Chen Yulong, Wan Shiming, Li Qing, Dong Xiaoru, Diao Jinghan, Liao Qing, Wang Gui-Ying, Gao Ze-Xia
Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, China.
Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China.
Front Cell Dev Biol. 2021 Feb 4;8:603815. doi: 10.3389/fcell.2020.603815. eCollection 2020.
Intermuscular bone (IB) occurs in the myosepta of teleosts. Its existence has an adverse influence on the edible and economic value of fish, especially for aquaculture species belonging to Cypriniformes. The growth mechanism of IBs is quite lacking. In this study, we firstly used single molecular real-time sequencing (SMRT) technology to improve the draft genome annotation and full characterization of the transcriptome for one typical aquaculture species, blunt snout bream (). The long non-coding RNA (lncRNA), microRNA (miRNA), and messenger RNA (mRNA) expression profiles in two IB growth stages (1 and 3 years old) were compared through transcriptome and degradome analyses. A total of 126 miRNAs, 403 mRNAs, and 353 lncRNAs were found to be differentially expressed between the two stages. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the significantly upregulated and in the MAPK/p53 signaling pathway and the significantly downregulated and in the extracellular matrix (ECM)-receptor pathway may play a key regulatory role in IB growth. Bioinformatics analysis subsequently revealed 14 competing endogenous RNA (ceRNA) pairs related to the growth of IBs, consisting of 10 lncRNAs, 7 miRNAs, and 10 mRNAs. Of these, dre-miR-24b-3p and dre-miR-193b-3p are core regulatory factors interacting with four lncRNAs and three mRNAs, the interaction mechanism of which was also revealed by subsequent experiments at the cellular level. In conclusion, our data showed that IBs had higher activity of cell apoptosis and lower mineralization activity in IB_III compared to IB_I via interaction of MAPK/p53 and ECM-receptor signaling pathways. The downregulated interacted with miR-24a-3p and lnc017705, decreased osteoblast differentiation and Ca deposition in the IB_III stage. Our identified functional mRNAs, lncRNAs, and miRNAs provide a data basis for in-depth elucidation of the growth mechanism of teleost IB.
肌间骨（IB）存在于硬骨鱼类的肌隔中。它的存在对鱼类的食用价值和经济价值有不利影响，尤其是对于鲤形目养殖鱼类。目前对肌间骨的生长机制了解甚少。在本研究中，我们首先使用单分子实时测序（SMRT）技术改进了一种典型养殖鱼类——团头鲂（）的基因组草图注释和转录组的全面表征。通过转录组和降解组分析，比较了肌间骨两个生长阶段（1岁和3岁）的长链非编码RNA（lncRNA）、微小RNA（miRNA）和信使RNA（mRNA）表达谱。发现两个阶段之间共有126个miRNA、403个mRNA和353个lncRNA差异表达。京都基因与基因组百科全书（KEGG）分析显示，丝裂原活化蛋白激酶/ p53信号通路中显著上调的 和 以及细胞外基质（ECM）-受体通路中显著下调的 和 可能在肌间骨生长中起关键调节作用。随后的生物信息学分析揭示了14对与肌间骨生长相关的竞争性内源RNA（ceRNA），由10个lncRNA、7个miRNA和10个mRNA组成。其中，dre-miR-24b-3p和dre-miR-193b-3p是与4个lncRNA和3个mRNA相互作用的核心调节因子，随后的细胞水平实验也揭示了它们的相互作用机制。总之，我们的数据表明，通过丝裂原活化蛋白激酶/ p53和细胞外基质-受体信号通路的相互作用，与IB_I相比，IB_III中的肌间骨细胞凋亡活性更高，矿化活性更低。下调的 与miR-24a-3p和lnc017705相互作用，在IB_III阶段降低了成骨细胞分化和钙沉积。我们鉴定出的功能性mRNA、lncRNA和miRNA为深入阐明硬骨鱼类肌间骨的生长机制提供了数据基础。
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