Exceptional fly and worm mirtrons exhibit strongly unpaired hairpin termini. It is generally accepted that a defined short 3′ overhang is critical for nuclear export of pre-miRNA hairpins via exportin 5. Consequently, a strongly unpaired hairpin base is unfavorable for pre-miRNA maturation. (A) The exceptional C. elegans mirtron mir-1019 exhibits a 2 + 5 hairpin overhang, but still exhibits a typical pattern of mirtronic reads corresponding specifically to the ends of the intron. (B) Similarly, the atypical D. melanogaster mirtron CG3225_in2 exhibits strong evidence for Dicer-1 cleavage despite a 4 + 7 hairpin overhang, including a rare read corresponding to the cleaved terminal loop (highlighted in blue). Reads from this intron exhibit evidence for loading to the siRNA effector AGO2 instead of the miRNA effector, AGO1. Head data including AGO1-IP and oxidized RNA (which enriches for mature AGO2-loaded siRNAs) were reported by Ghildiyal et al. (2010) and S2 cell data from AGO1-IP and AGO2-IP were reported by Czech et al. (2008); to permit comparison between the total and IP levels, these read numbers were normalized per million mapped reads in each library. Note that these worm and fly mirtrons are further atypical in that their mature cloned species derive from their 5p arms; this correlates with the strong thermodynamic asymmetry associated with their unpaired hairpin bases. These mirtrons are exceptional, and few other introns with similarly unpaired bases were productively converted into short cloned RNAs.
