Constructing CircRNA–miRNA–mRNA Regulatory Networks by Using GreenCircRNA Database

Circular RNA (circRNA) is a special class of endogenous RNA with a continuous loop structure, which plays important roles in metabolic processes. With the development of sequencing technology and algorithm for circRNA, more and more circRNA are identified in plants. However, the function of most plant circRNA remains unclear. In order to investigate the function of plant circRNA, we firstly build a plant circRNA database, named GreenCircRNA. Then we construct circRNA–miRNA–mRNA regulatory networks to infer the function of plant circRNA. Here, taking Arabidopsis thaliana as an example, we firstly show the method for identification of circRNA and construction of circRNA–miRNA–mRNA networks based on GreenCircRNA database, then perform a case study for identifying circRNAs and inferring their function in A. thaliana. Our method can be easily extended and applied to other plants.