The effect of DCL3 on mRNAs with miRNA hairpin-like structures in the 3′ UTR. Cre16.g694950 (serine/threonine kinase) (A) and Cre24.g755697 (aminoglycoside 3′-phosphotransferase) (B) have the respective cre-miR1169 and cre-miR1172 precursors in their 3′ UTR. A schematic representation of both genes is shown with their exons (gray boxes) and introns (black solid lines) at the bottom of each panel. Light gray (A4-1 parental line) and black (dcl3-1) hills represent sRNA and mRNA read counts. Both panels show the results for one replicate of A4-1 parental line and its dcl3-1 derivative knock out mutant. Overaccumulation (X-fold) of the indicated mRNA in dcl3-1 regarding the A4-1 parental line is indicated. Two additional samples from this parental and mutant line combination and a biological triplicate from E9-3 parental and dcl3-3 derivative lines showed the same trend in both miRNA and mRNA accumulation (Table 1; Supplemental Table S3).
