Figure S4: The secondary structure of pre-miR-21, showing passenger strand and loop section.
The loop and passenger sequences produced when the mature microRNA is excised from pre-miR-21 can be detected in deep-sequencing data, although they are not very abundant as they are degraded rapidly. In the replicate t = 0 (unstimulated) samples from our time course sequencing data from MCF7 cells, as well as in sequencing data from THP1 cells [S1], from which read counts are shown in this figure, the loop section always starts at the uracil that follows miR-21+C, and never at the cytosine that would follow canonical miR-21 if that isomiR were excised by DICER1, suggesting that miR-21+C is excised by DICER1. The passenger strand sequences are consistent with this, as the vast majority of these (974 of 995) would result in a 2-nt overhang with respect to miR-21+C (indicated in red), while only 21 reads start at the adenine that would produce a 2-nt overhang compared with canonical miR-21.
 
S1. Zhang H, Kolb FA, Jaskiewicz L, Westhof E, Filipowicz W (2004) Single processing center models for human Dicer and bacterial RNase III. Cell 118(1):57-68.