Efficacy is plotted on a log scale as mean destabilization of messages possessing the indicated sites corresponding to an introduced miRNA, as monitored on mRNA expression arrays (). Site-conservation analyses, site-depletion analyses, reporter-assay results, and proteomic results all indicate that these differences measured at the mRNA level correspond to similar relative differences in protein output (; ). The four seed-matched sites are colored as in . Nonconserved sites are considered together with conserved sites, and unless noted otherwise, only messages with single sites within the 3´ UTR are considered. The Y-axis is marked off in units corresponding to the mean efficacy of a single 7mer, considering both types of 7mers in aggregate (dashed lines).
(A) Mean efficacy of sites differentiated by their type. Efficacies of the four seed-matched sites () are plotted. To illustrate the contribution of seed pairing, also plotted are efficacies of 8mer sites with a single mismatch or wobble at nucleotides 3, 4, 5, 6 or 7 (open purple bar) and of the offset 6mer match (, open black bar).
(B) Mean efficacies of a single 7mer and dual 7mers. Both types of 7mer sites are considered in aggregate (black filled bars).
(C) Mean efficacy of sites differentiated based on their position in the message.
(D) Mean efficacy of sites differentiated based on their local AU content.
(E) Mean efficacy of sites differentiated based on potential for 3´-supplementary pairing.