Profiling the Spatial Expression Pattern and ceRNA Network of lncRNA, miRNA, and mRNA Associated with the Development of Intermuscular Bones in Zebrafish

Simple Summary Worldwide, many of the major economic fish have intermuscular bones (IBs). The existence of IBs leads to potential edible risks, lowers the quality of fish, and is not conducive for further processing and expanding the consumer market. The development of IBs is regulated by complex molecular networks, including mRNA-miRNA-lncRNA ceRNA networks. Using zebrafish as a model, this study revealed, for the first time, the spatial expression pattern and ceRNA networks of lncRNA, miRNA, and mRNA associated with IB development. In addition, we identified a series of key genes and pathways that may be involved in the formation and growth of IBs. Our findings provide new insights into the molecular mechanisms of IB development and clues for improving IB traits. Intermuscular bones (IBs) are small spicule-like bones in the muscular septum of fish, which affect their edible and economic value. The molecular mechanism of IB development is still uncertain. Numerous studies have shown that the ceRNA network, which is composed of mRNA, lncRNA, and miRNA, plays an important regulatory role in bone development. In this study, we compared the mRNA, lncRNA, and miRNA expression profiles in different IB development segments of zebrafish. The development of IBs includes two main processes, which are formation and growth. A series of genes implicated in the formation and growth of IBs were identified through gene differential expression analysis and expression pattern analysis. Functional enrichment analysis showed that the functions of genes implicated in the regulation of the formation and growth of IBs were quite different. Ribosome and oxidative phosphorylation signaling pathways were significantly enriched during the formation of IBs, suggesting that many proteins are required to form IBs. Several pathways known to be associated with bone development have been shown to play an important role in the growth of IBs, including calcium, ECM-receptor interaction, Wnt, TGF-beta, and hedgehog signaling pathways. According to the targeting relationship and expression correlation of mRNA, lncRNA, and miRNA, the ceRNA networks associated with the growth of IBs were constructed, which comprised 33 mRNAs, 9 lncRNAs, and 7 miRNAs. This study provides new insight into the molecular mechanism of the development of IBs.