PlantCircNet: a database for plant circRNA–miRNA–mRNA regulatory networks

Abstract

Circular RNA (circRNA) is a novel type of endogenous noncoding RNA with covalently closed loop structures, which are widely expressed in various tissues and have functional implications in cellular processes. Acting as competing endogenous RNAs (ceRNAs), circRNAs are important regulators of miRNA activities. The identification of these circRNAs underlines the increasing complexity of ncRNA-mediated regulatory networks. However, more biological evidence is required to infer direct circRNA–miRNA associations while little attention has been paid to circRNAs in plants as compared to the abundant research in mammals. PlantCircNet is presented as an integrated database that provides visualized plant circRNA–miRNA–mRNA regulatory networks containing identified circRNAs in eight model plants. The bioinformatics integration of data from multiple sources reveals circRNA–miRNA–mRNA regulatory networks and helps identify mechanisms underlying metabolic effects of circRNAs. An enrichment analysis tool was implemented to detect significantly overrepresented Gene Ontology categories of miRNA targets. The genomic annotations, sequences and isoforms of circRNAs were also investigated. PlantCircNet provides a user-friendly interface for querying detailed information of specific plant circRNAs. The database may serve as a resource to facilitate plant circRNA research. Several circRNAs were identified to play potential regulatory roles in flower development and response to environmental stress from regulatory networks related with miR156a and AT5G59720, respectively. This present research indicated that circRNAs could be involved in diverse biological processes. Database URL: http://bis.zju.edu.cn/plantcircnet/index.php

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“…3,40 In tumor research, the mechanism by which circular RNA acts as a miRNA "cavernous body" to regulate downstream target genes has been widely reported. 41 It has been found that a plurality of circular RNAs themselves contain at least one mi RNA binding site. 8 Therefore, it can act as a "sponge" of RNA to adsorb mi RNA, thereby regulating the expression of downstream target genes inhibited by mi RNA through the mechanism of competitive endogenous RNAs (ce RNAs).…”

Circular RNAs—The Road Less Traveled

“…AtcircDB, meanwhile, is meant exclusively for Arabidopsis circRNA (Ye et al, 2019). The PlantCircNet (Zhang P. et al, 2017) is meant for visualizing the plant circRNA-miRNA-mRNA interaction networks. Similarly, CircFunBase is the animal circRNA database and is a repository of functional circRNAs (Meng et al, 2019).…”

A comprehensive review of web-based resources of non-coding RNAs for plant science research

“…PlantCircNet is a visualized web-based database of plant circRNA, miRNA and mRNA regulatory networks, which can show querying detailed information of specific plant circRNAs in a user-friendly interface 128 . It contain identified circRNAs in eight model plants and can find significantly overrepresented Gene Ontology categories of miRNA targets by its enrichment analysis tool.…”