Abstract:

This study aimed to analyze the expression profiles of long non-coding RNAs (lncRNAs) in bovine muscle tissues during embryonic development, with the goal of identifying lncRNAs potentially involved in muscle development. Transcriptome sequencing was conducted on muscle tissue samples from 3 developmental stages (3-month-old fetuses, 6-month-old fetuses, and 9-month-old newborns obtained from genetically homogeneous Japanese Black cattle using embryo splitting techniques). Differential expression analysis was performed on the identified lncRNAs to screen key lncRNAs involved in embryonic muscle development. Subsequent bioinformatic analyses were carried out to predict the functions and target genes of these lncRNAs. Sequencing data revealed 9 913 differentially expressed lncRNAs and 3 079 differentially expressed mRNA transcripts across the developmental stages. Clustering analysis indicated that the highest number of differentially expressed lncRNAs and mRNAs occurred in the 3-month-old fetal muscle tissue. By identifying protein-coding genes located within 10 kb upstream or downstream of the differentially expressed lncRNAs, 2 064 cis-regulated target genes were predicted. A Venn diagram analysis comparing these target genes with the differentially expressed mRNAs identified 448 overlapping genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of these overlapping genes highlighted 99 lncRNAs and 27 candidate target mRNAs closely associated with muscle development. Short time-series expression miner (STEM) analysis of expression data revealed that both lncRNAs and mRNAs clustered into a significant profile characterized by an initial increase followed by a decrease in expression levels, encompassing 68 lncRNAs and 12 mRNAs. Finally, a regulatory network was constructed using Cytoscape based on cis-regulatory relationships based on the 68 lncRNAs and 12 mRNAs, suggesting that the majority of these lncRNAs may regulate genes such as SERP1, FXR1, and DVL3. The results showed that the 3-month-old period may be a critical period for bovine muscle development, and the 68 lncRNAs screened may affect the expression of corresponding target genes through competitive adsorption of corresponding miRNAs, thereby playing a regulatory role in the growth and development of bovine skeletal muscles at different stages.

Key words: RNA-Seq, bioinformatics analysis, bovine muscle tissue, lncRNA