Negative correlation between the expression of selected miRNA-like RNAs and their targets. (a) The expression of targets of miR169i.2-3p, miR169j.2, miR447a.3, miR839.2 and miR839.3 in a dcl1-9 mutant relative to that in the Ler wild type (WT), measured by realtime RT-PCR. (b) The expression level of the miR822.4-5p target in a dcl4-2 mutant relative to the Col-0 wide type. (c) The expression of two miR447a.3 targets and one miR839.2 target under the challenge of Pst DC3000 (avrRpt2) relative to that in the mock treatment. Actin was used as an internal control for delta Ct calculation. Error bars correspond to standard deviation data from three independent reactions. The experiments were repeated on three sets of biological samples and similar results were obtained. (d) Alignments of selected miRNA-like RNAs and some of their mRNA targets whose expression was compared in Dicer mutants and in the wide type (a, b) and under bacterial infection and under mock infection (c). Included are alignment scores and P-values of target signatures if miRNA-like RNAs had target degradation products in the three small RNA degradome datasets. The arrows are the target cleavage sites detected in the degradome data.