Prediction And Analysis Of Circular RNA In Caenorhabditis Elegans And Oryza Sativa

Circular RNA is a class of special RNA molecule with covalently closed 3ˊend and 5ˊend. It was generated by the way of back-splicing, which is quite different from normal linear RNA. Because of the particular structure, circular RNA is easily abandoned during the classical separate process, and this is also the reason why circular RNA was often ignored by scientists. With the development of next-generation sequencing and bioinformatics, circular RNA was identified in many eukaryotes. Caenorhabditis elegans is a model organism which has eukaryotic and prokaryotic characteristics both, circular RNA in C.elegans was reported but not analyzed deeply. On the other side, there are still no study about large scale of circular RNA in plants.By utilizing RNA-seq data and bioinformatics tools in different stages and conditions, we comprehensively revealed the general features of circular RNA in C.elegans and the relationship between circular RNA and linear RNA. At the same time, we predicted circular RNAs in Oryza sativa and Arabidopsis thaliana, compared the difference of circular RNA between plants and animals. The mainly ideas of our researches are described as below:1) Based on bioinformatics analysis of several development stages of RNase R treated RNA sequencing data in C.elegans, we totally found 1452 circular RNAs and defined them into different types, 1112 canonical exonic circular RNAs were selected for the further analysis.2) According to the site information of circular RNA, they are mainly composed by middle exon and usually contain multiple exons. The ratio of the first exon participates in circular RNA is higher than human. The exon length will be longer when a single exon cyclized. According to circular RNA flanking upstream and downstream intron sequence information, we found flanking intron length is longer than the average intron length and contains more reverse complementary matches. Combining the expression analysis result of RNA-seq data sets from different stages, we discovered that circular RNA is development stage specific, the expression of circular isoform and the linear isoform have no obvious correlationship.3) By analyzing the RNA-seq data sets of O.sativa and A.thaliana, we predicted 213 circular RNAs in O.sativa and 24 in A.thaliana. Most of them are consisted of mutiple exons, single cylized exon and the flanking intron have longer length as well. But the circular RNA flanking intron length is shorter than C.elegans, and the ratio of reverse complementary matches is lower than C.elegans. We assumed that the way circular RNA generate in plants is different from animals, the model of intron-pairing-driven circularization is not suitable in plants.4) The biological function of acting as mi RNA sponges is quite limited, we only find one circular RNA has the potential capacity in C.elegans.