Analysis of the accessibility of CLIP bound sites reveals that nucleation of the miRNA:mRNA pairing occurs preferentially at the 3′-end of the seed match

PACMIT's accessibility filter performs better when the location of the nucleation region is restricted to the 3′-end. (A) Mean log₂ fold changes in mRNA expression of miRNA targets predicted using the unrestricted and 3′-restricted location of the nucleation region as a function of its length n. (B) Mean log₂ fold changes in protein expression for the miRNA targets predicted using the different filters. mRNA and protein fold changes were taken from Selbach et al. (2008) and Baek et al. (2008). In both panels, stars below each bar denote the statistical significance (evaluated with the one-sided Wilcoxon rank sum test) of the difference between the corresponding log₂ fold change and the log₂ fold change obtained without any filter. (C) Precision vs. sensitivity curves are shown for several miRNA target prediction algorithms that consider the accessibility of the binding site. PACMIT unrestricted refers to PACMIT using the unrestricted location of the nucleation region with length n = 4, and PACMIT 3′-restricted refers to PACMIT using a nucleation region of length n = 4 restricted to the 3′-end of the seed match. The two curves labeled as PACCMIT correspond to the case in which in addition to accessibility, conservation of the seed match in chimp, rhesus and mouse is required.