PlantCircNet: a database for plant circRNA-miRNA-mRNA regulatory networks.

Peijing Zhang,Jitong Xue,Yongjing Liu,Ming Chen,Yincong Zhou,Xianwen Meng,Hongjun Chen

doi:10.1093/database/bax089

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

Highlights

Circular RNA is a new class of endogenous noncoding RNA, which was dismissed as molecular flukes or by-products of aberrant splicing for nearly 20 years [1,2,3,4]
Emerging evidence suggests that the majority of circRNAs are abundant, stable and conserved across species, are widespread in eukaryotic transcriptomes [10], and play important roles in diverse biological processes [9, 11]. They were reported as competing endogenous RNAs or miRNA sponges [12, 13], and they can regulate alternative splicing or transcription [14, 15]
We have presented PlantCircNet, a comprehensive database of plant circRNAs-associated regulatory networks

Summary

Introduction

Circular RNA (circRNA) is a new class of endogenous noncoding RNA, which was dismissed as molecular flukes or by-products of aberrant splicing for nearly 20 years [1,2,3,4]. Emerging evidence suggests that the majority of circRNAs are abundant, stable and conserved across species, are widespread in eukaryotic transcriptomes [10], and play important roles in diverse biological processes [9, 11]. They were reported as competing endogenous RNAs or miRNA sponges [12, 13], and they can regulate alternative splicing or transcription [14, 15]. Some evidence revealed that they have the potential to become promising biomarkers for disease diagnosis and prognosis [16, 17]

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Conclusion