Xu Shuangbin, Xiao Shijun, Qiu Changliang, Wang Zhiyong
Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, Fujian, PR China.
Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, Fujian, PR China.
Mar Genomics. 2017 Apr;32:71-78. doi: 10.1016/j.margen.2016.12.004. Epub 2017 Jan 6.
Circular RNA (circRNA) was first reported over thirty years ago. With the development of high-throughput sequencing technologies, circRNA has been identified in an increasing number of species. However, few studies on circRNA have been reported in teleost fish. Accumulating transcriptome and phenotype data enable us to probe the biological functions of circRNA in fish species. Here, we report the identification of circRNAs from RNA sequencing (RNA-seq) data in large yellow croaker (Larimichthys crocea), a commercially important marine fish in China and East Asia. Using the computational identification, 975 circular RNAs were detected, of which three were validated by experiments. GO and KEGG analyses revealed the biological functions of genes hosting the circRNAs were enriched in the progression of translation initiation, macromolecule metabolism and binding. Notably, we found that many circRNAs in large yellow croaker had abundant microRNA-binding sites. A total of 363 the identified circRNAs had more than five miRNA-binding sites, among which twenty-two had more than ten binding sites for the miRNA-430 and the let-7 family. Our study confirmed the presence of circRNAs in large yellow croaker for the first time, providing a valuable reference for circRNA identification in fish species. Meanwhile, this work confirmed that the RNA-seq data from the traditional linear transcriptome library could be used for preliminary circRNA identification, which may offer an important reference for preliminary circRNA investigations in other species.
环状RNA（circRNA）早在三十多年前就被首次报道。随着高通量测序技术的发展，越来越多物种中都鉴定出了circRNA。然而，硬骨鱼中关于circRNA的研究报道较少。不断积累的转录组和表型数据使我们能够探究circRNA在鱼类中的生物学功能。在此，我们报道了从大黄鱼（Larimichthys crocea）的RNA测序（RNA-seq）数据中鉴定circRNA，大黄鱼是中国和东亚一种具有重要商业价值的海水鱼。通过计算鉴定，共检测到975个环状RNA，其中3个通过实验得到验证。基因本体（GO）和京都基因与基因组百科全书（KEGG）分析显示，宿主基因的生物学功能在翻译起始、大分子代谢和结合过程中富集。值得注意的是，我们发现大黄鱼中的许多circRNA具有丰富的微小RNA（miRNA）结合位点。总共363个鉴定出的circRNA具有超过5个miRNA结合位点，其中22个对miRNA - 430和let - 7家族具有超过10个结合位点。我们的研究首次证实了大黄鱼中存在circRNA，为鱼类中circRNA的鉴定提供了有价值的参考。同时，这项工作证实了来自传统线性转录组文库的RNA-seq数据可用于circRNA的初步鉴定，这可能为其他物种的circRNA初步研究提供重要参考。
