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Development of a Novel Identification Tool and Functional Study for Circular RNAs
Circular RNA (circRNA) is a new member of non-coding RNA family that have attracted a lot of attention from biologists recently. Studies on circRNA include their genome-wide discovery in different species as well as the understanding of their biogenesis mechanisms and functions. However, currently there is only a limited amount of knowledge regarding the number and types of circRNAs in various organisms. Furthermore, the reliability of some circRNAs is even doubtful due to the limitation of current bioinformatics tools in identifying circRNA reads. The circRNA biogenesis mechanisms remain unclear though several models have been proposed to explain the generation of circRNAs. Except for the examples that a mouse circRNA (CDR1as) can impair the development of midbrain and that a circRNA from exon 6 of SEPALLATA3 in Arabidopsis can delay flowering, the other functions of circRNAs are not yet known. To explore as many authentic circRNAs and their supportive reads as possible, we developed a computational circRNA identification tool-CircDeepTop. Based on a thorough topological analysis of circRNA reads mapping patterns, CircDeepTop can identified many new circRNAs and more supportive reads than CIRI2, currently the best circRNA identification tool. Furthermore, CircDeepTop has stronger control in false positive rate. Analysis of circRNAs in diverse species revealed shared as well as species-specific features, some of which have not been reported previously. Overexpression of a circRNA, CircNPGR2, from exon 2 of NPGR2, significantly delayed flowering in Arabidopsis. Real-time qPCR showed that CircNPGR2 is overexpressed multiple times during flowering while the expression of its parental gene NPGR2 is reduced significantly, suggesting a negative regulation of CircNPGR2 on NPGR2. RNA-seq analysis indicated that the expression levels of hundreds of genes have been changed in the transgenic plants, most of which are up-regulated. Gene Ontology analysis found that most of these genes are associated to flowering related pathways. These results suggest that CircNPGR2 plays a role in suppressing the repression of most flowering related genes by NPGR2.
Yang, Weilong, "Development of a Novel Identification Tool and Functional Study for Circular RNAs" (2022). ETD collection for University of Nebraska-Lincoln. AAI29999257.