For consistency, in this manuscript we used the term "target" for any predicted mRNA gene of some known miRNA, accordingly "non-target" is used for the complement of predicted targets.
In theory, the technique is simple yet elegant: the complement of a target sequence of messenger ribonucleic acid (mRNA) encoding the protein of interest is used to disrupt translation or prevent translation initiation.
We give an example of a deviation from the expected thermodynamical behavior for the probe set 1091_at due to annotation problems, i.e., the surface-bound probe is not the exact complement of the target RNA sequence, because of errors present in public databases at the time when the array was designed.
Currently, 21mers from the reverse complement of the target transcript(s) are considered effective amiRNA candidates, if they have an "A" (sometimes also "U") at position 10 and display 5' instability (higher AU content at the 5' end and higher GC content at the 3' end).
Otherwise, the reverse complement of the target sequence was checked, and hits were reverted.
Although this complement of WNK8 target genes (which is based on altered transcript levels in the three mutants) is more stringently defined than the complement of the EDM2 target genes (which is only based on altered transcript levels in one mutant), the former is almost twice as large as the latter, suggesting that WNK8 may have a wider spectrum of biological roles than EDM2.
Reverse complement sequences of target (red) and PAM (shadowed) are shown on the reference sequence.
In line with this, we show that the components of this pathway do not show evidence of adaptive sequence evolution during the diversification of these species whereas the complement of putative downstream targets controlled by DAF-16 appear to vary between these species.
With this method, one can study brain regions or neurons in their intact state with their normal complement of inputs and targets.
Thus, the availability of different sets of mRNA targets in distinct cell types may contribute to the context specificity of miRNAs, and further work is required to identify the whole complement of miR-126 targets in hematopoietic stem versus progenitor cells.
