Deng Yang, Qin Yajuan, Yang Pan, Du Jianjun, Kuang Zheng, Zhao Yongxin, Wang Ying, Li Dayong, Wei Jianhua, Guo Xinyu, Li Lei, Yang Xiaozeng
Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, China.
Front Plant Sci. 2021 Dec 24;12:781836. doi: 10.3389/fpls.2021.781836. eCollection 2021.
MicroRNA (miRNA) is an important endogenous post-transcriptional regulator, while lettuce () is a leafy vegetable of global economic significance. However, there are few studies on miRNAs in lettuce, and research on miRNA regulatory network in lettuce is absent. In this study, through deep sequencing of small RNAs in different tissues, together with a reference genome, 157 high-confidence miRNA loci in lettuce were comprehensively identified, and their expression patterns were determined. Using a combination of computational prediction and high-throughput experimental verification, a set of reliable lettuce miRNA targets were obtained. Furthermore, through RNA-Seq, the expression profiles of these targets and a comprehensive view of the negative regulatory relationship between miRNAs and their targets was acquired based on a correlation analysis. To further understand miRNA functions, a miRNA regulatory network was constructed, with miRNAs at the core and combining transcription factors and miRNA target genes. This regulatory network, mainly composed of feed forward loop motifs, greatly increases understanding of the potential functions of miRNAs, and many unknown potential regulatory links were discovered. Finally, considering its specific expression pattern, as a hub gene was employed to illustrate the function of the regulatory network, and genetic experiments revealed its ability to increase the fresh weight and achene size of lettuce. In short, this work lays a solid foundation for the study of miRNA functions and regulatory networks in lettuce.
微小RNA（miRNA）是一种重要的内源性转录后调节因子，而生菜（）是具有全球经济意义的叶菜类蔬菜。然而，关于生菜中miRNA的研究较少，且缺乏对生菜miRNA调控网络的研究。在本研究中，通过对不同组织中的小RNA进行深度测序，并结合参考基因组，全面鉴定了生菜中157个高置信度的miRNA位点，并确定了它们的表达模式。通过计算预测和高通量实验验证相结合的方法，获得了一组可靠的生菜miRNA靶标。此外，通过RNA测序，基于相关性分析获得了这些靶标的表达谱以及对miRNA与其靶标之间负调控关系的全面认识。为了进一步了解miRNA的功能，构建了一个以miRNA为核心，结合转录因子和miRNA靶基因的miRNA调控网络。这个主要由前馈环基序组成的调控网络极大地增进了对miRNA潜在功能的理解，并发现了许多未知的潜在调控联系。最后，考虑到其特定的表达模式，将作为一个枢纽基因来阐明调控网络的功能，遗传实验揭示了它增加生菜鲜重和瘦果大小的能力。总之，这项工作为生菜中miRNA功能和调控网络的研究奠定了坚实基础。
