Integrated Comparative Transcriptome and circRNA-lncRNA-miRNA-mRNA ceRNA Regulatory Network Analyses Identify...

Area of Science:

• Animal Genomics
• Molecular Biology
• Meat Science

Background:

• Intramuscular fat (IMF) content is a crucial carcass trait in beef cattle, significantly impacting meat quality.
• The complex molecular mechanisms regulating IMF and fat metabolism in beef cattle remain incompletely understood.

Purpose of the Study:

• To identify candidate messenger RNAs (mRNAs) and regulatory RNAs involved in IMF and fat metabolism.
• To construct a competing endogenous RNA (ceRNA) network for understanding molecular regulation in longissimus dorsi muscle (LDM) tissue.
• To analyze these mechanisms across five diverse beef cattle breeds.

Main Methods:

• Comparative transcriptomic analysis of LDM tissue from five beef cattle breeds.
• Construction and analysis of a competing endogenous RNA (ceRNA) network.
• Integration of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses.
• Clustering analysis to identify key regulatory subnets.

Main Results:

• Identification of 34 circRNAs, 57 lncRNAs, 15 miRNAs, and 374 mRNAs.
• Detection of 7 key subnets comprising 16 circRNAs, 43 lncRNAs, 7 miRNAs, and 237 mRNAs.
• Enrichment analysis revealed significant GO terms related to IMF and identified key signaling pathways (metabolic, calcium, cGMP-PKG, thyroid hormone, oxytocin).
• Identification of MCU, CYB5R1, and BAG3 as important candidate marker genes for fat metabolism.

Conclusions:

• The study provides novel insights into the molecular mechanisms regulating IMF and fat metabolism in beef cattle.
• The developed ceRNA network and identified candidate genes offer a foundation for future research in meat quality improvement.
• Transcriptome profiles across breeds highlight genetic contributions to IMF variation.