A group I plant intron accumulates as circular RNA forms with extensive 5' deletions in vivo

Analysis by a PAGE approach for detecting small circular RNAs showed the existence of one such molecular species (RNA 1) accumulating at high levels in cherimoya. Sequencing of cDNA clones of RNA 1 revealed a size of 281 nt and a sequence identical to the 3'-terminal region of the 494-nt tRNALeu(UAA) group I intron from cherimoya. Northern blot hybridizations with a probe complementary to RNA 1 showed that this RNA coexists in vivo with its corresponding linear form, with the presumed full-length intron, and with minor amounts of two additional small circular species (RNAs 2 and 3). RNAs 2 and 3 had sizes of 216 and 156 nt, respectively, and sequences identical to different moieties of the 3'-terminal region of the tRNALeu(UAA) intron. The three cyclization sites giving rise to RNAs 1, 2, and 3, located within loop 8, are preceded by CUU or UUU trinucleotides and followed by sequences capable of forming base pairing interactions with the internal guide sequence characteristic of group I introns. The good correlation observed between the stabilities of these interactions and the in vivo accumulation levels of the corresponding cherimoya circular RNAs support the hypothesis that they emerge through a common mechanism similar to that advanced previously for the generation of circular RNAs derived from other group I introns. The lack of interactions of similar stabilities in tobacco, in which no circular RNAs derived from the tRNALeu(UAA) intron were detected, is consistent with this proposal, although other factors are also probably important in the synthesis and accumulation of the small circular RNAs in cherimoya.