Fig. 6

Mechanism of shifting RNA cleavage upstream of a stem-loop in IR4. a Secondary structure predicted for IR4 and a schematic diagram of mutation. The cleavage site is indicated by red arrows. b, c Effect of deletion of various elements of the secondary structure of IR4, as analyzed by Northern blotting (b) and qRT-PCR (c). d Cleavage sites of IR4 and IR4ΔSL1 were precisely identified by primer extension assay. The nucleotide sequences encompassing cleavage sites were listed on the right side of the panel. Cleavage sites are indicated by red arrows. (e) The schematic diagram of IR4 derivatives. f, g Effect of replacement of IR4-SL1 and IR4-SL2 with other stem-loops, as analyzed by Northern blotting (f) and qRT-PCR (g). Black arrows highlight the positions of bands that correspond to transcripts as indicated on the right side of the panel of Northern blotting results. 16S rRNA was used as a loading control. Error bars indicate the standard deviation of the mean from experiments done in triplicate