq) 和单细胞 RNA-seq (scRNA-seq) 来研究肌发生过程中的 AS 图谱。我们的 Iso-seq 数据鉴定了 61146 个全长异构体，代表 11682 个表达基因，其中超过 52%是新的。我们鉴定了 38022 个 AS 事件，其中大多数事件改变编码序列并表现出阶段特异性剪接模式。我们通过 scRNA-seq 分析鉴定了不同类型肌肉细胞中的 AS 动态，揭示了在细胞类型之间经历差异剪接的收缩肌系统和细胞骨架的关键基因。基因剪接分析表明，AS 作为一种调节剂，独立于整体基因表达的变化而起作用。剪接因子 TRA2B 的两种异构体通过触发 TGFBR2 的 AS 以不同方式调节经典 TGF-β信号级联来发挥不同的作用。我们的研究为肌发生提供了有价值的转录组资源，并揭示了 AS 及其在肌发生过程中的调控的复杂性。
