Effects of seed match type and conservation on mRNA repression for miRNAs and siRNAs. (A) Seed match types and numbering system, illustrated for miR-1. Positions in the miRNA are numbered 5′-3′. (Seed match 6 mer) WC inverse complement of miRNA bases 2–7; (A1) presence of adenosine opposite miRNA base 1; (M8) WC match to miRNA base 8. (B) CDFs (cumulative distribution functions) of LFCs (log2 fold change) for mRNAs containing indicated miR-124 seed match types (colored lines and labels) or no miR-124 seed matches (gray line) following transfection of miR-124. (Solid vertical gray line) The LFC above which 97.5% of the no-seed-match mRNA set falls. (Inset bar plot) nLFC (normalized log2 fold change) values for each seed match type with error bars indicating standard error. Data for panels B–E are from Lim et al. (2005). Plots include only mRNAs containing exactly one miR-124 seed match, and thus the seed match type sets are mutually exclusive. The distribution of mRNA expression values did not differ significantly between seed match type sets (P > 0.05 by rank sum test). All seed match types except the 6 mer have distributions significantly different from the no-seed-match class (P < 0.005 by rank sum test). (C) CDFs of LFCs for mutually exclusive mRNA sets containing conserved (red) or nonconserved (blue) extended seed matches to miR-124, or no seed matches (gray); the conserved and nonconserved sets are significantly different (P < 0.001 by rank sum test). The “nonconserved” mRNA set contains exclusively nonconserved seed matches; the “conserved” mRNAs may also contain nonconserved seed matches. The nonconserved set was sampled to match the conserved set in seed match type and count, overall UTR conservation, and initial mRNA expression level (Supplemental Fig. S2). (D) Same as B for miR-1. All seed match type classes are significantly different from the no-seed-match class (P < 10−4 by rank sum test). (E) Same as C for miR-1. The CDFs of conserved and nonconserved mRNA sets are significantly different (P < 0.01 by rank sum test). (F) Same as B for pooled set of 33 “effective” siRNAs that begin with non-U bases (Supplemental Material). Additional seed match classes containing M1 are shown (triangles). All seed match types have distributions significantly different from the no-seed-match class (P < 10−14 by rank sum test). (G) Same analysis and controls as C for pooled set of siRNAs. The CDFs of conserved and nonconserved mRNA sets are not significantly different (P > 0.05 by rank sum test). See Supplemental Table S1 for additional statistics.
