Identification And Analysis Of Non-coding Circular RNAs In Plants

Recent studies in animals have found a kind of non-coding RNA molecule called circular RNA (circRNA) produced by splicing complex with one or more exons of the gene. In animals and human cells, circular RNA has miRNA sponge function, regulating its parent gene functions and also it was reported that the formation of circular RNA depends on both sides of the intron complementary sequence. However, the situation of circular RNA in plants is unknown. Using the current softwares or algorithms developed for animals or humans, the accuracy of the prediction of circular RNA in plant is relatively low and the sensitivity is not high. In this study we choose the model plant Arabidopsis and rice and try to answer whether circular RNA exists in plants, what its characteristics are and how they work, and then develop a suitable software for predicting circular RNA in plants, which will lay the foundation for the research on plant circular RNA. The results are as follows:(1) Using the rRNA-deplete RNA-seq data, circRNAs (12,037 and 6,012) were identified in Oryza sativa and Arabidopsis thaliana, respectively, with 56%(10/18,10 is validated number of circRNA,18 is total selected number of circRNA) of the sampled rice exonic circRNA validated experimentally. Parent genes of over 700 exonic circRNAs were orthologues between rice and Arabidopsis, suggesting conservation of circRNA 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 fcund 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.(2) A new circRNA prediction method called PcircRNA_finder is developed in plants. Using the simulated data and real RNA-seq data, we show that the software has good sensitivity, and can be more comprehensive to find out the circular RNA. It can be used to distinguish and predict circular RNA with alternative donor/acceptor sites with minor changes. At the same time, the software has a good output, and gives a more detailed information on the circular RNA, which facilitate the follow-up of experimental verification and the functional study of circular RNA.