Characterization of multiple circular RNAs derived from a plant viroid-like RNA by sequence deletions and duplications.

Northern blot hybridizations with a probe complementary to a 275-nt circular RNA isolated from carnation plants revealed that this RNA co-exists in vivo with minor amounts of other small circular RNAs. Sequencing of cDNA clones of nine RNA species demonstrated deletions and duplications of the predominant 275-nt RNA. Minor sequence heterogeneities were observed at the crossover sites. Deletions mapped to three arms of the cruciform structure of lowest free energy obtained previously for the parental 275-nt RNA, whereas repeats encompassed mostly regions of the arm where deletions were not found. Some of the deleted and duplicated regions corresponded to sequences forming part of the two hammerhead structures involved in the in vitro self-cleavage of the plus and minus strands of the 275-nt RNA. A copy choice model is proposed for the emergence of deletions and duplications, where the RNA polymerase with the nascent strand dissociates from the template at regions rich in secondary and possibly tertiary structures, and reinitiates synthesis at different upstream and downstream positions.