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Background <p>Huaxi Cattle is a newly developed beef cattle breed in China with independent intellectual property rights. It exhibits internationally advanced levels of daily weight gain, slaughter rate, and net meat yield. Although circular RNA (circRNA) expression has been shown to be highly tissue- and species-specific, the circRNA profiles across different developmental stages of Huaxi cattle muscle remain poorly characterized.</p> Results <p>In the study, we collected longissimus dorsi muscle samples from newborn (NB), young (YG), and adult (AD) Huaxi cattle for RNA sequencing (RNA-seq). A total of 28,013 circRNAs were identified. Differential expression (DE) analysis revealed 633, 41, and 578 DE circRNAs in the YG vs. NB, AD vs. YG, and AD vs. NB comparison groups, respectively. Four DE circRNAs were common across all three comparison groups. Gene Ontology (GO) enrichment analysis of the host genes of DE circRNAs showed that biological process (BP) terms in the YG vs. NB group were predominantly related to metabolic processes. In the AD vs. YG group, BP terms were primarily associated with limb morphogenesis, whereas in the AD vs. NB group, BP terms were mostly linked to muscle development. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis identified 14 significant pathways, including adhesion junctions and tight junctions in the YG vs. NB group. In the AD vs. YG group, pathways such as FoxO signaling, calcium signaling, and RNA transport were enriched. In the AD vs. NB group, significant pathways included propanoate metabolism, MAPK signaling, and mTOR signaling. Reverse Transcription-PCR (RT-PCR) amplification and Sanger sequencing confirmed back-splicing in seven circRNAs. The RNase R resistance assay demonstrated that these circRNAs were more stable than linear mRNA controls. Furthermore, our circRNA-seq and quantitative PCR (qPCR) results were consistent across all three developmental stages. Notably, novel_circ_0018908 was found to play a crucial role in muscle tissue development.</p> Conclusions <p>This study enriches the circRNA library during skeletal muscle development in Huaxi cattle. Furthermore, novel_circ_0018908 was identified as a pivotal circRNA involved in the regulation of skeletal muscle development, providing valuable molecular targets for further study.</p>

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Exploring the landscape of circular RNAs in the development of skeletal muscle in Huaxi cattle

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年10月15日

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  • Xin Hu,
  • Fugui Jiang,
  • Haijian Cheng,
  • Wei You,
  • Yahui Wang,
  • Junya Li,
  • Lupei Zhang,
  • Enliang Song

摘要

Background

Huaxi Cattle is a newly developed beef cattle breed in China with independent intellectual property rights. It exhibits internationally advanced levels of daily weight gain, slaughter rate, and net meat yield. Although circular RNA (circRNA) expression has been shown to be highly tissue- and species-specific, the circRNA profiles across different developmental stages of Huaxi cattle muscle remain poorly characterized.

Results

In the study, we collected longissimus dorsi muscle samples from newborn (NB), young (YG), and adult (AD) Huaxi cattle for RNA sequencing (RNA-seq). A total of 28,013 circRNAs were identified. Differential expression (DE) analysis revealed 633, 41, and 578 DE circRNAs in the YG vs. NB, AD vs. YG, and AD vs. NB comparison groups, respectively. Four DE circRNAs were common across all three comparison groups. Gene Ontology (GO) enrichment analysis of the host genes of DE circRNAs showed that biological process (BP) terms in the YG vs. NB group were predominantly related to metabolic processes. In the AD vs. YG group, BP terms were primarily associated with limb morphogenesis, whereas in the AD vs. NB group, BP terms were mostly linked to muscle development. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis identified 14 significant pathways, including adhesion junctions and tight junctions in the YG vs. NB group. In the AD vs. YG group, pathways such as FoxO signaling, calcium signaling, and RNA transport were enriched. In the AD vs. NB group, significant pathways included propanoate metabolism, MAPK signaling, and mTOR signaling. Reverse Transcription-PCR (RT-PCR) amplification and Sanger sequencing confirmed back-splicing in seven circRNAs. The RNase R resistance assay demonstrated that these circRNAs were more stable than linear mRNA controls. Furthermore, our circRNA-seq and quantitative PCR (qPCR) results were consistent across all three developmental stages. Notably, novel_circ_0018908 was found to play a crucial role in muscle tissue development.

Conclusions

This study enriches the circRNA library during skeletal muscle development in Huaxi cattle. Furthermore, novel_circ_0018908 was identified as a pivotal circRNA involved in the regulation of skeletal muscle development, providing valuable molecular targets for further study.