Shangguan Aishao, Yang Juan, Zhang Nian, Tao Hu, Zhang Feng, Xu Tian, Chen Mingxin, Xiong Qi
Key Laboratory of Animal Embryo Engineering and Molecular Breeding of Hubei Province, Institute of Animal Sciences and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China.
Key Laboratory of Animal Embryo Engineering and Molecular Breeding of Hubei Province, Institute of Animal Sciences and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China.
Genomics. 2025 Jul;117(4):111059. doi: 10.1016/j.ygeno.2025.111059. Epub 2025 May 21.
Alternative splicing (AS) plays a crucial role in the post-transcriptional regulation of gene expression, influencing skeletal muscle growth and development. However, research into transcriptomic landscape of AS and its key isoforms associated with skeletal muscle in goats is comparatively limited compared with other livestock species such as pigs. In this study, longissimus dorsi muscles from 4 Macheng black goats and 4 Boer goats were used to perform Oxford Nanopore Technologies full-length sequencing and Illumina RNA-seq. A total of 91,874 unique full-length non-chimeric sequences and 10,955 novel isoforms were identified. Subsequently, we detected 13,866 AS events and 1702 novel long non-coding RNAs (lncRNAs), with exon skipping (4024, 29.02 %) being the most prevalent AS event. In addition, a total of 2267 differentially expressed isoforms (DEIs) were identified between Macheng black and Boer goats. Among these DEIs, 1301 isoforms were up-regulated and 966 were down-regulated in Macheng black goats. Functional enrichment analyses revealed that these DEIs were predominantly associated with pathways related to skeletal muscle development, cellular metabolic processes, and genetic information processing. Notably, we identified LUC7L-201 as an important isoform that negatively regulates cell proliferation and differentiation in goat primary myoblasts, as demonstrated by overexpression experiments. Overall, this study enhances our understanding of the transcriptomic diversity underlying skeletal muscle growth and development in goats, providing valuable insights for future research and potential applications in livestock management.
可变剪接（Alternative splicing，AS）在基因表达的转录后调控中起着关键作用，影响骨骼肌的生长和发育。然而，与猪等其他家畜物种相比，关于山羊AS转录组图谱及其与骨骼肌相关的关键异构体的研究相对有限。在本研究中，采集了4只麻城黑山羊和4只波尔山羊的背最长肌，用于进行牛津纳米孔技术全长测序和Illumina RNA测序。共鉴定出91,874条独特的全长非嵌合序列和10,955条新异构体。随后，我们检测到13,866个可变剪接事件和1702条新的长链非编码RNA（lncRNA），其中外显子跳跃（4024个，占29.02%）是最常见的可变剪接事件。此外，在麻城黑山羊和波尔山羊之间共鉴定出2267个差异表达异构体（DEI）。在这些DEI中，麻城黑山羊中有1301个异构体上调，966个异构体下调。功能富集分析表明，这些DEI主要与骨骼肌发育、细胞代谢过程和遗传信息处理相关的通路有关。值得注意的是，过表达实验表明，我们鉴定出LUC7L-201是一种重要的异构体，它对山羊原代成肌细胞的增殖和分化具有负调控作用。总体而言，本研究增进了我们对山羊骨骼肌生长发育背后转录组多样性的理解，为未来的研究以及家畜管理中的潜在应用提供了有价值的见解。
