1. Genome-wide identification and analysis of long noncoding RNAs in longissimus muscle tissue from Kazakh cattle and Xinjiang brown cattle.
- Author
-
Xiang-Min Yan, Zhe Zhang, Jian-Bo Liu, Na Li, Guang-Wei Yang, Dan Luo, Yang Zhang, Bao Yuan, Hao Jiang, and Jia-Bao Zhang
- Subjects
- *
LINCRNA , *REVERSE transcriptase polymerase chain reaction , *ERECTOR spinae muscles , *CELLULAR signal transduction , *PI3K/AKT pathway , *CATTLE , *FALSE discovery rate - Abstract
Objective: In recent years, long noncoding RNAs (lncRNAs) have been identified in many species, and some of them have been shown to play important roles in muscle development and myogenesis. However, the differences in lncRNAs between Kazakh cattle and Xinjiang brown cattle remain undefined; therefore, we aimed to confirm whether lncRNAs are differentially expressed in the longissimus dorsi between these two types of cattle and whether differentially expressed lncRNAs regulate muscle differentiation. Methods: We used RNAseq technology to identify lncRNAs in longissimus muscles from these cattle. The expression of lncRNAs were analyzed using StringTie (1.3.1) in terms of the fragments per kilobase of transcript per million mapped reads values of the encoding genes. The differential expression of the transcripts in the two samples were analyzed using the DESeq R software package. The resulting false discovery rate was controlled by the Benjamini and Hochberg's approach. KOBAS software was utilized to measure the expression of different genes in Kyoto encyclopedia of genes and genomes pathways. We randomly selected eight lncRNA genes and validated them by quantitative reverse transcription polymerase chain reaction (RTqPCR). Results: We found that 182 lncRNA transcripts, including 102 upregulated and 80 downregulated transcripts, were differentially expressed between Kazakh cattle and Xinjiang brown cattle. The results of RTqPCR were consistent with the sequencing results. Enrichment analysis and functional annotation of the target genes revealed that the differentially expressed lncRNAs were associated with the mitogenactivated protein kinase, Ras, and phosphatidylinositol 3kinase (PI3k)/Akt signaling pathways. We also constructed a lncRNA/mRNA coexpression network for the PI3k/Akt signaling pathway. Conclusion: Our study provides insights into cattle muscleassociated lncRNAs and will contribute to a more thorough understanding of the molecular mechanism underlying muscle growth and development in cattle. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF