Systematic identification of long noncoding RNAs related to cattle muscle development. Bos taurus

Long noncoding RNAs are of crucial importance in diverse biological processes such as cell-cycle regulation, genomic imprinting, and cell differentiation. However, limit studies on the overall expression status of lncRNAs during muscle development have been conducted. To explore the potential functions of lncRNAs in cattle muscle development, we employed Ribo-Zero-Seq to systematically identify lncRNAs expressed in embryonic (90 day), neonatal (3-day-old) and adult (24-month-old) longissimus muscle (LM) of Qinchuan steers. We finally defined 7692 high-confidence lncRNAs. Further data analyses showed that a total of 401 lncRNAs were differentially expressed among three tested samples, including H19, linc-MD1 and TCONS_00154844. Interestingly, the chromosomal location of linc-MD1 and TCONS_00154844 is overlapped with miR-206/miR-133b or miR-1-2/miR-133a-2 cluster, respectively. miR-1, miR-133 and miR-206 are the most extensively studied miRNAs involved in myogenesis. The genomic close positional relationship between linc-MD1 and miR-206/miR-133b, TCONS_00154844 and miR-1-2/miR-133a-2 strongly indicated that these lncRNAs may play crucial roles in muscle development. GO annotation and KEGG analyses demonstrated that the lncRNAs-targeted mRNAs were related to myogenic differentiation, including metabolic pathways, regulation of actin cytoskeleton, and PI3K-Akt signaling pathway. Our findings complement the reference genome annotation of cattle, which might further aid the lncRNAs cloning and biological functional analyses.