title: Widespread noncoding circular RNAs in plants.
abstract: A large number of noncoding circular RNAs (circRNAs) with regulatory potency have been identified in animals, but little attention has been given to plant circRNAs. We performed genome-wide identification of circRNAs in Oryza sativa and Arabidopsis thaliana using publically available RNA-Seq data, analyzed and compared features of plant and animal circRNAs. circRNAs (12037 and 6012) were identified in Oryza sativa and Arabidopsis thaliana, respectively, with 56% (10/18) of the sampled rice exonic circRNAs validated experimentally. Parent genes of over 700 exonic circRNAs were orthologues between rice and Arabidopsis, suggesting conservation of circRNAs in plants. The introns flanking plant circRNAs were much longer than introns from linear genes, and possessed less repetitive elements and reverse complementary sequences than the flanking introns of animal circRNAs. Plant circRNAs showed diverse expression patterns, and 27 rice exonic circRNAs were found to be differentially expressed under phosphate-sufficient and -starvation conditions. A significantly positive correlation was observed for the expression profiles of some circRNAs and their parent genes. Our results demonstrated that circRNAs are widespread in plants, revealed the common and distinct features of circRNAs between plants and animals, and suggested that circRNAs could be a critical class of noncoding regulators in plants.
authors.affiliation: Institute of Crop Sciences, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Chu-Yu
authors.initials: CY
authors.lastname: Ye
authors.affiliation: Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Li
authors.initials: L
authors.lastname: Chen
authors.affiliation: Institute of Crop Sciences, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Chen
authors.initials: C
authors.lastname: Liu
authors.affiliation: CSIRO Agriculture Flagship, Black Mountain Laboratories, Canberra, ACT, 2601, Australia.
authors.forename: Qian-Hao
authors.initials: QH
authors.lastname: Zhu
authors.affiliation: Institute of Crop Sciences, Zhejiang University, Hangzhou, 310058, China.|Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Longjiang
authors.initials: L
authors.lastname: Fan
mesh_terms: D000818:Animals; D017360:Arabidopsis / Q000235:genetics; D001483:Base Sequence; D018744:DNA, Plant; D005091:Exons; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D007438:Introns; D012275:Oryza / Q000235:genetics; D010944:Plants / Q000235:genetics*; D012313:RNA; D012326:RNA Splicing; D000079962:RNA, Circular; D022661:RNA, Untranslated; D012689:Sequence Homology, Nucleic Acid; D013312:Stress, Physiological / Q000235:genetics
chemical_list: D018744:DNA, Plant; D000079962:RNA, Circular; D022661:RNA, Untranslated; D012313:RNA
keywords: Arabidopsis thaliana; Oryza sativa; back splicing; circular RNA (circRNA); exonic circRNA; noncoding RNA