Transcriptome profiling and alternative splicing analysis of skeletal muscle in Pseudocaranx dentex: insights into slow-twitch and fast-twitch muscle specialization
文献类型： 外文期刊
作者： Wang, Huan 1 ; Li, Ang 1 ; An, Changting 1 ; Che, Shuai 1 ; Huang, Rong 1 ; Liu, Shufang 1 ; Zhuang, Zhimeng 1 ;
作者机构： 1.Chinese Acad Fishery Sci, Yellow Sea Fisheries Res Inst, State Key Lab Mariculture Biobreeding & Sustainabl, Qingdao 266071, Peoples R China
2.Qingdao Marine Sci & Technol Ctr, Lab Marine Fisheries Sci & Food Prod Proc, Qingdao 266237, Peoples R China
关键词： Pseudocaranx dentex; Slow-twitch muscle (SM); Fast-twitch muscle (FM); Alternative splicing; Iso-Seq; Muscle specialization
期刊名称：INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES （ 影响因子：8.5； 五年影响因子：8.7 ）
ISSN： 0141-8130
年卷期： 2025 年 312 卷
页码：
收录情况： SCI
摘要： Alternative splicing (AS) plays a crucial role in regulating muscle type specialization characteristics in mammals but has been rarely explored in teleost. In this study, we combined Iso-Seq and RNA-Seq technologies to profile the transcriptome and AS landscape of slow-twitch muscle (SM) and fast-twitch muscle (FM) in a migratory teleost, Pseudocaranx dentex. We identified 24,096 full-length transcripts and 14,346 isoforms in SM, and 18,483 full-length transcripts and 10,541 isoforms in FM, revealing extensive transcript and isoform diversity. The 3086 differentially expressed transcripts (DETs) were found to contribute to metabolic and contractile differences between SM and FM. Additionally, we detected 5761 AS events in SM and 4543 in FM, with skipped exons (SE) and intron retention (IR) being the predominant AS types. Furthermore, 325 differentially AS genes (DASGs) were found to regulate differences in metabolic processes, organelles organization, cellular component organization, and microtubule-based processes. Importantly, transcripts of tnni2, capzb, neb, and pdlim5 produced by AS with significant expression differences between SM and FM were determined to associate with sarcomere assembly. This study provides the first comprehensive view of transcriptome complexity and splice variants in teleost skeletal muscle and sheds light on the molecular mechanisms underlying muscle type specialization through post-transcriptional regulation.
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